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At least 1,531 records · Page 85Linked to original sources
USGS2017

Long-term monitoring data provide evidence of declining species richness in a river valued for biodiversity conservation

Free-flowing river segments provide refuges for many imperiled aquatic biota that have been extirpated elsewhere in their native ranges. These biodiversity refuges are also foci of conservation concerns because species persisting within isolated habitat fragments may be particularly vulnerable to local environmental change. We have analyzed long-term (14- and 20-y) survey data to assess evidence of fish species declines in two southeastern U.S. rivers where managers and stakeholders have identified potentially detrimental impacts of current and future land uses. The Conasauga River (Georgia and Tennessee) and the Etowah River (Georgia) form free-flowing headwaters of the extensively dammed Coosa River system. These rivers are valued in part because they harbor multiple species of conservation concern, including three federally endangered and two federally threatened fishes. We used data sets comprising annual surveys for fish species at multiple, fixed sites located at river shoals to analyze occupancy dynamics and temporal changes in species richness. Our analyses incorporated repeated site-specific surveys in some years to estimate and account for incomplete species detection, and test for species-specific (rarity, mainstem-restriction) and year-specific (elevated frequencies of low- or high-flow days) covariates on occupancy dynamics. In the Conasauga River, analysis of 26 species at 13 sites showed evidence of temporal declines in colonization rates for nearly all taxa, accompanied by declining species richness. Four taxa (including one federally endangered species) had reduced occupancy across the Conasauga study sites, with three of these taxa apparently absent for at least the last 5 y of the study. In contrast, a similar fauna of 28 taxa at 10 sites in the Etowah River showed no trends in species persistence, colonization, or occupancy. None of the tested covariates showed strong effects on persistence or colonization rates in either river. Previous studies and observations identified contaminants, nutrient loading, or changes in benthic habitat as possible causes for fish species declines in the Conasauga River. Our analysis provides baseline information that could be used to assess effectiveness of future management actions in the Conasauga or Etowah rivers, and illustrates the use of dynamic occupancy models to evaluate evidence of faunal decline from time-series data.

Georgia↗
USGS1981

Birds of the St. Croix River valley: Minnesota and Wisconsin

The St. Croix River Valley encompasses nearly 11,550 km2 in east-central Minnesota and northwestern Wisconsin. A wide range of habitats are available for birds including upland oak, lowland deciduous, maple-basswood, lowland and upland coniferous forests, natural basin wetlands, and grasslands. Situated in the north-central region of the United States, the valley is a biological 'crossroads' for many species. Because of the mixed affinities of plant communities, the valley includes the northern and southern range limits for a number of species. Also, because the valley lies near the forest-prairie transition zone, many typical western breeding species (e.g. pintail, western meadowlark, yellow-headed blackbird) breed in proximity to typical eastern species such as tufted titmouse, eastern meadowlark, and cardinal. From 1966 to 1980, I conducted extensive surveys of avian distribution and abundance in the St. Croix River Valley. I have supplemented the results of these surveys with published and unpublished observations contributed by many ornithologists. These additional data include compilations from Christmas Bird Counts sponsored by the National Audubon Society and from the Breeding Bird Survey coordinated by the U.S. Fish and Wildlife Service. Three hundred fourteen species have been recorded in the study area; data are presented on the migration period, nesting season distribution, winter distribution, relative abundance, and habitat use of each species. Recognizing the uniqueness of the area, and its importance not only to wildlife but also to man, the U.S. Congress designated the St. Croix a National Scenic Riverway. This action provided a considerable degree of protection to lands along and directly adjacent to the river. Unfortunately, no similar legal measure exists to protect lands away from the river. With the exception of the northern quarter of the St. Croix River Valley, agricultural interests have made significant inroads into the habitat base. The continuing expansion of the nearby Minneapolis-St. Paul metropolitan region has degraded or destroyed many woodlots, upland fields, and wetlands. In numerous instances, degradation of natural habitats has influenced the abundance and distribution of bird species. Because of these changes, both the Federal government and State Departments of Natural Resources have listed several species in various categories based on their current status. In the St. Croix River Valley, seven species are endangered, eight are threatened, and 29 are watch or priority status in either or both states. Data presented in this report are of value to land managers, land use specialists, and ornithologists, in assessing current and projected habitat alterations on the avifauna of this valley. The St. Croix River bisects a large region of western Wisconsin and east central Minnesota that exhibits a wide range of habitat types. This region supports not only birds, but many mammals, fishes, reptiles and amphibians, and several thousand species of vascular and nonvascular plants. The river itself is relatively clean through most of its course, and its natural flow is interrupted by only two small dams. Because the river lies within a 1-day drive of nearly 10 million people (Waters 1977), use of the area for recreational purposes is extremely heavy. Recreational pursuits include sunbathing, boating, and wild river kayaking in the summer, and ice fishing and cross-country skiing in the winter. The large number of unique and highly fragile habitats that exist there may never be compatible with the uses and abuses of the land that go with expanding human populations. Through the efforts of a number of citizens concerned with the quality of their environment and the foresightedness of several local, State, and Federal legislators, a portion of the upper St. Croix River Valley (hereafter termed 'the Valley') was established as a National Wild and Scenic River. Through establishment of t

North American Fauna↗
USGS2016

mizuRoute version 1: A river network routing tool for a continental domain water resources applications

