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Well installation, single-well testing, and particle-size analysis for selected sites in and near the Lost Creek Designated Ground Water Basin, north-central Colorado, 2003-2004

This report describes results from a groundwater data-collection program completed in 2003-2004 by the U.S. Geological Survey in support of the South Platte Decision Support System and in cooperation with the Colorado Water Conservation Board. Two monitoring wells were installed adjacent to existing water-table monitoring wells. These wells were installed as well pairs with existing wells to characterize the hydraulic properties of the alluvial aquifer and shallow Denver Formation sandstone aquifer in and near the Lost Creek Designated Ground Water Basin. Single-well tests were performed in the 2 newly installed wells and 12 selected existing monitoring wells. Sediment particle size was analyzed for samples collected from the screened interval depths of each of the 14 wells. Hydraulic-conductivity and transmissivity values were calculated after the completion of single-well tests on each of the selected wells. Recovering water-level data from the single-well tests were analyzed using the Bouwer and Rice method because test data most closely resembled those obtained from traditional slug tests. Results from the single-well test analyses for the alluvial aquifer indicate a median hydraulic-conductivity value of 3.8 x 10-5 feet per second and geometric mean hydraulic-conductivity value of 3.4 x 10-5 feet per second. Median and geometric mean transmissivity values in the alluvial aquifer were 8.6 x 10-4 feet squared per second and 4.9 x 10-4 feet squared per second, respectively. Single-well test results for the shallow Denver Formation sandstone aquifer indicate a median hydraulic-conductivity value of 5.4 x 10-6 feet per second and geometric mean value of 4.9 x 10-6 feet per second. Median and geometric mean transmissivity values for the shallow Denver Formation sandstone aquifer were 4.0 x 10-5 feet squared per second and 5.9 x 10-5 feet squared per second, respectively. Hydraulic-conductivity values for the alluvial aquifer in and near the Lost Creek Designated Ground Water Basin generally were greater than hydraulic-conductivity values for the Denver Formation sandstone aquifer and less than hydraulic-conductivity values for the alluvial aquifer along the main stem of the South Platte River Basin reported by previous studies. Particle sizes were analyzed for a total of 14 samples of material representative of the screened interval in each of the 14 wells tested in this study. Of the 14 samples collected, 8 samples represent the alluvial aquifer and 6 samples represent the Denver Formation sandstone aquifer in and near the Lost Creek Designated Ground Water Basin. The sampled alluvial aquifer material generally contained a greater percentage of large particles (larger than 0.5 mm) than the sampled sandstone aquifer material. Alternatively, the sampled sandstone aquifer material generally contained a greater percentage of fine particles (smaller than 0.5 mm) than the sampled alluvial aquifer material consistent with the finding that the alluvial aquifer is more conductive than the sandstone aquifer in the vicinity of the Lost Creek Designated Ground Water Basin.

Open-File Report

Water resources inventory of Connecticut Part 2: Shetucket River Basin

The Shetucket River basin has a relatively abundant supply of water of generally good quality which is derived from precipitation that has fallen on the basin. Annual precipitation has ranged from about 30 inches to 75 inches and has averaged about 45 inches over a 35-year period. Approximately 20 inches of water are returned to the atmosphere each year by evaporation and transpiration; the remainder of the annual precipitation either flows overland to streams or percolates downward to the water table and ultimately flows out of the basin in the Shetucket River or as underflow through the deposits beneath. During the autumn and winter months precipitation normally is sufficient to cause a substantial increase in the amount of water stored underground and in surface reservoirs within the basins whereas in the summer most of the precipitation is lost through evaporation and transpiration, resulting in sharply reduced streamflow and lowered groundwater levels. The mean monthly storage of water in the basin on an average is 3.5 inches higher in November than it is in June. The amount of water that flows out of the basin in the Shetucket River represents the total amount of water potentlally available for use by man. Annual runoff from the entire basin above the Quinebaug River has ranged from about 13 to 42 inches since 1929, and has averaged about 23 inches (300 billion gallons). Although runoff indicates the total amount of water potentially available, it is usually not economically or legally feasible for man to use all of it. On the other hand, with increased development, It is possible that some water will be reused several times. The water available may be tapped as it flows through the area or is temporarily stored in streams, lakes, and aquifers. The amounts that can be developed vary from place to place and time to time, depending on the amount of precipitation, on the size of drainage area, on the thickness, permeability and areal extent of aquifers, and on the variations in chemical and physical quality of the water. Differences in streamflow from point to point are due primarily to differences in the proportion of stratified drift in the drainage basin above each point, which affect the timing of streamflow, and to differences in precipitation, which affect the amount of streamflow. Information on streamflow from gaging stations may be extended to ungaged sites by accounting for both of these factors ,in calculations. Future floods on the upper Willimantic River or the Shetucket River are unlikely to cause major damage so long as buildings are not constructed below the highest flood elevations to be expected with the present system of reservoirs for flood control. Ground water can be obtained from wells almost anywhere in the Shetucket River basin, but the amount obtainable from individual wells at any particular point depends upon the type and water-bearing properties of the aquifers present. For practical purposes, the earth materials in the basin comprise three aquifers--stratified drift, till, and bedrock, Stratified drift is the only aquifer generally capable of yielding more than 100 gpm to individual wells. This aquifer covers about 18 percent of the basin and occurs chiefly In lowlands where it overlies till or bedrock. Coefficient of permeability of the coarse-grained unit of stratified drift averages about 1,900 gpd per sq ft. Drilled, screened wells tapping this unit, are known to yield from 200 to 675 gpm. Dug wells in coarse-grained stratified drift should supply at least 2 gpm per foot of drawdown over an 8-hour period. Fine-grained stratified drift has an average coefficient of permeability of about 400 gpd per sq ft and can usually yield to dug wells supplies sufficient for household use. Till and bedrock are widespread in extent but can provide only small to moderate water supplies. Till is tapped chiefly by dug wells; permanent supplies of more than 200 gpd can be obtained from dug wells at a majority of sites in areas of till, but there are many sites where the till is too impermeable or too thin to provide this much water throughout the year. The coefficient of permeability of till ranges from about 0.2 gpd per sq ft to 55 gpd per sq it. Bedrock Is tapped chiefly by drilled wells, about 90 percent of which will supply at least 3 gpm. Very few, however, will supply more than 50 gpm. The amount of ground water potentially available In an area depends upon the amount of groundwater outflow, the amount of ground water in storage, and the quantity of water available by Induced infiltration from streams and lakes. From data on permeability, saturated thickness, recharge, yield from aquifer storage, well performance, and streamflow, preliminary estimates of ground-water availability can be made for any point in the basin. Long-term yields estimated for 15 areas especially favorable for development of large ground-water supplies ranged from 1.3 to 61.8 mgd. Detailed site studies to determine optimum yields, drawdowns, and spacing of individual wells are needed before major ground-water development is undertaken In these or other areas. The chemical quality of water in the Shetucket basin Is generally good to excellent. Samples of naturally occurring surface water collected from 32 sites contained less than 61 ppm of dissolved solids and less than 32 ppm of hardness. Water from wells is more highly mineralized than naturally occurring water from streams. Even so only 7 percent of wells sampled yielded water with more than 200 ppm of dissolved sol-ids and only 9 percent yielded water with more than 120 ppm of hardness. Even in the major rivers, which are used to transport industrial waste, the dissolved mineral content is less than 100 ppm and hardness rarely exceeds 40 ppm. One notable exception occurs in the lower reaches of Little River where an exceptional amount of industrial waste is discharged into the river near Versailles. This waste is particularly noticeable during low streamflow. Iron and manganese In both ground water and surface water are the only constituents whose concentrations commonly exceed recommended limits for domestic and industrial use. Most wells in the basin yield clear water with little or no iron or manganese, but distributed among them are wells with ground water that contains enough of these dissolved constituents to be troublesome for most uses. iron concentrations in naturally occurring stream water exceeded 0.3 ppm under tow-flow conditions at 20 percent of the sites sampled. Large concentrations of iron in stream water result from discharge of iron-bearing ground water or from the discharge of water from swamps. In swamps the iron is released largely from decaying vegetation. Ground water more than 30 feet below the land surface has a relatively constant temperature, usually between 48°F and 50°F. Water temperature in very shallow wells may fluctuate from about 38°F in February or March to about 55°F in late summer. Water temperature in the larger streams fluctuates much more widely, ranging from 32°F at least for brief periods in winter, to about 85°F occasionally during The quantity of suspended sediment transported by streams in the basin is negligible, though amounts large enough to be troublesome may occur locally at times. The total amount of water used In the Shetucket Rlver basin for all purposes during 1961 was about 5,810 million gallons~ which is equivalent to 208 gpd per person, Public water systems supplied the domestic needs of nearly half the population of the basin; 10 systems were sampled, all of which provided water of better quality than the U.S. Public Health Service suggests for drinking water standards.