This paper describes the first version of a stand-alone runoff routing tool, mizuRoute. The mizuRoute tool post-processes runoff outputs from any distributed hydrologic model or land surface model to produce spatially distributed streamflow at various spatial scales from headwater basins to continental-wide river systems. The tool can utilize both traditional grid-based river network and vector-based river network data. Both types of river network include river segment lines and the associated drainage basin polygons, but the vector-based river network can represent finer-scale river lines than the grid-based network. Streamflow estimates at any desired location in the river network can be easily extracted from the output of mizuRoute. The routing process is simulated as two separate steps. First, hillslope routing is performed with a gamma-distribution-based unit-hydrograph to transport runoff from a hillslope to a catchment outlet. The second step is river channel routing, which is performed with one of two routing scheme options: (1) a kinematic wave tracking (KWT) routing procedure; and (2) an impulse response function – unit-hydrograph (IRF-UH) routing procedure. The mizuRoute tool also includes scripts (python, NetCDF operators) to pre-process spatial river network data. This paper demonstrates mizuRoute's capabilities to produce spatially distributed streamflow simulations based on river networks from the United States Geological Survey (USGS) Geospatial Fabric (GF) data set in which over 54 000 river segments and their contributing areas are mapped across the contiguous United States (CONUS). A brief analysis of model parameter sensitivity is also provided. The mizuRoute tool can assist model-based water resources assessments including studies of the impacts of climate change on streamflow.

Geoscientific Model Development↗
USGS1989

Hydrological, morphometrical, and biological characteristics of the connecting rivers of the International Great Lakes: a review

The connecting channels of the Great Lakes are large rivers (1, 200-9, 900 m3 • s-1) with limited tributary drainage systems and relatively stable hydrology (about 2:1 ration of maximum to minimum flow). The rivers, from headwaters to outlet, are the St. Marys, St. Clair, Detroit, Niagara, and St. Lawrence. They share several characteristics with certain other large rivers: the fish stocks that historically congregated for spawning or feeding have been overfished, extensive channel modification have been made, and they have been used as a repository for domestic and industrial wastes and for hydroelectric energy generation. Levels of phosphorus, chlorophyll a, and particulate organic matter increase 3- to 5-fold from the St. Marys River to the St. Lawrence River. Biological communities dependent on nutrients in the water column, such as phytoplankton, periphyton, and zooplankton similarly increase progressively downstream through the system. The standing crop of emergent macrophytes is similar in all of the rivers, reflecting the relatively large nutrient pools in the sediments and atmosphere. Consequently, emergent macrophytes are an important source of organic matter (67% of total primary production) in the nutrient poor waters of the St. Marys River, whereas phytoplankton production dominates (76%) in the enriched St. Lawrence River. Submersed and emergent macrophytes and the associated periphyton are major producers of organic matter in the connecting channels. Another major source of organic matter (measured as ash free dry weight, AFDW) in the Detroit River is sewage, introduced at a rate of 26, 000 t per year. The production of benthos ranges from a low 5.4 g AFDW•m-2 in the Detroit River to a high of 15.5 g AFDW•m-2 in the St. Marys River. The rivers lack the organic transport from riparian sources upstream but receive large amounts of high quality phytoplankton and zooplankton from the Great Lakes.

Canadian Special Publication of Fisheries and Aqua↗
USGS2013

Status and trends monitoring of the mainstem Columbia River: sample frame development and review of programs relevant to the development of an integrated approach to monitoring

Implementing an Integrated Status and Trends Monitoring program (ISTM) for the mainstem Columbia River will help identify trends in important natural resources and help us understand the long-term collective effects of management actions. In this report, we present progress towards the completion of a stepwise process that will facilitate the development of an ISTM for the mainstem Columbia River. We discuss planning and regulatory documents that can be used to identify monitoring goals and objectives and present existing monitoring and research activities that should be considered as the development of a Columbia River ISTM proceeds. We also report progress towards the development of sample frames for the Columbia and Snake Rivers and their floodplains. The sample frames were formulated using Digital Elevation Models (DEM’s) of the river channel and upland areas and a Generalized Random-Tessellation Stratified (GRTS) algorithm for an area based resource to generate “master sample(s).” Working with the Pacific Northwest Aquatic Monitoring Partnership (PNAMP) we facilitated the transfer of the sample frames to the PNAMP “Monitoring Sample Designer” tool. We then discuss aspects of response and survey designs as they pertain to the formulation of a mainstem Columbia River ISTM. As efforts to formulate an ISTM for the mainstem Columbia River proceed, practitioners should utilize the extensive literature describing the planning and implementation of fish and wildlife mitigation and recovery efforts in the Columbia River Basin. While we make progress towards establishing an ISTM framework, considerable work needs to be done to formulate an ISTM program for the mainstem Columbia River. Long-term monitoring programs have been established for other large rivers systems; scientists that have experience planning, implementing, and maintaining large river monitoring efforts such as those in the Colorado, Illinois, and Mississippi Rivers should be consulted and involved as efforts proceed.

Idaho;Oregon;Washington↗
USGS1958

Ground-water resources in the tri-state region adjacent to the Lower Delaware River

The purpose of this report is to appraise and evaluate the groundwater resources of a tri-state region adjacent to the lower Delaware River that is centered around Philadelphia, Pa., and Camden, N. J., and includes Wilmington, Del., and Trenton, N.J. Specifically, the region includes New Castle County, Del.; Burlington, Camden, Gloucester, Mercer, and Salem Counties in New Jersey; and Bucks, Chester, Delaware, Montgomery, and Philadelphia Counties in Pennsylvania. The peculiar advantages of ground water, such as its availability in many places without the necessity for expensive pipelines and its relatively uniform temperature and quality, make it an especially valuable resource in an industrial area. Large, readily available supplies of good, fresh water have contributed substantially to the recent rapid industrial growth of the lower Delaware River basin and will be vital to its continued prosperity. The major part of these supplies is drawn from the streams passing through the region, but very large quantities of ground water also are used. The region is divided almost equally by the Fall Line, which extends in a southwesterly direction along the general course of the Delaware River from Trenton, N.J., to Wilmington, Del., and beyond. Northwest of the Fall Line is a region of consolidated rocks in which ground water occurs mainly in cracks, crevices, and openings created or enlarged by weathering. The capacity of the various geologic formations to yield water depends largely upon the degree to which they have been fractured and weathered. The yield of individual wells in this part of the region is generally small to moderate and not readily predictable. Ground water in this part of the region is generally low in dissolved minerals and suitable for many uses without treatment. Southeast of the Fall Line lie the unconsolidated rocks of the Coastal Plain. Ground water occurs in these rocks largely in the pore spaces between the individual mineral grains. The major formations and the principal aquifers are rather uniform in their water-bearing characteristics over large areas. The yield of individual wells is moderate to very large and may be predicted with a reasonable degree of assurance. Sufficient quantities of ground water are available in most places for all ordinary purposes. The chemical quality of the ground water from the Coastal Plain aquifers is generally acceptable for most uses, but objectionable quantities of iron or other minerals are found in some places, and some waters have a low pH and are corrosive. More than 40 distinct geologic formations occur in the region. They range in age from Precambrian to Recent. Nearly all will yield some water to wells. However, only about a dozen yield water freely enough to be considered major aquifers. Of these, the sands of the Raritan and Magothy formations have been developed most intensively, and the Cohansey sand appears to have the greatest capacity for additional development. The present withdrawal of ground water in the region is estimated to average more than 200 mgd, of which more than half is drawn from the aquifers in the Raritan and Magothy formations. It is estimated that additional supplies of ground water, aggregating more than 1 billion gallons a day, can be developed within the region. Furthermore, substantial additional quantities can be developed outside the region for use within it if the need should ever arise. Induced recharge from the Delaware River supplies a substantial portion of the total water drawn from the Raritan and Magothy formations. In some areas, the quality of the water from these aquifers is approaching that of the river. Increased withdrawals of water from wells along the river will tend to increase induced recharge. Thus, the maintenance of a good quality of water in the river, which is desirable for many other reasons, is imperative if the quality of the ground-water supply is to be maintained. The proposed deepening of the Delaware River channel from Philadelphia to Trenton will greatly increase the opportunity for the interchange of water between the river and the adjacent aquifers. Whether this will be beneficial or detrimental to the ground-water supplies will depend upon the quality of the water in that reach of the river. If an acceptable quality of river water is maintained, the groundwater resources of the region will be augmented. If salt water from the ocean or excessive contamination from other sources should render the river water undesirable as a source of recharge, actual and potential ground-water supplies aggregating about 250 mgd would be endangered. The danger of salt-water encroachment into the aquifers normally yielding fresh water may limit the optimum yield of some of the most important aquifers in the region. Encroachment may come either from salt water in the surface-water bodies of the region or from parts of the aquifers, normally containing salt water. The protection of ground-water supplies against salt-water encroachment can be maintained only by constant vigilance, careful distribution of the pumping from the aquifers, regular sampling of outpost wells in exposed localities, and adjustment of rates of pumping in the light of changing conditions. The maximum beneficial utilization of the ground-water resources cannot be accomplished in haphazard fashion. It must be planned and controlled on the basis of sound, current information about the hydrology of the various aquifers. Continued and, in some areas, intensified investigations of the ground-water resources of the region should form the basis for such planning and control.

New Jersey, Pennsylvania, Delaware↗
USGS2014

Population trends of smallmouth bass in the upper Colorado River basin with an evaluation of removal effects