Connecticut

Multivariate Statistical Models for Predicting Sediment Yields from Southern California Watersheds

Debris-retention basins in Southern California are frequently used to protect communities and infrastructure from the hazards of flooding and debris flow. Empirical models that predict sediment yields are used to determine the size of the basins. Such models have been developed using analyses of records of the amount of material removed from debris retention basins, associated rainfall amounts, measures of watershed characteristics, and wildfire extent and history. In this study we used multiple linear regression methods to develop two updated empirical models to predict sediment yields for watersheds located in Southern California. The models are based on both new and existing measures of volume of sediment removed from debris retention basins, measures of watershed morphology, and characterization of burn severity distributions for watersheds located in Ventura, Los Angeles, and San Bernardino Counties. The first model presented reflects conditions in watersheds located throughout the Transverse Ranges of Southern California and is based on volumes of sediment measured following single storm events with known rainfall conditions. The second model presented is specific to conditions in Ventura County watersheds and was developed using volumes of sediment measured following multiple storm events. To relate sediment volumes to triggering storm rainfall, a rainfall threshold was developed to identify storms likely to have caused sediment deposition. A measured volume of sediment deposited by numerous storms was parsed among the threshold-exceeding storms based on relative storm rainfall totals. The predictive strength of the two models developed here, and of previously-published models, was evaluated using a test dataset consisting of 65 volumes of sediment yields measured in Southern California. The evaluation indicated that the model developed using information from single storm events in the Transverse Ranges best predicted sediment yields for watersheds in San Bernardino, Los Angeles, and Ventura Counties. This model predicts sediment yield as a function of the peak 1-hour rainfall, the watershed area burned by the most recent fire (at all severities), the time since the most recent fire, watershed area, average gradient, and relief ratio. The model that reflects conditions specific to Ventura County watersheds consistently under-predicted sediment yields and is not recommended for application. Some previously-published models performed reasonably well, while others either under-predicted sediment yields or had a larger range of errors in the predicted sediment yields.

Open-File Report

Groundwater-flow model of the Treasure Valley, southwestern Idaho, 1986–2015

Most of the population of the Treasure Valley and the surrounding area of southwestern Idaho and easternmost Oregon depends on groundwater for domestic supply, either from domestic or municipal-supply wells. Current and projected rapid population growth in the area has caused concern about the long-term sustainability of the groundwater resource. In 2016, the U.S. Geological Survey, in cooperation with the Idaho Water Resource Board and the Idaho Department of Water Resources, began a project to construct a numerical groundwater-flow model of the westernmost portion of the western Snake River Plain aquifer system, called the Treasure Valley. The development of the model was guided by several objectives, including: to improve the understanding of groundwater and surface water interactions; to facilitate conjunctive water management; to provide a tool for water resources planning; and to provide a tool for water allocation. The model was constructed with a spatial scale and level of detail that aimed to meet these objectives while balancing the sometimes-competing goals of fast runtimes, numerical stability, usability, and parsimony. The Treasure Valley Groundwater Flow Model (TVGWFM) is a three-dimensional finite-difference numerical model constructed using MODFLOW 6 (Langevin and others, 2017, Documentation for the MODFLOW 6 Groundwater Flow Model: U.S. Geological Survey Techniques and Methods, book 6, chap. A55, 197 p., https://doi.org/10.3133/tm6A55 ). The model covers the westernmost portion of the western Snake River Plain and is discretized into a regular grid of 64 by 65 cells with a side length of 1 mile and 6 layers of varying depth and active area. A historical model period was developed consisting of 360 month-long stress periods for 1986–2015. The model builds upon previous modeling efforts by adding a transient period, incorporating new head and discharge observations to constrain parameters, incorporating information from the hydrogeologic framework model (HFM) of Bartolino (2019, Hydrogeologic framework of the Treasure Valley and surrounding area, Idaho and Oregon: U.S. Geological Survey Scientific Investigations Report 2019–5138, https://doi.org/10.3133/sir20195138 ) and incorporating refined estimates of evapotranspiration and irrigation classification of lands in the study area. The TVGWFM includes all significant components of recharge to and discharge from the aquifer. Inflows include canal seepage, irrigation and precipitation recharge, mountain-front recharge, rivers and stream seepage, and seepage from Lake Lowell. Outflows include discharge to agricultural drainage ditches, discharge to rivers and streams, pumping, and discharge to Lake Lowell. Each recharge or discharge component is represented separately using individual MODFLOW 6 packages. Parameter values were derived with a combination of trial-and-error steps and automated parameter estimation using PEST software (Doherty, J.E., 2005, PEST, model-independent parameter estimation–User manual: Watermark Numerical Computing, https://pesthomepage.org/documentation ). Parameter estimates were constrained with several types of observation data, including water levels, water level changes, vertical water level differences, drain discharges, change in drain discharges, river seepage, seepage from Lake Lowell, and change in seepage from Lake Lowell. Material properties from the hydrogeologic framework were also used to assign the minimum and maximum values of some parameters. A final parameter realization was reached that minimized residuals between the observed and modelled values for the various observation groups. Mean residuals for the observation groups were 15.4 feet (ft) for water levels, 0.2 ft for water level changes, 19.4 ft for vertical water level differences, −3.9 cubic feet per second (ft 3 /s) for drain discharges, 0.0 ft 3 /s for changes in drain discharge, 45.0 ft 3 /s for river seepage, −40.1 ft 3 /s for Lake Lowell seepage, and 126.3 ft 3 /s for changes in Lake Lowell seepage. The quality of the model’s fit to observations varied spatially, with notable areas of under- or over-simulation of water levels present to the northwest and southwest of Lake Lowell, in the foothills along the eastern model boundary, and near the City of Eagle. Trends were observed in the residuals of many of the observation groups, indicating that the model is missing or not fully reproducing some phenomena that are observed in the system. The TVGWFM can be used as a tool for water resource planning, for understanding the interactions of groundwater and surface water at a basin scale, and for facilitating conjunctive management, but may lack the precision needed for water rights administration at a local scale. Additional sources of uncertainty or limitations of the model are noted. The quantity and spatial distribution of canal seepage and infiltration of irrigation water recharge, the largest sources of recharge to the system, are unknown and approximated indirectly. There is poor understanding of how canal seepage and incidental recharge change as land is converted from agricultural (irrigated) to suburban (semi-irrigated). These uncertainties will affect any scenarios that investigate changes to land use or irrigation practices. Finally, the model has relatively high water-level residuals around and to the southwest of Lake Lowell and should not be used to estimate water level effects in that region. The model was built with multiple, broadly expressed objectives and did not optimize performance for specific uses. However, the model and the tools included in an associated data release provide ample flexibility to improve the model for future uses. Adjustments and improvements could be made by refining the model in an area of interest, collecting additional calibration data, applying more rigorous boundary conditions, or re-estimating model parameters to optimize model performance for a specific model forecast.

Idaho

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 2020 Report)

A primary focus of the Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and have identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance 2015; Breed et al. 2018; Winkler et al. 2018). Many of the most complex information needs relate to identifying the appropriate sources of plant species that can successfully establish in dryland environments, like the Colorado Plateau, where precipitation is generally low and highly variable. Providing this information requires synergistic research efforts that build upon insight gained from earlier investigations. The U.S. Geological Survey (USGS) Southwest Biological Science Center’s (SBSC’s) research activities that supported CPNPP in FY20 followed the FY20 Statement of Work to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is outlined in the 2019-2023 5-Year Research Strategy (hereafter referred to as the 5-year plan). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance, 2015), Department of Interior Secretarial Order #3347 ( Conservation Stewardship and Outdoor Recreation ), and Bureau of Land Management Leadership Priority #1 ( Create a conservation stewardship legacy second only to Teddy Roosevelt ). Research activities in FY20 centered on landscape genomics, implementing a common garden experiment near Vernal, UT, conducting experimental treatments using the GRID (Germination for Restoration Information and Decision-making) framework, and collecting seeds and leaf tissues in the field in preparation for future experiments. These activities were supported by five biological science technicians. The SARS-CoV-2 pandemic delayed some aspects of the FY20 workplan, especially for contract laboratory services and the construction of the GRID garden in Flagstaff, AZ. However, goals were largely met, and the overall progress of research remains on track with respect to the 5-year plan. While Dr. Rob Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY20, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, Matt Jones, and Daniel Winkler, spent a considerable amount of time providing expertise and support for individual projects. Work activities performed in support of each goal are discussed in turn.

Arizona, Colorado, New Mexico, Utah

Supporting the development and use of native plant materials for restoration on the Colorado Plateau (Fiscal Year 19 Report)

A primary focus of the Bureau of Land Management’s (BLM’s) Colorado Plateau Native Plant Program (CPNPP) is to identify and develop appropriate native plant materials (NPMs) for current and future restoration projects. Multiple efforts have characterized the myriad challenges inherent in providing appropriate seed resources to enable effective, widespread restoration and have identified a broad suite of research activities to provide the information necessary to overcome those challenges (e.g., Plant Conservation Alliance 2015; Breed et al. 2018; Winkler et al. 2018). Many of the most complex information needs relate to identifying the appropriate sources of plant species that can successfully establish in dryland environments, like the Colorado Plateau, where low and highly variable precipitation is standard. Providing this information requires synergistic research efforts in which results from earlier investigations inform the design of subsequent investigations. The U.S. Geological Survey Southwest Biological Science Center’s (SBSC’s) research activities in FY19 followed an FY19 Statement of Work to support a research framework that is continually adapting based on the needs of the restoration community and results from previous investigations; the long-term research framework is outlined in the 2019-2023 5-Year Research Strategy (hereafter referred to as the 5-year plan). This research framework provides support for the National Seed Strategy for Rehabilitation and Restoration (Plant Conservation Alliance, 2015), Department of Interior Secretarial Order #3347 (Conservation Stewardship and Outdoor Recreation), and Department of Interior Leadership Priority #1 (Create a conservation stewardship legacy second only to Teddy Roosevelt). Research activities in FY19 centered on landscape genetics, collecting seeds in preparation for experimental common gardens, and planning and trials in support of experimental drought gardens. These activities were supported by three biological technicians, one of which was jointly funded by the Ecological Society of America for six pay periods. Most of the field-related activities, including plant trait measurement, seed/tissue collecting, and GRID (Germination for Restoration Information and Decision-making) experimental treatments at the Canyonlands Research Center near Moab, UT were assigned to these technicians. Contrary to the drought conditions the pervaded the Colorado Plateau in FY18, plentiful spring precipitation resulted in easily-collected plant tissue and seed collections. However, the cool and wet spring delayed the phenology of early blooming species, which caused difficulties for timing seed collecting. Furthermore, seed collecting for late blooming species was difficult because of lower than average monsoon precipitation. While Dr. Rob Massatti was the only scientist supported by the SBSC-CPNPP agreement in FY19, other scientists, including Drs. John Bradford, Seth Munson, Mike Duniway, Sasha Reed, and Daniel Winkler, spent a considerable amount of time providing expert guidance and support for individual projects. Work activities performed in support of each 5-year plan goal are discussed in turn.

Arizona, Colorado, New Mexico, Utah

Regional analysis of ground-water recharge

A modeling analysis of runoff and ground-water recharge for the arid and semiarid southwestern United States was performed to investigate the interactions of climate and other controlling factors and to place the eight study-site investigations into a regional context. A distributed-parameter water-balance model (the Basin Characterization Model, or BCM) was used in the analysis. Data requirements of the BCM included digital representations of topography, soils, geology, and vegetation, together with monthly time-series of precipitation and air-temperature data. Time-series of potential evapotranspiration were generated by using a submodel for solar radiation, taking into account topographic shading, cloudiness, and vegetation density. Snowpack accumulation and melting were modeled using precipitation and air-temperature data. Amounts of water available for runoff and ground-water recharge were calculated on the basis of water-budget considerations by using measured- and generated-meteorologic time series together with estimates of soil-water storage and saturated hydraulic conductivity of subsoil geologic units. Calculations were made on a computational grid with a horizontal resolution of about 270 meters for the entire 1,033,840 square-kilometer study area. The modeling analysis was composed of 194 basins, including the eight basins containing ground-water recharge-site investigations. For each grid cell, the BCM computed monthly values of potential evapotranspiration, soil-water storage, in-place ground-water recharge, and runoff (potential stream flow). A fixed percentage of runoff was assumed to become recharge beneath channels operating at a finer resolution than the computational grid of the BCM. Monthly precipitation and temperature data from 1941 to 2004 were used to explore climatic variability in runoff and ground-water recharge. The selected approach provided a framework for classifying study-site basins with respect to climate and dominant recharge processes. The average climate for all 194 basins ranged from hyperarid to humid, with arid and semiarid basins predominating (fig. 6, chapter A, this volume). Four of the 194 basins had an aridity index of dry subhumid; two of the basins were humid. Of the eight recharge-study sites, six were in semiarid basins, and two were in arid basins. Average-annual potential evapotranspiration showed a regional gradient from less than 1 m/yr in the northeastern part of the study area to more than 2 m/yr in the southwestern part of the study area. Average-annual precipitation was lowest in the two arid-site basins and highest in the two study-site basins in southern Arizona. The relative amount of runoff to in-place recharge varied throughout the study area, reflecting differences primarily in soil water-holding capacity, saturated hydraulic conductivity of subsoil materials, and snowpack dynamics. Climatic forcing expressed in El Niño and Pacific Decadal Oscillation indices strongly influenced the generation of precipitation throughout the study area. Positive values of both indices correlated with the highest amounts of runoff and ground-water recharge.

Professional Paper

Effects of building a sand barrier berm to mitigate the effects of the Deepwater Horizon oil spill on Louisiana marshes

The State of Louisiana requested emergency authorization on May 11, 2010, to perform spill mitigation work on the Chandeleur Islands and on all the barrier islands from Grand Terre Island eastward to Sandy Point to enhance the capability of the islands to reduce the movement of oil from the Deepwater Horizon oil spill to the marshes. The proposed action-building a barrier berm (essentially an artificial island fronting the existing barriers and inlets) seaward of the existing barrier islands and inlets-'restores' the protective function of the islands but does not alter the islands themselves. Building a barrier berm to protect the mainland wetlands from oil is a new strategy and depends on the timeliness of construction to be successful. Prioritizing areas to be bermed, focusing on those areas that are most vulnerable and where construction can be completed most rapidly, may increase chances for success. For example, it may be easier and more efficient to berm the narrow inlets of the coastal section to the west of the Mississippi River Delta rather than the large expanses of open water to the east of the delta in the southern parts of the Breton National Wildlife Refuge (NWR). This document provides information about the potential available sand resources and effects of berm construction on the existing barrier islands. The proposed project originally involved removing sediment from a linear source approximately 1 mile (1.6 km) gulfward of the barrier islands and placing it just seaward of the islands in shallow water (~2-m depth where possible) to form a continuous berm rising approximately 6 feet (~2 m) above sea level (North American Vertical Datum of 1988–NAVD88) with an ~110-yd (~100-m) width at water level and a slope of 25:1 to the seafloor. Discussions within the U.S. Geological Survey (USGS) and with others led to the determination that point-source locations, such as Hewes Point, the St. Bernard Shoals, and Ship Shoal, were more suitable "borrow" locations because sand content is insufficient along a linear track offshore from most of Louisiana's barrier islands. Further, mining sediment near the toe of the barrier island platform or edge of actively eroding barrier islands could create pits in the seafloor that will capture nearshore sand, thereby enhancing island erosion, and focus incoming waves (for example, through refraction processes) that could yield hotspots of erosion. In the Breton NWR, the proposed berm would be continuous from just south of Hewes Point to Breton Island for approximately 100 km with the exception of several passages for vessel access. Proposed volume estimates by sources outside of the USGS suggest that the structure in the Breton NWR would contain approximately 56 million cubic yards (42.8 m 3 ) of sandy material. In the west, the berm would require approximately 36 million cubic yards (27.5 m 3 ) of sandy material because this area has less open water than the area to the east of the delta. The planned berm is intended to protect the islands and inland areas from oil and would be sacrificial; that is, it will rapidly erode through natural processes. It is not part of the coastal restoration plan long discussed in Louisiana to rebuild barrier islands for hurricane protection of mainland infrastructure and habitat.

Louisiana

Hydrodynamic simulations of physical aquatic habitat availability for Pallid Sturgeon in the Lower Missouri River, at Yankton, South Dakota, Kenslers Bend, Nebraska, Little Sioux, Iowa, and Miami, Missouri, 2006-07

The objective of this study was to assess the sensitivity of habitat availability in the Lower Missouri River to discharge variation, with emphasis on habitats that might support spawning of the endangered pallid sturgeon. We constructed computational hydrodynamic models for four reaches that were selected because of evidence that sturgeon have spawned in them. The reaches are located at Miami, Missouri (river mile 259.6–263.5), Little Sioux, Iowa (river mile 669.6–673.5), Kenslers Bend, Nebraska (river mile 743.9–748.1), and Yankton, South Dakota reach (river mile 804.8–808.4). The models were calibrated for a range of measured flow conditions, and run for a range of discharges that might be affected by flow modifications from Gavins Point Dam. Model performance was assessed by comparing modeled and measured water velocities. A selection of derived habitat units was assessed for sensitivity to hydraulic input parameters (drag coefficient and lateral eddy viscosity). Overall, model results were minimally sensitive to varying eddy viscosity; varying lateral eddy viscosity by 20 percent resulted in maximum change in habitat units of 5.4 percent. Shallow-water habitat units were most sensitive to variation in drag coefficient with 42 percent change in unit area resulting from 20 percent change in the parameter value; however, no habitat unit value changed more than 10 percent for a 10 percent variation in drag coefficient. Sensitivity analysis provides guidance for selecting habitat metrics that maximize information content while minimizing model uncertainties. To assess model sensitivities arising from topographic variation from sediment transport on an annual time scale, we constructed separate models from two complete independent surveys in 2006 and 2007. The net topographic change was minimal at each site; the ratio of net topographic change to water volume in the reaches at 95 percent exceedance flow was less than 5 percent, indicating that on a reach-average basis, annual topographic change contributed little to habitat area variation. Net erosion occurred at Yankton (the upstream reach) and because erosion was distributed uniformly, there was little affect on many habitat metrics. Topographic change was spatially nonuniform at Little Sioux and Kenslers Bend reaches. Shallow water habitat units and some reach-scale patch statistics (edge density, patch density, and Simpson’s Diversity Index) were affected by these changes. Erosion dominated at the downstream reach but habitat metrics did not vary substantially from 2006 to 2007. Among habitat metrics that were explored, zones of convergent flow were identified as areas that most closely correspond to spawning habitats of other sturgeon species, as identified in the scientific literature, and that are consistent with sparse data on pallid sturgeon spawning locations in the Lower Missouri River. Areas of convergent zone habitat varied little with discharges that would be associated with spring pulsed flows, and relations with discharge changed negligibly between 2006 and 2007. Other habitat measures show how physical habitat varies with discharge and among the four reaches. Wake habitats defined by velocity gradients seem to correspond with migration pathways of adult pallid sturgeon. Habitats with low Froude-number correspond to low energy areas that may accumulate passively transporting particles, organic matter, and larval fish. Among the modeled reaches, Yankton had substantially longer water residence time for equivalent flow exceedances than the other three modeled reaches. Longer residence times result from greater flow resistance in the relatively wide, shallow channel and may be associated with longer residence times of passively transported particulate materials.