Smallmouth bass Micropterus dolomieu were rare in the upper Colorado River basin until the early 1990’s when their abundance dramatically increased in the Yampa River sub-basin. Increased abundance was due primarily to colonization from Elkhead Reservoir, which was rapidly drawn down twice, first to make improvements to the dam (1992) and a second time for reservoir expansion (2005), and allowed escapement of resident bass to the river through an unscreened outlet. Elkhead Reservoir is located on Elkhead Creek, a tributary of the Yampa River. The rapid Elkhead Reservoir drawdown in 1992 was followed by a period of drought years with low, early runoff in the Yampa River sub-basin that benefitted smallmouth bass reproduction. This combination of factors allowed smallmouth bass to establish a self-sustaining population in the Yampa River. Subsequently, successful recruitment allowed smallmouth bass to disperse upstream and downstream in the Yampa River and eventually move into the downstream Green River. Smallmouth bass were also likely introduced, by unknown means, into the upper Colorado River and have since dispersed in this sub-basin. The rapid increase of smallmouth bass in the upper Colorado River basin overlapped with significant reductions in native fish populations in some locations. The threat to these native fishes initiated intensive mechanical removal of smallmouth bass by the Upper Colorado River Endangered Fish Recovery Program. In general, three factors explain fluctuating patterns in smallmouth bass density in the upper Colorado River basin in the last decade: reductions due to electrofishing removal, bass recovery after exploitation due to recruitment and immigration, and changes due to environmental factors not related to electrofishing and other management actions. Our analyses indicated that smallmouth bass densities were substantially reduced in most years by 7 electrofishing removal efforts. Less often, but dramatically in some cases, environmental effects were also responsible for significant declines in smallmouth bass densities in some reaches. Abundant year classes of young smallmouth bass produced in low flow and warm years such as 2007 have potential to overwhelm removal efforts, and the year class persists for one or more years. Nonetheless, it appears that increased electrofishing removal efforts from 2007 to 2011 resulted in sustained reductions in density of smallmouth bass sub-adults and adults throughout the upper basin despite environmental conditions that favored smallmouth bass reproduction in some years (e.g. 2007 and 2009), subsequent recruitment into sub-adult and adult age classes, and movement of smallmouth bass which previously (prior to increases in electrofishing removal efforts) allowed densities to recover in some reaches. We recommend that removal efforts continue in most areas of the upper basin but that the Recovery Program consider allocating effort based on population trends and suspected areas of highest smallmouth bass reproduction. For instance, reproduction, recruitment, and movement of smallmouth bass allowed densities to recover in some reaches, particularly Little Yampa Canyon. Smallmouth bass population recovery implies that areas such as Little Yampa Canyon itself or adjacent reaches (especially upstream), may provide important habitat for age-0 production. We recommend continued assessment of smallmouth bass populations in reaches where reproduction or age-1 nurseries are suspected, such as Little Yampa Canyon and the adjacent upstream reach. It may also be necessary to expand monitoring to areas surrounding suspected sources of smallmouth bass reproduction and increase electrofishing removal effort in these reaches.

Colorado, Utah↗
USGS2019

Integrated hydrologic modeling of the Salinas River, California, for sustainable water management

The Salinas River is the largest river in California’s Central Coast region. Groundwater resources of the Salinas River basin are used to meet water supply needs, including crop irrigation and municipal water supply. Two large multipurpose reservoirs also supply irrigation and municipal water uses. Historical imbalances between supply and demand have resulted in sinking groundwater levels, seawater intrusion, regulatory actions on pumping, adjudication, and requirements for minimum in-stream fish flows. Present needs include finding replacement water supplies and improving watershed management to comply with legal mandates, adapt to future climate variability and landuse conversions, and improve environmental conditions. The Salinas Valley Integrated Hydrologic Model (SVIHM) was developed to help water managers evaluate and adjust to projected impacts on water supplies and demands in the Salinas Valley watershed caused by changes in land use, population, and climate. The SVIHM includes four modeling components: (1) the Basin Characterization Model (BCM), (2) the Hydrologic Simulation Program – FORTRAN (HSPF), (3) MODFLOW - One Water Hydrologic Model (MF-OWHM), and (4) the Surface Water Operations (SWO) package. The BCM and HSPF components compose the Salinas Valley Watershed Model (SVWM). The 4,530 square-mile (mi2) SVWM domain encompasses the entire Salinas River watershed, as well as coastal drainages adjacent to the Salinas River outflow, and includes two separate and connected HSPF model domains, the 2,540 mi2 upper Salinas River and the 1,990 mi2 lower Salinas River models. SVWM (1) simulates the water budget for the entire Salinas River basin containing both the SVIHM domain as well as the mountainous terrain of the tributary headwater areas not included in the SVIHM; and (2) was used to develop the 148 boundary inflows for the SVIHM. Simulated evapotranspiration (ET) is the largest component of the water budget after precipitation, with a 71-year average basin-wide ET of 13.9 in/yr, compared to the basin-wide average precipitation of 18.4 in/yr. Simulated ET ranges from 15 to 29 in/yr along the western side of the SVWM to less than 10 in/yr throughout the valley floor and in the southeast part of the Salinas River watershed. The simulated total 71-year average inflow to the SVIHM was 890 ft3/sec (about 640,000 acre-feet per year), with the highest average inflow of 270 ft3/sec simulated for the Nacimiento River; whereas, the simulated 71-year average streamflow at the mouth of the Salinas River was only about 190 ft3/sec, indicating that most of the streamflow generated in the Salinas River basin is lost to channel seepage. The lack of sustained baseflow causes streamflow to be highly sensitive to the temporal variability in precipitation, especially during the drier periods, and this increases the importance of developing adequate reservoir management, flow augmentation, and conjunctive water use scenarios for potential future drought periods and potentially increased temporal variability in precipitation.