Scientific Investigations Report

Surface-water quality and suspended-sediment quantity and quality within the Big River Basin, southeastern Missouri, 2011-13

Missouri was the leading producer of lead in the United States—as well as the world—for more than a century. One of the lead sources is known as the Old Lead Belt, located in southeast Missouri. The primary ore mineral in the region is galena, which can be found both in surface deposits and underground as deep as 200 feet. More than 8.5 million tons of lead were produced from the Old Lead Belt before operations ceased in 1972. Although active lead mining has ended, the effects of mining activities still remain in the form of large mine waste piles on the landscape typically near tributaries and the main stem of the Big River, which drains the Old Lead Belt. Six large mine waste piles encompassing more than 2,800 acres, exist within the Big River Basin. These six mine waste piles have been an available source of trace element-rich suspended sediments transported by natural erosional processes downstream into the Big River. A study was performed by the U.S. Geological Survey in cooperation with U.S. Environmental Protection Agency, Region 7, to calculate and characterize suspended-sediment quantity and quality within the Big River basin after reclamation of the mine waste piles ended in 2012. Streamflow and suspended sediments were quantified and sampled at two locations along a 68-mile reach of the Big River between Bonne Terre and Byrnes Mill, Missouri. The results will help regulatory agencies, such as the U.S. Environmental Protection Agency and U.S. Fish and Wildlife Service, determine impaired reaches and ecosystems for remedial and restoration efforts. Continuous stream stage, water temperature, and turbidity, and discrete suspended-sediment concentration data were collected at the two sites between October 2011 and September 2013. Suspended-sediment samples were collected during various hydrologic conditions to develop a regression model between discrete suspended-sediment concentration and continuous turbidity. Suspended sediments collected during stormflow events were analyzed for concentrations of trace elements such as barium, cadmium, lead, and zinc within two sediment size fractions. Event loads and annual loads of suspended sediment and select trace elements in suspended sediments also were calculated. Suspended-sediment loads computed by the regression model increased downstream from about 201,000 tons at the upstream site to about 355,000 tons at the downstream site during the study period. Stormflow-event-based (hereinafter referred to as “event-based”) suspended-sediment loads ranged from 180 to 32,000 tons at the upstream sampling site and 390 to 53,000 tons at the downstream site along the Big River. Although only seven stormflow events at the upstream site and six at the downstream site were sampled, the event-based suspended-sediment loads accounted for nearly 30 percent of the total suspended-sediment loads computed at both sites, indicating most of the suspended sediment transported through the Big River occurs during higher streamflows. Sediment quality guidelines, known as the threshold effect concentration and the probable effect concentration, used to assess toxicity of trace-element concentrations in sediments were compared to the cadmium, lead, and zinc concentrations in suspended sediment samples collected during stormflow events. All concentrations of cadmium, lead, and zinc in event-based suspended sediment samples exceeded the threshold and probable effect concentrations. Lead and zinc concentrations in the sediment size fraction less than 0.063 millimeters also exceeded the toxic effect threshold, above which sediment is considered to be heavily polluted causing adverse effects on sediment-dwelling organisms. Concentrations of cadmium and zinc in event-based suspended sediment samples were notably higher in samples from the upstream site than samples from the downstream site, indicating the sources of sediments enriched in these trace elements decrease in the downstream area of the watershed. The reduction in concentration of cadmium and zinc could be from dissolution of the constituents during transport or possibly a decrease in downstream source material. The lead concentration exceedance of the probable effects concentration as well as the threshold effects concentration indicates that lead-rich suspended sediments in the fraction less than 0.063 millimeters are readily available within the Big River Basin for transport. These sediments remain in the system from historical mining, and as the reclamation of mine waste piles in the upstream area of the watershed reduce additional sediment loadings, these fine sediments may be continually released as the river scours the streambed and erodes stream banks causing the lead-rich suspended sediment to remain in a state of equilibrium. Barium concentrations in suspended-sediments were nearly twice as high in stormflow event samples collected at the downstream site as compared to samples from the upstream site. The source of barium in the Big River could be from Mineral Fork and Mill Creek, which flow through the historical barite (barium sulfate, also known as tiff) mining district in Washington County, and discharge into the Big River between the two study sites. Total trace-element loads and yields in suspended sediments were computed from the sampled events for each year in the study. The total barium loads in suspended sediments were higher for sampled events collected at the downstream site than the upstream site during both study years. Cadmium and zinc loads in suspended sediments were lower at the downstream site than the upstream site, although the decrease in total load was not substantial during the study period. Lead loads in suspended sediments were lower at the downstream site during the first study year, with a slightly higher load downstream in the second year though the increase from upstream to downstream was small. Event-based yields were higher at the upstream site, indicating that readily available sediment sources are closer to the upstream site where more mining affected areas are located. The estimates determined during large precipitation events indicate that large sources of suspended sediments with large concentrations of trace elements are still available for transport within the Big River.

Missouri

Results of a workshop concerning assessment of the functions of bottomland hardwoods

The U.S. Environmental Protection Agency (EPA) is authorized under Section 404 of the Clean Water Act (33 U.S.C. 1344) to participate in the regulation of the discharge of dredged or fill material into waters of the United States. This regulatory authority is exercised in partnership with the U.S. Army Corps of Engineers, which has responsibility for permit issuance, and in consultation with the U.S. Fish and Wildlife Service and the National Marine Fisheries Service. Through amendments to the original statute, a series of legal actions and court decisions, and the development of operating guidance among the responsible agencies, Section 404 has evolved into the primary mechanism afforded Federal authorities for the protection of wetlands. EPA recognizes the importance of wetlands in achieving the goals of the Clean Water Act, which are to protect and maintain the chemical, physical, and biological integrity of the Nation’s waters. EPA Administrator Lee Thomas has identified wetlands protection as among the highest of Agency priorities. EPA recognizes that bottomland hardwood (BLH) wetlands have vital and unique attributes that, if lost, would severely impact the physical, chemical, and biological integrity of the Nation's waters. As part of a broad program to better protect the Nation's wetlands, EPA has therefore identified bottomland hardwood wetlands as a priority resource requiring special attention on a national basis. Recognizing the importance of implementing an effective, nationally consistent, and scientifically defensible regulatory program, EPA, in October 1984, issued Interim Operating Guidance to its field personnel for implementing the Section 404 regulatory program in bottomland hardwood wetlands. With the goal of improving and finalizing that guidance, EPA is sponsoring a series of workshops designed to answer key questions concerning BLH wetlands, based on the best scientific and technical information currently available. The first two workshops were directed toward summarizing existing scientific and technical knowledge concerning the functions of BLH ecosystems, the characteristics that are important to each function, and the impact of various development activities on those characteristics. The first workshop, which was held in St. Francisville, Louisiana, in December, 1984, examined a wetland zonation concept as a framework for gaining a greater understanding of BLH structure and function. The workshop set out to determine whether characterization of BLH resources as a series of relatively distinct zones, defined by concomitant variation in hydrologic regime, soils, and vegetation, might provide the basis for a useful and scientifically sound regulatory framework. For examp1e, if certain zones are of particular importance to one or more wetland functions that the Clean Water Act was intended to protect, then the zonation concept might be useful from the perspective of how various activities should be regulated. Discussions during the first workshop, however, indicated that the zonation concept provides, at best, only an incomplete picture of the structure and function of BLH ecosystems. In many cases, BLH functions are not limited to or closely correlated with particular zones and, furthermore, many factors other than zone are important determinants of BLH functions. With these responses in mind, the second workshop, held at Lake Lanier, Georgia, in July, 1985, was designed to elicit information on two questions. First, if zones are not an adequate framework for understanding the functions of BLH systems, what characteristics (predictors) can be used to assess the extent to which a particular site performs these functions? And second, what are the impacts of various development activities that often occur in BLH ecosystems on those characteristics and thus on the functions themselves? At the second workshop, individual workgroups dealing with particular subject areas (e.g., hydrology, water quality, fisheries, wildlife, ecosystem processes, and cultural/recreational/economic resources) were able to identify site characteristics that are important determinants of the performance of various functions. For example, the Hydrology Workgroup identified flood storage as one of three major hydrologic functions that BLH ecosystems perform. The workgroup then identified the most important characteristic (e.g., surface area of the site, soil saturation, and others) that determine flood storage and the likely impact of several common activities (e.g., conversion to soybean production and levee construction) on these characteristics. Some of the workgroups also provided estimates of the aggregate impact of activities, acting through all of the characteristics, on certain functions. The workgroups also identified key characteristics that could be used to identify high-value wetlands for various functions. In addition, the workgroups pointed out a number of topics needing further examination and discussion. First, all of the workgroups identified the need to develop the technical basis and information sources to address the problem of cumulative impacts in the regulatory process. Second, most of the workgroups noted the important of contextual variables in assessing the function of a particular site. For example, the location of a BLH site in relationship to other tracts of habitat is an important variable for many wildlife species. Similarly, the extent to which a site retains or transforms contaminants is depended not only on the characteristics of the site, but also on its position in a watershed relative to contaminant inputs. And finally, several of the workgroups pointed out that assessing the impact of an activity on a function is not as simple as "adding up" the impact on individual characteristics, but may depend instead on complex interactions among characteristics. Addressing these questions, as summarized in the objectives and discussions that follow, was the focus of the third workshop, the results of which are described in this report.

Report

Hydrologic conditions and water-quality conditions following underground coal mining in the North Fork of the Right Fork of Miller Creek drainage basin, Carbon and Emery Counties, Utah, 2004-2005

In 2004 and 2005, the U.S. Geological Survey, in cooperation with the Bureau of Land Management, reassessed the hydrologic system in and around the drainage basin of the North Fork of the Right Fork (NFRF) of Miller Creek, in Carbon and Emery Counties, Utah. The reassessment occurred 13 years after cessation of underground coal mining that was performed beneath private land at shallow depths (30 to 880 feet) beneath the NFRF of Miller Creek. This study is a follow-up to a previous USGS study of the effects of underground coal mining on the hydrologic system in the area from 1988 to 1992. The previous study concluded that mining related subsidence had impacted the hydrologic system through the loss of streamflow over reaches of the perennial portion of the stream, and through a significant increase in dissolved solids in the stream. The previous study also reported that no substantial differences in spring-water quality resulted from longwall mining, and that no clear relationship between mining subsidence and spring discharge existed. During the summers of 2004 and 2005, the USGS measured discharge and collected water-quality samples from springs and surface water at various locations in the NFRF of Miller Creek drainage basin, and maintained a streamflow-gaging station in the NFRF of Miller Creek. This study also utilized data collected by Cyprus–Plateau Mining Corporation from 1992 through 2001. Of thirteen monitored springs, five have discharge levels that have not returned to those observed prior to August 1988, which is when longwall coal mining began beneath the NFRF of Miller Creek. Discharge at two of these five springs appears to fluctuate with wet and dry cycles and is currently low due to a drought that occurred from 1999–2004. Discharge at two other of the five springs did not increase with increased precipitation during the mid-1990s, as was observed at other monitored springs. This suggests that flowpaths to these springs may have been altered by land subsidence caused by underground coal mining. Analysis of possible impacts to the fifth spring were inconclusive due to a lack of data collected during the mid-1990s. Discharge at eight other monitored springs in the study area appears to be controlled mainly by climatic fluctuations and was generally near the value measured prior to 1988. Discharge at one of these eight springs is significantly greater than that measured during the longwall mining period. Concentrations of magnesium, calcium, sulfate, and dissolved solids at one undermined spring were elevated in relation to other springs in the study area. Dissolved solids concentration at this spring ranged from 539–709 milligrams per liter. Dissolved-solids concentration for all other springs in the study area ranged from 163 to 360 milligrams per liter and was near the median value measured prior to longwall mining beneath the NFRF of Miller Creek drainage basin. Baseflow measured at a streamflow-gaging station on the NFRF of Miller Creek located downstream of the mined area during the summer of 2004 was near 5 gallons per minute. Baseflow in 2005 increased to 7–8 gallons per minute, due to increased precipitation. This is slightly greater than the range of baseflow measured near the end of the longwall mining period which was approximately 3–5 gallons per minute. Seepage investigations carried out in the summer of 2004 and 2005 along the NFRF of Miller Creek showed a net loss of surface flow along the studied reach. Specific areas within the study reach had streamflow losses prior to longwall mining, however, the study reach as a whole was observed to gain in discharge when measured in 1986–1988, immediately before longwall mining began. The area where the greatest loss in discharge from the NFRF of Miller Creek occurred corresponds to an area where overburden (material overlying a deposit of useful geological materials or bedrock) is between 700 and 210 feet thick. Overburden thickness at the place where the streambed first dried up was approximately 600 feet thick. In 2004, approximately 1,600 ft of the streambed of the NFRF of Miller Creek was dry. Only 300 feet of the streambed was dry during the wetter year of 2005. Prior to longwall mining, no dry reaches were observed, though seepage loss was documented. Average discharge measured at a tributary to the NFRF of Miller Creek has increased from 1.6 gallons per minute measured during longwall mining to 7.2 gallons per minute measured in 2004–2005. During both years of this study, the lower reach of the stream regained flow from this tributary and from seepage gains. Water quality in the lower reach of the NFRF of Miller Creek downstream of the longwall-mined area, showed significantly higher concentrations of magnesium, calcium, sulfate, and strontium, in relation to water in the upper reach of the NFRF of Miller Creek and to the springs sampled in the area. Dissolved-solids concentration measured in the lower reach of the stream in 2004 and 2005 ranged from 1,880 to 2,220 milligrams per liter, while sulfate concentrations ranged from 1,090 to 1,320 mg/L. The maximum contaminant level for drinking water in the state of Utah for dissolved solids and sulfate is 2,000 and 1,000 mg/L respectively. Concentrations of these ions are slightly greater than those measured during and just following mining beneath the NFRF of Miller Creek drainage basin, but are significantly higher than those measured prior to mining. With the exception of strontium, dissolved metals concentrations in the NFRF of Miller Creek were similar to those measured in area springs. pH in the creek and at all spring sites was near neutral. Qualitative observations of the creek bottom suggest that mining-related activities have had little effect on vegetative growth.

Utah

Groundwater flow model for Western Chippewa County–Including analysis of water resources related to industrial sand mining and irrigated agriculture

A groundwater flow model for western Chippewa County, Wisconsin, was developed by the Wisconsin Geological and Natural History Survey (WGNHS) and the U.S. Geological Survey (USGS) using the computer program MODFLOW. The model is the result of a five-year groundwater study commissioned by Chippewa County in 2012 to evaluate the effects of industrial sand mining and irrigated agriculture on the county’s water resources. The study incorporates existing data and newly acquired data from fieldwork conducted within the study area. The groundwater model may be useful for future investigations, such as evaluation of proposed high-capacity well sites, development of municipal wellhead protection plans, and studies that seek to further quantify surface water-groundwater relationships. The model conceptualizes the hydrostratigraphy of western Chippewa County as six stacked layers. Each layer is distinct, beginning with unlithified glacial material at the surface, and alternating between sandstones (that act as aquifers) and shale units (that serve as aquitards). The model is bounded below by Precambrian crystalline bedrock and its perimeter was derived from a regional-scale groundwater flow model. The MODFLOW model represented average conditions during 2011–2013 with “steady-state” assumptions, meaning that simulated water levels do not fluctuate seasonally or from year to year. Steady-state models simplify natural variability, making results of scenario simulations easier to interpret and compare while also maximizing effects of stressors because the simulated stress is always applied (not halted after a few months or years). Model calibration used the parameter estimation code (PEST), and calibration targets included heads (groundwater levels) and streamflows. Calibration focused on 2011–2013 because a large amount of head and streamflow data were available for that period. The MODFLOW model explicitly simulates all sources and sinks of water, including groundwater/surface-water interaction with streamflow routing. Model input included estimates of aquifer hydraulic conductivity and a spatial groundwater recharge distribution developed using a GIS-based soil-water-balance (SWB) model applied to the model area. Groundwater withdrawals were simulated for 269 high-capacity wells across the entire model domain, which includes western Chippewa County and adjacent portions of Dunn, Barron, and Rusk Counties. Collectively, these wells withdrew about 1.14 million gallons per year between 2011 and 2013. Once the model was calibrated, it was applied to two distinct scenarios of increased groundwater withdrawals: one evaluating hydrologic effects of more intensive industrial sand mining and the second evaluating the hydrologic effects of more intensive agricultural irrigation practices. Each scenario was developed with input from Chippewa County and a stakeholder group established expressly for this study. The scenarios were designed to represent reasonable future buildout conditions for both mining and irrigated agriculture. The mining scenario underscores the potential hydrologic effects related to changing land-use practices (i.e., hilltops and farmland becoming sand mines), while the irrigated agriculture scenario illustrates the potential hydrologic effects of intensifying existing land-use practices (i.e., installing new wells to irrigate farm fields). While each scenario evaluated distinctly different conditions, modeling results demonstrated the potential of both scenarios to lower the water table and reduce baseflows in headwater streams within the modeled area. In the case of irrigated agriculture, hydrologic effects were associated directly with groundwater withdrawals. By assuming that irrigation did not decrease, this steady-state simulation represented a sustained future effect. By contrast, hydrologic effects of industrial sand mining were the result of both groundwater withdrawals at mines and land-use changes that effectively reduced recharge to groundwater over distinct phases of active mining. This scenario included a post-mining phase, during which groundwater withdrawals stopped and mined areas were reclaimed to undeveloped prairie grass cover. If reclamation to undeveloped prairie indeed occurs as simulated, long-term increases in the water table and stream baseflows are possible. In this sense, the scenario representing build out of irrigated agriculture led to long-term baseflow declines while the future buildout of industrial sand mining led to declines that dissipated following mine reclamation to undisturbed prairie. Future investigations in similar hydrogeologic settings may find the following insights gleaned from this study useful: ❚❚ The characterization of hydrogeologic properties, delineation of hydrogeologic units, and calibration of groundwater flow models benefited from incorporation of accurate well construction reports, high-quality borehole geophysical logs, and streamflow gaging data. ❚❚ Infiltration testing performed in active mining areas provided evidence that reducing the degree and extent of compaction and enhancing areas designed to retain and infiltrate stormwater runoff could potentially reduce runoff and increase groundwater recharge. ❚❚ Similarly, reclaiming mined areas to prairie grasses would be expected to reduce runoff and increase groundwater recharge by reducing compaction and improving soil structure and vegetation that can slow runoff and enhance infiltration.