California↗
USGS2020

Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River Fall Chinook Salmon ESU: January 2019 - December 2019

The portion of the Snake River fall Chinook salmon Oncorhynchus tshawytscha evolutionary significant unit (ESU) that spawns upstream of Lower Granite Dam transitioned from low to high abundance during 19922019 in association with U.S. Endangered Species Act recovery efforts and other federally mandated actions. This annual report focuses on (1) numeric and habitat use responses by natural- and hatchery-origin spawners, (2) phenotypic and numeric responses by natural-origin juveniles, and (3) use of a small unmanned aerial system (sUAS) to search for fall Chinook salmon redds and carcasses. Spawners have located and used most of the available spawning habitat and that habitat is gradually approaching redd capacity. Timing of spawning and fry emergence have been relatively stable, but effects of density dependence are evident in juvenile life stages. Apparent abundance of juvenile fall Chinook salmon has increased and we noted the following responses: parr dispersal from riverine rearing habitat into Lower Granite Reservoir has become earlier; growth rate (g/d) and dispersal size of parr declined; and passage timing of smolts from the two Snake River reaches has become earlier and downstream movement rate faster. These findings coupled with stock-recruitment analyses presented in this report provide evidence for density-dependence in the Snake River reaches and in Lower Granite Reservoir that was influenced by the expansion of the recovery program. The long-term goal is to use this information in a comprehensive modeling effort to conduct action-effectiveness and uncertainty research and to inform Fish Population, Hydrosystem, Harvest, Hatchery, and Predation and Invasive Species Management Research, Monitoring, and Evaluation (RM&E) progams. In 2019, the U.S. Geological Survey (USGS) shifted survey efforts in the Snake River toward deepwater redd searches and fish collection for parentage-based tagging (PBT) analyses because all unmanned aerial system (UAS) activities were suspended by the Department of the Interior two weeks into the spawning season. We counted 81 deepwater redds at 17 of the 29 sites surveyed. Redd depths averaged 3.6 m. We collected a total of 123 live fall Chinook salmon from 16 unique geographic locations that spanned 55 river kilometers. Forty-six fish were recovered at Eureka Bar (rkm 307.1) and Kirby Creek (rkm 352.0), which accounted for 37% of all collected fish in 2019. Most (73 fish) post-spawned salmon were collected from early to mid-November just after peak spawning. A summary of 2019 PBT results can be found in Appendix A.1. In 2019, we PIT tagged subyearling fall Chinook salmon in both the Snake and Clearwater rivers. In the Snake River, we tagged 410 fish with 8-mm tags, 666 fish with 9-mm tags, and 1,082 fish 12-mm tags. During seining, our recapture rate of previously tagged fish was slightly higher in the lower reach at 11.4% than in the upper reach at 10.6%. In an effort to represent more of the population through tagging, we tagged fish as small as 45 mm with 8-mm tags at one site in the upper reach. This allowed us to increase the number of fish tagged in that reach by 17.7%. An additional 10.6% of collected fish could have been tagged in the lower reach had we used 8-mm tags in that reach. In the Clearwater River, we tagged 2,451 subyearlings and recaptured 260 (10.6%) fish in the river and 66 fish (48 tagged by USGS, 18 tagged by the Nez Perce Tribe) at Lower Granite Dam during October to provide information for growth estimation. Within riverine habitats, growth in both length and mass were higher for fish tagged with 8-mm tags than with 9- and 12-mm tags. Estimated growth in length and mass of subyearlings was higher in Lower Granite Reservoir than in riverine habitats. We adapted existing statistical models used to estimate abundance of steelhead and spring/summer Chinook salmon for fall Chinook salmon passing Lower Granite Dam. Run reconstruction efforts to date at Lower Granite Dam for Snake River fall Chinook salmon have provided estimates of the number of returning adults but with no measure of uncertainty about the estimates. The objective of this study was to estimate the abundance, with uncertainty, of marked (coded-wire tagged CWT or adipose clipped) and unmarked fall Chinook salmon past Lower Granite Dam for return years 20032018. Estimating uncertainty is important for informing the state-space life cycle model (Chapter 5), which incorporates both observation and process uncertainty into parameter estimates. The coefficient of variation (CV) for log- abundance was 1.0% or less in all years, whereas the CV for abundance averaged 4.2% and ranged from 1.4% to 10.4% among years. Over the past five years, we have been developing a two-stage state-space life-cycle model for naturally produced fall Chinook salmon in the Snake River basin. Initial efforts focused on generating juvenile and adult abundance estimates, with estimates of uncertainty, for informing the life-cycle model. In this report we 1) describe the statistical life-cycle model and improvements made since our last report to the Independent Scientific Advisory Board (ISAB), 2) estimate the effects of covariates on key demographic parameters, and 3) use the fitted life- cycle model to simulate population trajectories under hydrosystem actions proposed for the NOAA 2020 Biological Opinion (hereafter, the Proposed Action). Major recent advancements to the model include revised juvenile abundance estimates, the ability to estimate smolt-to-adult return rates (SAR) separately for subyearling and yearling juvenile fall Chinook salmon, and improvements in the observation model for estimating age, sex, and outmigration structure in adult returns. We examined the effect of numerous environmental, hydrosystem, and ocean covariates on key demographic parameters but only a few covariates were significant. For the adult-to-juvenile transition, we found the maximum weekly river flows during the winter egg- incubation period had a significant negative effect on the juvenile outmigrant abundance from that brood year. For subyearling outmigrants, percent spill during the summer had a significant positive effect on SAR and the mean winter PDO (Pacific Decadal Oscillation) had a significant negative effect on SAR. For yearling outmigrants, NPGO (North Pacific Gyre Oscillation) had a significant positive effect on SAR. We used the fitted model to simulate population trajectories under the Proposed Action, and the median 10-year geometric mean abundance was 8,222 female spawners (interquartile range: 2,592 26,714). Overall, the probability of quasi- extinction (probability of falling below 50 female spawners for 4 consecutive years) was low, with only 1.6% of all simulations having a quasi-extinction probability >0.95. Although quasi-extinction probability was low, we did not assess the additional effect of climate change, which would be expected to increase quasi-extinction probability.