Wisconsin

Geology, water-quality, hydrology, and geomechanics of the Cuyama Valley groundwater basin, California, 2008--12

To assess the water resources of the Cuyama Valley groundwater basin in Santa Barbara County, California, a series of cooperative studies were undertaken by the U.S. Geological Survey and the Santa Barbara County Water Agency. Between 2008 and 2012, geologic, water-quality, hydrologic and geomechanical data were collected from selected sites throughout the Cuyama Valley groundwater basin. Geologic data were collected from three multiple-well groundwater monitoring sites and included lithologic descriptions of the drill cuttings, borehole geophysical logs, temperature logs, as well as bulk density and sonic velocity measurements of whole-core samples. Generalized lithologic characterization from the monitoring sites indicated the water-bearing units in the subsurface consist of unconsolidated to partly consolidated sand, gravel, silt, clay, and occasional cobbles within alluvial fan and stream deposits. Analysis of geophysical logs indicated alternating layers of finer- and coarser-grained material that range from less than 1 foot to more than 20 feet thick. On the basis of the geologic data collected, the principal water-bearing units beneath the monitoring-well sites were found to be composed of younger alluvium of Holocene age, older alluvium of Pleistocene age, and the Tertiary-Quaternary Morales Formation. At all three sites, the contact between the recent fill and younger alluvium is approximately 20 feet below land surface. Water-quality samples were collected from 12 monitoring wells, 27 domestic and supply wells, 2 springs, and 4 surface-water sites and were analyzed for a variety of constituents that differed by site, but, in general, included trace elements; nutrients; dissolved organic carbon; major and minor ions; silica; total dissolved solids; alkalinity; total arsenic and iron; arsenic, chromium, and iron species; and isotopic tracers, including the stable isotopes of hydrogen and oxygen, activities of tritium, and carbon-14 abundance. Of the 39 wells sampled, concentrations of total dissolved solids and sulfate from 38 and 37 well samples, respectively, were greater than the U.S. Environmental Protection Agency’s secondary maximum contaminant levels. Concentrations greater than the maximum contaminant levels for nitrate were observed in five wells and were observed for arsenic in four wells. Differences in the stable-isotopic values of hydrogen and oxygen among groundwater samples indicated that water does not move freely between different formations or between different zones within the Cuyama Valley. Variations in isotopic composition indicated that recharge is derived from several different sources. The age of the groundwater, expressed as time since recharge, was between 600 and 38,000 years before present. Detectable concentrations of tritium indicated that younger water, recharged since the early 1950s, is present in parts of the groundwater basin. Hydrologic data were collected from 12 monitoring wells, 56 domestic and supply wells, 3 surface-water sites, and 4 rainfall-gaging stations. Rainfall in the valley averaged about 8 inches annually, whereas the mountains to the south received between 12 and 19 inches. Stream discharge records showed seasonal variability in surface-water flows ranging from no-flow to over 1,500 cubic feet per second. During periods when inflow to the valley exceeds outflow, there is potential recharge from stream losses to the groundwater system Water-level records included manual quarterly depth-to-water measurements collected from 68 wells, time-series data collected from 20 of those wells, and historic water levels from 16 wells. Hydrographs of the manual measurements showed declining water levels in 16 wells, mostly in the South-Main zone, and rising water levels in 14 wells, mostly in the Southern Ventucopa Uplands. Time-series hydrographs showed daily, seasonal, and longer-term effects associated with local pumping. Water-level data from the multiple-well monitoring sites indicated seasonal fluctuations as great as 80 feet and water-level differences between aquifers as great as 40 feet during peak pumping season. Hydrographs from the multiple-well groundwater monitoring sites showed vertical hydraulic gradients were upward during the winter months and downward during the irrigation season. Historic hydrographs showed water-level declines in the Southern-Main, Western Basin, Caliente Northern-Main, and Southern Sierra Madre zone ranging from 1 to 7 feet per year. Hydrographs of wells in the Southern Ventucopa Uplands zone showed several years with marked increases in water levels that corresponded to increased precipitation in the Cuyama Valley. Investigation of hydraulic properties included hydraulic conductivity and transmissivity estimated from aquifer tests performed on 63 wells. Estimates of horizontal hydraulic conductivity ranged from about 1.5 to 28 feet per day and decreased with depth. The median estimated hydraulic conductivity for the older alluvium was about five times that estimated for the Morales Formation. Estimates of transmissivity ranged from 560 to 163,400 gallons per day per foot and decreased with depth. The median estimated transmissivity for the younger alluvium was about three times that estimated for the older alluvium. Geomechanical analysis included land-surface elevation changes at five continuously operating global positioning systems (GPS) and land-subsidence detection at five interferometric synthetic aperture radar (InSAR) reference points. Analysis of data collected from continuously operating GPS stations showed the mountains to the south and west moved upward about 1 millimeter (mm) annually, whereas the station in the center of the Southern-Main zone moved downward more than 7 mm annually, indicating subsidence. It is likely that this subsidence is inelastic (permanent) deformation and indicates reduced storage capacity in the aquifer sediments. Analysis of InSAR data showed local and regional changes that appeared to be dependent, in part, on the time span of the interferogram, seasonal variations in pumping, and tectonic uplift. Long-term InSAR time series showed a total maximum detected subsidence rate of approximately 12 mm per year at one location and approximately 8 mm per year at a second location, while short-term InSAR time series showed maximum subsidence of about 15 mm at one location and localized maximum uplift of about 10 mm at another location.

California

Groundwater/surface-water interactions in the Partridge River Basin and evaluation of hypothetical future mine pits, Minnesota

The Partridge River Basin (PRB) covers 156 square miles in northeastern Minnesota with headwaters in the Mesabi Iron Range. The basin is characterized by extensive wetlands, lakes, and streams in poorly drained and often thin glacial material overlying Proterozoic bedrock. To better understand the interaction between these extensive surface water features and the groundwater system, a three-dimensional, steady-state, groundwater-flow model of the PRB was developed by the U.S. Geological Survey in cooperation with the Great Lakes Indian Fish & Wildlife Commission using the finite-difference computer code MODFLOW-NWT. The model simulates steady-state base flow in streams and groundwater interactions using the streamflow routing (SFR2) package. Existing mining features including tailings basins, stockpiles, pumped mine pits, and flooded mine pits were simulated using either high hydraulic conductivity zones or the drain (DRN) package. The unsaturated zone flow (UZF) package was used to better represent the groundwater system in areas with a high water table and for wetlands often associated with such areas. UZF typically is used to represent unsaturated zone processes but also can simulate the rejection of recharge and groundwater discharge to the land surface when the water table is near land surface. The steady-state model used data from the 2011 to 2013 period when 2011 high-resolution land surface (light detecting and ranging [lidar]) data were available that reflected land-surface and water elevations from mining activity in the basin. The parameter-estimation software suite PEST_HP was used to obtain a best fit of the modeled to measured groundwater levels, streamflow, pit inflow rates, and mapped peat deposits. The PEST calibration used the target residuals from two models with the same model parameters and targets from two separate periods: (1) a 1995–2015 calibration model, which provided a larger number of calibration targets, and (2) a 2011–2013 mining conditions model, which included calibration targets that reflected conditions consistent with the modeled mine-workings topography. Calibration of the PRB model resulted in ranges of glacial horizontal hydraulic conductivity parameters that generally agreed with literature values and other models of the region. Horizontal hydraulic conductivity of the bedrock was higher in the upper bedrock layers where numerous and continuous fractures have been observed and lower in the deeper bedrock layers. Average basin-wide calibrated infiltration was 5.3 inches per year. An average of 4.6 inches per year of infiltration crosses the water table and becomes recharge and 0.7 inch per year is rejected by UZF due to saturated conditions at the land surface. Simulated groundwater runoff (the sum of rejected recharge and groundwater seepage to the land surface) can either be routed to streams or removed from the model as evapotranspiration. The calibrated model indicates relatively shallow groundwater-flow paths dominating and approximately 50 percent of the stream base flow coming from groundwater runoff. The 2011–2013 mining conditions model was then used to develop five model scenarios simulating the response of the groundwater and surface-water system to potential hydrologic stress. The purpose of these mine pit scenarios is to present a possible workflow to quantify a model’s uncertainty for a given model forecast and serve as a possible guide for initial data collection that may improve a future model’s ability to make such a forecast. The scenarios included one scenario with the currently existing Peter Mitchell pit at final buildout and flooded to an elevation of 1,500 feet, and four scenarios with a hypothetical, new mine pit plus the flooded Peter Mitchell at final buildout. The five model scenarios were used to forecast streamflow at six locations in the PRB, pit inflow rates for the new mine pits and the flooded Peter Mitchell pit, and the average depth to water in 12 wetlands. A linear uncertainty analysis was performed using information from the PEST calibration and tools in the PyEMU python package to assess model uncertainty propagation to the model forecasts. Streamflows generally were reduced with future mining and the greatest streamflow reductions occurred from the flooded Peter Mitchell Pit, probably due to its large size. Average depth to groundwater in wetlands was most affected the closer the wetland was to a new mine pit. Linear uncertainty methods were also used to evaluate data worth, which is the ability for potential new groundwater elevation observations to reduce the uncertainty in scenario forecasts. Data worth was performed for a grid of new hydraulic head observations. Overall, areas with nonnegligible data worth generally corresponded to wetland areas with no groundwater seepage to land surface from UZF. These model behaviors indicated that the land-surface boundary condition simulated by the UZF package was pinning the groundwater elevations to the land surface in areas with groundwater seepage (33 percent of the 2011–2013 base conditions model) such that the sensitivity to new observations in these areas was minimal. Therefore, representing wetlands as boundary conditions minimized the usefulness of data worth calculations because wetland areas were present over a large part of the model domain. Probabilistic capture zones were estimated for each of the mines in the model scenarios. A capture zone represents the area contributing recharge to a model feature, like a well or a mine pit, and can be calculated by forward tracking particles from the water table. By using Monte Carlo techniques, it is possible to generate estimated capture zones that include the probability of recharge capture given the uncertainty present in the model. Monte Carlo techniques use randomly generated model parameter sets sampled from a plausible parameter range to create many possible realizations. The resulting capture zone arrays were calculated by tallying the total number of realizations in which a particle from a model cell was captured by the feature. Probabilities from the Monte Carlo runs ranged from 1 (captured in 100 percent of the runs) near the pits to 0 (captured in 0 percent of the runs) at the edges of the capture zone. Capture zones were not always spatially continuous; for example, the capture zone for the proposed mine pits south of the flooded Peter Mitchell pit was discontinuous with capture surrounding the proposed mine pit and north of the flooded Peter Mitchell pit. This northern section represents deeper groundwater flow paths that originate in the topographic high, move under the flooded pit, and discharge into the proposed pit. This pattern of capture indicates the possibility of some deeper flow through the upper fractured bedrock when the shallow groundwater flow system is modified. These results underscore that future site-specific applications of the base condition model require the input of site-specific data and recalibration to focus on the site of interest.

Minnesota

Pesticides in groundwater in the Anacostia River and Rock Creek watersheds in Washington, D.C., 2005 and 2008

The U.S. Geological Survey (USGS), in cooperation with the District Department of the Environment, conducted a groundwater-quality investigation to (a) determine the presence, concentrations, and distribution of selected pesticides in groundwater, and (b) assess the presence of pesticides in groundwater in relation to selected landscape, hydrogeologic, and groundwater-quality characteristics in the shallow groundwater underlying the Anacostia River and Rock Creek watersheds in Washington, D.C. With one exception, well depths were 100 feet or less below land surface. The USGS obtained or compiled ancillary data and information on land use (2001), subsurface sediments, and groundwater samples from 17 wells in the lower Anacostia River watershed from September through December 2005, and from 14 wells in the lower Anacostia River and lower Rock Creek watersheds from August through September 2008. Twenty-seven pesticide compounds, reflecting at least 19 different types of pesticides, were detected in the groundwater samples obtained in 2005 and 2008. No fungicides were detected. In relation to the pesticides detected, degradate compounds were as or more likely to be detected than applied (parent) compounds. The detected pesticides chiefly reflected herbicides commonly used in urban settings for non-specific weed control or insecticides used for nonspecific haustellate insects (insects with specialized mouthparts for sucking liquid) or termite-specific control. Detected pesticides included a combination of pesticides currently (2008) in use, banned or under highly restricted use, and some that had replaced the banned or restricted-use pesticides. The presence of banned and restricted-use pesticides illustrates their continued persistence and resistance to complete degradation in the environment. The presence of the replacement pesticides indicates the susceptibility of the surficial aquifer to contamination irrespective of the changes in the pesticides used. A preliminary review of the data collected in 2005 and 2008 indicated that differences in the surficial geology, land use (as a surrogate for pesticide use), and above-average precipitation for most of 2004 through 2008, as well as differences in the number and performance of USGS laboratory methods used, could have led to more pesticides detected in groundwater samples collected in 2008 than in groundwater samples collected in 2005. Thus, although data from both years of collection were used for interpretive analysis, emphasis was placed on the analysis of the data obtained in 2008. The presence of pesticides in shallow groundwater (less than approximately 100 ft (feet), or 30 m (meters), below land surface) indicated at least the upper surficial aquifer in Washington, D.C. was susceptible to contamination. One or more herbicides or insecticides were detected in groundwater samples collected from 50 percent of the shallow wells sampled in 2005, and from 62 percent of the shallow wells sampled in 2008. Differences among types of pesticides in shallow groundwater were apparent. The most frequently detected class of herbicides was the s-triazine compounds—atrazine, simazine, or prometon, or the atrazine-degradate compounds—2-chloro-4-ethylamino-6-amino-s-triazine (desethylatrazine or CIAT) and 2-chloro-4-isopropylamino-6-amino-s-triazine (hydroxyatrazine or OIET). The next most frequently detected classes of herbicides were the chloroacetanilides, including metolachlor and acetochlor, and the ureic herbicides, including diuron (and degradate, 3,4-dichloroaniline), fluometuron, metsulfuron methyl, sulfameturon, bromacil, and tebuthiuron. Insecticides also were detected, but less frequently than herbicides, with one or more insecticides present in groundwater samples from 38 percent of shallow wells sampled in 2008. Detected insecticides included parent or degradate compounds commonly used for either nonspecific or haustellate (sucking) insects, including chlorpyrifos and dichlorodiphenyldichloroethane (p,p’-DDD; a degradate of dichlorodiphenyltrichloroethane, DDT), and for termite control, including dieldrin, chlordane, heptachlor epoxide, (a degradate of heptachlor), fipronil, and the sulfone and sulfide degradates of fipronil. The concentrations of individual pesticides in shallow groundwater in both years were low. Maximum concentrations were no greater than a few tenths of a microgram per liter (μg/L); typical concentrations often were less than 0.1 μg/L. Multiple pesticides, however, commonly were present in groundwater. For example, in 2008, approximately 88 percent (7 of 8) of the wells that yielded a sample with at least one detectable pesticide contained five or more pesticides. The highest number of detections occurred in a groundwater sample from well WE Ca 32, which is located in a highly developed urban area; this sample contained 15 different pesticide residues. In relation to human and aquatic health, no pesticide concentration in either 2005 or 2008 exceeded Federal drinking-water standards. Groundwater samples from a few sites, however, contained levels of chiefly banned or restricted-use pesticides that exceeded other human-health and (or) aquatic-health guidelines. For example, concentrations of dieldrin in 2008 groundwater samples from three wells—WE Ca 32 (0.028 μg/L), WE Ba 11 (0.016 μg/L), and WW Ac 8 (0.014 μg/L)—fell within the range of concern for 2004 Federally approved non-regulatory USGS Health-Based Assessment benchmarks (0.002 to 0.2 μg/L), and exceeded earlier (1999) Federal criteria for drinking water (0.000052 μg/L). Other individual compounds whose concentrations exceeded 1999 Federal guidelines for samples from one or more of these three sites, or another site, included p,p’-DDD, dichlorodiphenyldichloroethylene (p,p’-DDE; another degradate of DDT), chlordane, and heptachlor epoxide. Pesticide concentrations in groundwater also were compared to three aquatic-health guidelines for freshwater (United States, Great Lakes, or Canada). One or more of these guidelines were exceeded in groundwater samples obtained in 2005 or 2008 for one or more of the compounds chlordane, dieldrin, heptachlor epoxide, p,p’-DDE, p,p’-DDD, and chlorpyrifos. The spatial distribution of pesticides in the shallow groundwater appeared to be related, in part, to land use, a surrogate for pesticide use. Although most of the wells sampled in this study are in parklands or other relatively open and accessible space, multiple pesticides most often were detected in 2008 groundwater samples collected from wells where a considerable percentage (in excess of 60 percent) of the land within a 500-m radius is developed space (residential, commercial, or other urban infrastructure). Insecticides were detected in wells surrounded by at least 50 percent, and most commonly by more than 80 percent, development. Well WE Ca 32, the site associated with the highest number of pesticide residues in groundwater (8 herbicides and 7 insecticides), is in a small residential park, where 99 percent of the surrounding land is well-maintained residential and commercial development. The vertical distribution of detected pesticides in shallow groundwater appeared to be related, in part, to depth below land surface, surficial-bedrock type, and differences in the chemistry of shallow groundwater. Pesticides were detected at relatively shallow depths in wells that may not have fully penetrated the shallow aquifer. For wells in which at least one pesticide was detected, the median depth below land surface to the top of the well screen was 5.8 m, and the maximum depth was 8.5 m. Among the types of surficial materials in which wells were completed—alluvium, terrace deposits, or Potomac Formation sub- or outcrops in the Coastal Plain Province, and saprolite or fractured bedrock (Laurel and Sykesville Formations) underlying saprolite in the Piedmont Province—no pesticides were detected in groundwater associated with wells completed in the alluvium or fractured bedrock. Detections occurred in some but not all wells completed in the other surficial materials. Overall, the pattern in occurrence appeared related to the local permeability of these sediments and groundwater chemistry. Groundwater with multiple pesticide detections tended to occur in permeable sediments (absent any appreciable overlying clay, silt, or clay-silt layers), in conjunction with other common urban contaminants (elevated chloride in excess of tens to hundreds of milligrams per liter (mg/L), and oxic, rather than reduced, groundwater as evidenced by elevated (in excess of 5 mg/L) concentrations of nitrate). The results of this investigation were compared to results from two other similar and recent studies on pesticide occurrence in the shallow aquifer. These included a study in the nearby Maryland and Delaware Coastal Plain Physiographic Province and one in the Maryland and Virginia Piedmont Physiographic Province. Results from these studies were similar to the current study in relation to (a) the types, frequencies, concentrations, and mixtures of pesticides detected; (b) compounds that exceeded human-and aquatic-health criteria; and (c) the occurrence and distribution of pesticides within the surficial aquifer in relation to depths, sediment types, and groundwater chemistries.

Washington D.C.