Idaho, Oregon, Washington↗
USGS2011

Sediment dynamics in the restored reach of the Kissimmee River Basin, Florida: A vast subtropical riparian wetland

Historically, the Kissimmee River Basin consisted of a broad nearly annually inundated riparian wetland similar in character to tropical Southern Hemisphere large rivers. The river was channelized in the 1960s and 1970s, draining the wetland. The river is currently being restored with over 10 000 hectares of wetlands being reconnected to 70 river km of naturalized channel. We monitored riparian wetland sediment dynamics between 2007 and 2010 at 87 sites in the restored reach and 14 sites in an unrestored reference reach. Discharge and sediment transport were measured at the downstream end of the restored reach. There were three flooding events during the study, two as annual flood events and a third as a greater than a 5-year flood event. Restoration has returned periodic flood flow to the riparian wetland and provides a mean sedimentation rate of 11.3 mm per year over the study period in the restored reach compared with 1.7 mm per year in an unrestored channelized reach. Sedimentation from the two annual floods was within the normal range for alluvial Coastal Plain rivers. Sediment deposits consisted of over 20% organics, similar to eastern blackwater rivers. The Kissimmee River is unique in North America for its hybrid alluvial/blackwater nature. Fluvial suspended-sediment measurements for the three flood events indicate that a majority of the sediment (70%) was sand, which is important for natural levee construction. Of the total suspended sediment load for the three flood events, 3%–16% was organic and important in floodplain deposition. Sediment yield is similar to low-gradient rivers draining to the Chesapeake Bay and alluvial rivers of the southeastern USA. Continued monitoring should determine whether observed sediment transport and floodplain deposition rates are normal for this river and determine the relationship between historic vegetation community restoration, hydroperiod restoration, and sedimentation.

Florida↗
USGS2024

Declining geomorphic diversity and potential adaptive management opportunities on a highly regulated reach of the Bighorn River, Montana

Rivers downstream from dams often experience decreased flow variability and disrupted sediment transport. We investigated a highly regulated 35.5-kilometre reach of the Bighorn River, downstream from Yellowtail Dam, emplaced in 1965. This dam created a thriving trout fishery, but more recently, side channel networks and habitat diminished. We document how the Bighorn River's anabranching morphology responded to flow regulation and a near cessation of sediment supply. Geomorphic diversity drastically decreased since 1939 and the Bighorn River abandoned numerous side channels. By 1980, geomorphic loss slowed, and the river became laterally static. The 1980 river and side channel network could represent the maximum areal extent of a downscaled morphology, maintained through restoration and adaptive management. However, side channel restoration alone will not return natural alluvial processes to this river reach. The Bighorn River needs sediment to reinstate dynamic lateral movement, even within a downscaled morphology. Sediment augmentation is an option, but more complex to implement on rivers where potential downstream impacts and landowners must be considered. The decline of geomorphic diversity and potential adaptive management solutions on the Bighorn River has wide applicability to numerous dammed rivers, where similar changes to the flow and sediment transport regime are common.

Montana, Wyoming↗
USGS2014

A quantitative life history of endangered humpback chub that spawn in the Little Colorado River: variation in movement, growth, and survival

While the ecology and evolution of partial migratory systems (defined broadly to include skip spawning) have been well studied, we are only beginning to understand how partial migratory populations are responding to ongoing environmental change. Environmental change can lead to differences in the fitness of residents and migrants, which could eventually lead to changes in the frequency of the strategies in the overall population. Here, we address questions concerning the life history of the endangered Gila cypha (humpback chub) in the regulated Colorado River and the unregulated tributary and primary spawning area, the Little Colorado River. We develop eight multistate models for the population based on three movement hypotheses, in which states are defined in terms of fish size classes and river locations. We fit these models to mark–recapture data collected in 2009–2012. We compare survival and growth estimates between the Colorado River and Little Colorado River and calculate abundances for all size classes. The best model supports the hypotheses that larger adults spawn more frequently than smaller adults, that there are residents in the spawning grounds, and that juveniles move out of the Little Colorado River in large numbers during the monsoon season (July–September). Monthly survival rates for G. cypha in the Colorado River are higher than in the Little Colorado River in all size classes; however, growth is slower. While the hypothetical life histories of life-long residents in the Little Colorado River and partial migrants spending most of its time in the Colorado River are very different, they lead to roughly similar fitness expectations when we used expected number of spawns as a proxy. However, more research is needed because our study period covers a period of years when conditions in the Colorado River for G. cypha are likely to have been better than has been typical over the last few decades.