Plankton communities and summertime declines in algal abundance associated with low dissolved oxygen in the Tualatin River, Oregon

Phytoplankton populations in the Tualatin River in northwestern Oregon are an important component of the dissolved oxygen (DO) budget of the river and are critical for maintaining DO levels in summer. During the low-flow summer period, sufficient nutrients and a long residence time typically combine with ample sunshine and warm water to fuel blooms of cryptophyte algae, diatoms, green and blue-green algae in the low-gradient, slow-moving reservoir reach of the lower river. Algae in the Tualatin River generally drift with the water rather than attach to the river bottom as a result of moderate water depths, slightly elevated turbidity caused by suspended colloidal material, and dominance of silty substrates. Growth of algae occurs as if on a “conveyor belt” of streamflow, a dynamic system that is continually refreshed with inflowing water. Transit through the system can take as long as 2 weeks during the summer low-flow period. Photosynthetic production of DO during algal blooms is important in offsetting oxygen consumption at the sediment-water interface caused by the decomposition of organic matter from primarily terrestrial sources, and the absence of photosynthesis can lead to low DO concentrations that can harm aquatic life. The periods with the lowest DO concentrations in recent years (since 2003) typically occur in August following a decline in algal abundance and activity, when DO concentrations often decrease to less than State standards for extended periods (nearly 80 days). Since 2003, algal populations have tended to be smaller and algal blooms have terminated earlier compared to conditions in the 1990s, leading to more frequent declines in DO to levels that do not meet State standards. This study was developed to document the current abundance and species composition of phytoplankton in the Tualatin River, identify the possible causes of the general decline in algae, and evaluate hypotheses to explain why algal blooms diminish in midsummer. Plankton and water-quality sample data from 2006 to 2008 were combined with parts of a larger discrete-sample and continuous water-quality monitoring dataset and examined to identify patterns in water-quality and algal conditions since 1991, with a particular emphasis on 2003–08. Longitudinal plankton surveys were conducted in 2006–08 at six sites between river miles (RM) 24.5 and 3.4 at 2- to 3-week intervals, or 5–6 per season, and in-situ bioassay experiments were conducted in 2008 to examine the potential effects of wastewater treatment facility (WWTF) effluent and phosphorus additions on phytoplankton biomass and algal photosynthesis. Phytoplankton and zooplankton community composition, streamflow, and water-quality data were analyzed using multivariate statistical techniques to gain insights into plankton dynamics to determine what factors might be most tied to the abundance and characteristics of the phytoplankton assemblages, and identify possible causes of their declines. The connection between low-DO events and algal declines was clearly evident, as bloom crashes were nearly always followed by periods of low DO. Algal blooms occurred each year during 2006–08, producing maximum chlorophyll-a (Chl-a) values in June or July generally in the range of 50–80 micrograms per liter (µg/L). Bloom crashes and absence of sufficient algal photosynthesis in mid- to late-summer contributed to minimum DO concentrations that were less than the State standard of 6.5 milligrams per liter (mg/L) based on the 30-day mean daily concentration, for 62–74 days each year. At times, the absolute minimum State standard (4 mg/L DO) also was not met. To learn more about why low-DO events occurred, specific algal declines during 2003–08 were scrutinized to determine their likely causal factors. From this information, a series of hypotheses were formulated and evaluated in terms of their ability to explain recent declines in algal populations in the river in late summer. Meteorological, streamflow, turbidity, water temperature, and conductance conditions in the Tualatin River during the 2006–08 summer seasons were not atypical. Natural flow comprised the majority (70–80 percent) of flow each year during spring, but then reduced to 38–40 percent during midsummer when WWTF effluent—which contributed as much as 36 percent—and flow augmentation releases comprised a greater fraction of the flow. Summer 2008 was unusual, however, in the prolonged influence from the Wapato Lake agricultural area near Gaston in the upper part of the basin. The previous winter flooding and levee breach at Wapato Lake caused a much greater area of inundation. As a result, drainage from this area continued into July, much later than normal. A subsequent algal bloom in Wapato Lake then seeded the upper Tualatin River, and this drainage had a profound effect on the downstream plankton community. A large blue-green algae bloom developed—the largest in recent memory—prompting a public health advisory for recreational contact for about two weeks. Algal growths and surface blooms are a common feature of the Tualatin River. Most of the dominant algae have growth forms and morphologies that are well suited for planktonic life, employing spines and gas vacuoles to resist settling, forming colonies, and producing mucilage (or toxins) to resist zooplankton grazing. In 2006–08, 143 algal taxa were identified in 117 main-stem samples; diatoms and green algae were more diverse than blue-green, golden, and cryptophyte algae, although these later groups sometimes dominated the overall volumetric abundance (biovolume). The most frequently occurring taxa, occurring in 97–99 percent of samples, were flagellated cryptophytes Cryptomonas erosa and Rhodomonas minuta. Other important algal taxa included centric diatoms Stephanodiscus, Cyclotella, and Melosira species and colonial green algae Scenedesmus and Actinastrum. These taxa comprised the majority of the algal biovolume during much of the growing season. A general seasonal trend in the phytoplankton assemblages was observed, with dominance by filamentous centric diatoms Stephanodiscus and Melosira in spring and early summer, and flagellated cryptophytes and green algae, particularly Chlamydomonas sp., in late-summer; or, in 2008, dominance by blue-green algae Anabaena flos-aquae and Aphanizomenon flos-aquae during the Wapato Lake bloom event. There were 99 zooplankton taxa identified from the Tualatin River in 2006–08, composed primarily of cladocerans, copepods, and rotifers. A seasonal increase in zooplankton abundance was observed in early summer just as or shortly after the phytoplankton population began to increase, with populations growing to 15,000−120,000 organisms per cubic meter in the lower river. Zooplankton abundance showed a predictable and distinct longitudinal downstream increase, particularly downstream of Highway 99W (RM 11.6). Although grazing rates were not measured, the data suggest that, at times, zooplankton grazing may affect algal abundance and species composition in the Tualatin River, with diatoms becoming relatively less abundant and flagellated cryptophytes and green algae relatively more abundant during periods when zooplankton densities were highest. Multivariate statistical analyses identified soluble reactive phosphorus (SRP), natural flow, flow augmentation, and WWTF effluent as important factors influencing Tualatin River phytoplankton populations, with zooplankton density (particularly rotifers and copepods), specific conductance, chloride, and water temperature also having an important influence. Although SRP was highly correlated with the plankton communities, that correlation was likely the result of high or low algal activity (uptake) as SRP concentrations were often reduced to low levels during blooms. While previous studies have already established that phosphorus, among other factors such as flow, places a theoretical cap on the size of the phytoplankton population in the river, sometimes algal declines occur when SRP concentrations are apparently sufficient. To identify alternative causal factors, additional analyses were performed without SRP to focus on other water-quality parameters, zooplankton density, and flow factors. Considering data for all 3 years and including just those samples from the lower Tualatin River not affected by the 2008 Wapato Lake drainage event, three factors (percentage of reservoir flow augmentation, total natural flow, and rotifer density) best explained variations in the phytoplankton assemblages. Analyses focusing on the possible causes of algal declines included the above multivariate analyses, scrutiny of 10 specific instances of declines in algal populations during 2003–08 including several bloom–crash sequences, and analyses of historic routine watershed monitoring data from Clean Water Services. Six factors were hypothesized to be important in causing bloom crashes or impeding blooms from rebounding in August: (1) light limitation from cloudy weather, (2) a reduction in the plankton inocula or “seed” entering the lower river from upstream sources, (3) increased summer streamflows, (4) changes in the dominant sources of flow as the percentage of flow augmentation and WWTF discharges have increased, (5) zooplankton grazing, and (6) low concentrations of bioavailable phosphorus (<0.015 milligram per liter). All of these hypotheses are supported in some fashion by the available data and statistical analyses. Zooplankton grazing, short-term declines in photosynthesis from cloudy weather, total flow as it affects residence time, and the dominant source of flow are primary factors responsible for the low-DO events caused by declines in algae in the lower Tualatin River during late summer. Cloudy weather and increased turbidity are known to inhibit algal growth in the Tualatin River, and slight increases in turbidity in recent years may be a problem. Upstream sources of algae are critical in determining the characteristics and size of downstream populations, as illustrated by the Wapato Lake bloom in 2008, but more data are needed from upstream to fully define the importance of this connection. The sources of flow, through their differential contribution of plankton inocula (quality and amount), were, at times, important factors affecting phytoplankton populations. While SRP concentrations were often most highly correlated with phytoplankton species community, the bioavailability of phosphorus is still somewhat unknown and there are several sources to consider. Preliminary bioassay tests suggested that while treated wastewater effluent may stimulate algae at 30 percent concentrations, negative effects (or decreased stimulation) on Chl-a and DO production may occur at concentrations of 50 percent. Targeted data collection and future research will be needed to further understand the importance of these factors on Tualatin River phytoplankton. While the data and analysis completed for this report provide insights into future research and monitoring that would be useful to continue, additional monitoring of turbidity, Chl-a, and plankton abundance and species composition in the upper part of the basin would enhance our understanding of plankton dynamics and factors affecting phytoplankton abundance in the lower river. Assessment of the key upstream sources of algal inocula via surveys of the major flow sources as well as tributaries and wetlands would provide useful information for the management of river water quality. Other studies that could prove useful for developing management strategies include targeted experiments to evaluate the bioavailability of phosphorus from a variety of sources. New research on phytoplankton–zooplankton interactions, and studies of planktivorous fish, might also provide insight about food web dynamics and potential “top-down” effects of fish predation on the plankton communities. In addition, further development of neural-network or other water-quality models would help to evaluate management strategies and provide forecasts of water-quality conditions. Finally, periodic future reassessments of the available data with the multivariate statistical tools used in this study would be helpful to assess whether and how plankton communities are changing, and to continue to shed light on the importance of factors shaping the plankton. Although certain types and sizes of algal blooms are undesirable, minimum phytoplankton populations are an important part of aquatic food webs and are needed to maintain healthy levels of DO in the river. By understanding the sources, characteristics, causal factors, and responses of the plankton communities, management strategies can be developed to improve DO conditions in the lower Tualatin River during the important summer low-flow period.

Oregon

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California