Colorado River;Little Colorado River↗
USGS2017

Carbon dynamics of river corridors and the effects of human alterations

Research in stream metabolism, gas exchange, and sediment dynamics indicates that rivers are an active component of the global carbon cycle and that river form and process can influence partitioning of terrestrially derived carbon among the atmosphere, geosphere, and ocean. Here we develop a conceptual model of carbon dynamics (inputs, outputs, and storage of organic carbon) within a river corridor, which includes the active channel and the riparian zone. The exchange of carbon from the channel to the riparian zone represents potential for storage of transported carbon not included in the “active pipe” model of organic carbon (OC) dynamics in freshwater systems. The active pipe model recognizes that river processes influence carbon dynamics, but focuses on CO 2 emissions from the channel and eventual delivery to the ocean. We also review how human activities directly and indirectly alter carbon dynamics within river corridors. We propose that dams create the most significant alteration of carbon dynamics within a channel, but that alteration of riparian zones, including the reduction of lateral connectivity between the channel and riparian zone, constitutes the most substantial change of carbon dynamics in river corridors. We argue that the morphology and processes of a river corridor regulate the ability to store, transform, and transport OC, and that people are pervasive modifiers of river morphology and processes. The net effect of most human activities, with the notable exception of reservoir construction, appears to be that of reducing the ability of river corridors to store OC within biota and sediment, which effectively converts river corridors to OC sources rather than OC sinks. We conclude by summarizing knowledge gaps in OC dynamics and the implications of our findings for managing OC dynamics within river corridors.

Ecological Monographs↗
USGS2021

Lake sturgeon seasonal movements in regulated and unregulated Missouri River tributaries

Spatio-temporal movement patterns of aquatic organisms drive many ecological processes. However, dams block migrations and alter the hydrologic and thermal regimes influencing movement behaviour of freshwater fishes. In North America, many recovering southern Lake Sturgeon populations occur in rivers with hydroelectric dams, but few studies have examined the impact of hydrologic alteration on their seasonal movements. We conducted a 3-year telemetry study of 96 adult and subadult Lake Sturgeon to compare their migratory responses to temperature and hydrology in adjacent regulated and unregulated tributaries of the Missouri River. Many other populations of Lake Sturgeon use tributaries primarily for spring spawning; however, in our study, Lake Sturgeon used Missouri River tributaries during 78% of the year. Differences in river size, hydrologic and thermal regimes in the regulated Osage River may have contributed to the greater year-round residency, later initiation, more frequent directional changes and longer duration of spring migrations compared to the unregulated Gasconade River. Lake Sturgeon made spring upstream migrations at temperatures of 13–19°C and elevated discharges in both rivers. However, Osage River migrants responded less to changes in discharge or temperature during spring migrations, especially those that overwintered at upstream locations. Fall tributary migrations occurred in the Osage River at rising or high discharges but were uncommon in the Gasconade River. Our identification of the influences of abiotic variables on the timing, duration and extent of Lake Sturgeon seasonal migrations can help guide management of habitat and hydrology in regulated rivers to recover migratory fishes globally.

Missouri↗
USGS2021

Exploration of the 2016 Yellowstone River fish kill and proliferative kidney disease in wild fish populations

Proliferative kidney disease (PKD) is an emerging disease that recently resulted in a large mortality event of salmonids in the Yellowstone River (Montana, USA). Total PKD fish mortalities in the Yellowstone River were estimated in the tens of thousands, which resulted in a multi‐week river closure and an estimated economic loss of US$500,000. This event shocked scientists, managers, and the public, as this was the first occurrence of the disease in the Yellowstone River, the only reported occurrence of the disease in Montana in the past 25 yr, and arguably the largest wild PKD fish kill in the world. To understand why the Yellowstone River fish kill occurred, we used molecular and historical data to evaluate evidence for several hypotheses: Was the causative parasite Tetracapsuloides bryosalmonae a novel invader, was the fish kill associated with a unique parasite strain, and/or was the outbreak caused by unprecedented environmental conditions? We found that T. bryosalmonae is widely distributed in Montana and have documented occurrence of this parasite in archived fish collected in the Yellowstone River prior to the fish kill. T. bryosalmonae had minimal phylogeographic population structure, as the DNA of parasites sampled from the Yellowstone River and distant water bodies were very similar. These results suggest that T. bryosalmonae could be endemic in Montana. Due to data limitations, we could not reject the hypothesis that the fish kill was caused by a novel and more virulent genetic strain of the parasite. Finally, we found that single‐year environmental conditions are insufficient to explain the cause of the 2016 Yellowstone River PKD outbreak. Other regional rivers where we documented T. bryosalmonae had similar or even more extreme conditions than the Yellowstone River and similar or more extreme conditions have occurred in the Yellowstone River in the recent past, yet mass PKD mortalities have not been documented in either instance. We conclude by placing these results and unresolved hypotheses into the broader context of international research on T. bryosalmonae and PKD, which strongly suggests that a better understanding of bryozoans, the primary host of T. bryosalmonae , is required for better ecosystem understanding.

Montana↗
USGS2023

High potential but low achievement: Frequent disturbance constrains the light use efficiency of river ecosystems

We rarely consider light limitation in ecosystem productivity, yet light limitation is a major constraint on river autotrophy. Because the light that reaches benthic autotrophs must first pass through terrestrial vegetation and an overlying water column that can be loaded with sediments or colored organic material, there is strong selection for river autotrophs to have high light use efficiencies (LUEs), that is, the efficiency at which light energy is converted to biomass. In contrast to prior studies that have estimated river LUE on single days, we calculated continuous LUE over more than 6 full years for 64 free-flowing rivers across the United States. This dataset represents the largest compilation of continuous estimates of daily rates of gross primary productivity (GPP) and daily light inputs from which we calculated daily estimates of LUE. Early estimates of LUE in rivers found that clearwater springs with stable flows could achieve LUEs of 4%, much higher than LUEs reported for terrestrial plants. We found that 53% of the rivers in our dataset have LUEs that exceed 4% on at least one day of their time series. Because of the high variability in daily LUE, measurements taken on any given day may misrepresent a river ecosystem's annual LUE. Though most rivers share a high potential, the mean annual LUE of all rivers in our dataset is much lower, only 0.5%. We found that rivers with more variable flow regimes had lower annual LUEs, which indicates that LUE is constrained by hydrologic disturbances that remove, bury, or shade autotrophic biomass. Comparisons of LUE across ecosystems allow us to reframe our view of rivers, by recognizing the high efficiency with which they convert light to biomass compared with lentic, marine, and terrestrial ecosystems.

conterminous United States↗
USGS2000

Biomarker response and health of polychlorinated biphenyl- and chlordane-contaminated paddlefish from the Ohio River Basin, USA

Fifty paddlefish ( Polyodon spathula ) collected from two sites on the Ohio River and from one site on the Cumberland River, USA, were examined to determine gonad polychlorinated biphenyl (PCB) and chlordane concentrations, amounts of plasma sex steroids (testosterone and estradiol), hepatic microsomal ethoxyresorufin- O -deethylase (EROD) activity, and the presence of immunoreactive cytochrome P450 1A (CYP1A) protein. Percent hatch and liver, spleen, and kidney histology were also determined. Gonad PCB and chlordane concentrations were significantly higher in Ohio River paddlefish than in Cumberland River paddlefish. Gonad PCB and chlordane concentration and gonad percent lipid were correlated in Ohio River paddlefish. Five of 10 Ohio River egg samples exceeded the Food and Drug Administration's action limit for chlordane (0.30 μg/g). Polychlorinated biphenyl congener-specific analysis detected predominantly the tetra-, penta-, and hexachlorobiphenyls in paddlefish testes. Plasma testosterone levels were significantly lower in males collected from the upper Ohio River site than those collected from the lower part of the river. There was no measurable hepatic microsomal EROD activity in any of the 50 paddlefish collected from the three sites. Western blotting analysis confirmed that a rabbit antitrout CYP1A1 IgG antibody did not recognize a CYP1A protein in paddlefish liver microsomes. Percent hatch was not significantly different in eggs collected from the Cumberland (88–96%) and Ohio Rivers (90–95%). Histological analysis of liver, spleen, and kidney detected the presence of hepatic steatosis and hemosiderosis, splenic lymphoid cell depletion, and hyperplasia of interrenal and chromaffin tissues. Immunosuppression, hepatic metabolic disorders, and altered neuroendocrine function may be occurring in Ohio River paddlefish. Results presented here suggest that organochlorine exposure may be jeopardizing the long-term health of Ohio River paddlefish and that additional investigation of contaminant effects on immune system function and hormone levels in paddlefish is warranted.

Alabama, Georgia, Illinois, Indiana, Kentucky, Mar↗
USGS2015

Rethinking the longitudinal stream temperature paradigm: region-wide comparison of thermal infrared imagery reveals unexpected complexity of river temperatures

Prevailing theory suggests that stream temperature warms asymptotically in a downstream direction, beginning at the temperature of the source in the headwaters and leveling off downstream as it converges to match meteorological conditions. However, there have been few empirical examples of longitudinal patterns of temperature in large rivers due to a paucity of data. We constructed longitudinal thermal profiles (temperature versus distance) for 53 rivers in the Pacific Northwest (USA) using an extensive dataset of remotely sensed summertime river temperatures and classified each profile into one of five patterns of downstream warming: asymptotic (increasing then flattening), linear (increasing steadily), uniform (not changing), parabolic (increasing then decreasing), or complex (not fitting other classes). We evaluated (1) how frequently profiles warmed asymptotically downstream as expected, and (2) whether relationships between river temperature and common hydroclimatic variables differed by profile class. We found considerable diversity in profile shape, with 47% of rivers warming asymptotically, and 53% having alternative profile shapes. Water temperature did not warm substantially over the course of the river for coastal parabolic and uniform profiles, and for some linear and complex profiles. Profile classes showed no clear geographical trends. The degree of correlation between river temperature and hydroclimatic variables differed among profile classes, but there was overlap among classes. Water temperature in rivers with asymptotic or parabolic profiles was positively correlated with August air temperature, tributary temperature and velocity, and negatively correlated with elevation, August precipitation, gradient, and distance upstream. Conversely, associations were less apparent in rivers with linear, uniform, or complex profiles. Factors contributing to the unique shape of parabolic profiles differed for coastal and inland rivers, where downstream cooling was influenced locally by climate or cool water inputs, respectively. Potential drivers of shape for complex profiles were specific to each river. These thermal patterns indicate diverse thermal habitats that may promote resilience of aquatic biota to climate change. Without this spatial context, climate change models may incorrectly estimate loss of thermally suitable habitat.

California, Idaho, Oregon, Washington↗