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Benthic processes affecting contaminant transport in Upper Klamath Lake, Oregon

Executive Summary Multiple sampling trips during calendar years 2013 through 2015 were coordinated to provide measurements of interdependent benthic processes that potentially affect contaminant transport in Upper Klamath Lake (UKL), Oregon. The measurements were motivated by recognition that such internal processes (for example, solute benthic flux, bioturbation and solute efflux by benthic invertebrates, and physical groundwater-surface water interactions) were not integrated into existing management models for UKL. Up until 2013, all of the benthic-flux studies generally had been limited spatially to a number of sites in the northern part of UKL and limited temporally to 2–3 samplings per year. All of the benthic invertebrate studies also had been limited to the northern part of the lake; however, intensive temporal (weekly) studies had previously been completed independent of benthic-flux studies. Therefore, knowledge of both the spatial and temporal variability in benthic flux and benthic invertebrate distributions for the entire lake was lacking. To address these limitations, we completed a lakewide spatial study during 2013 and a coordinated temporal study with weekly sampling of benthic flux and benthic invertebrates during 2014. Field design of the spatially focused study in 2013 involved 21 sites sampled three times as the summer cyanobacterial bloom developed (that is, May 23 , June 13 , and July 3, 2013). Results of the 27-week, temporally focused study of one site in 2014 were summarized and partitioned into three periods (referred to herein as pre-bloom, bloom and post-bloom periods), each period involving 9 weeks of profiler deployments, water column and benthic sampling. Partitioning of the pre-bloom, bloom, and post-bloom periods were based on water-column chlorophyll concentrations and involved the following date intervals, respectively: April 15 through June 10 , June 17 through August 13 , and August 20 through October 16, 2014. To examine dissolved-solute (0.2-micrometer [μm] filtered) benthic flux, sets of nonmetallic pore-water profilers (U.S. Patent 8,051,727 B1) were deployed. In 2013, the deployment of profilers at 21 UKL sites occurred at the beginning of the annual cyanobacterial bloom of Aphanizomenon flos–aquae (AFA), in the middle of the bloom period, and at the peak of the bloom. Coordinated benthic invertebrate collections also were made. Based on results from 2013, weekly deployments of profilers and collection of benthic invertebrate samples from late spring to early autumn were used to estimate temporal trends in solute flux and benthic invertebrate densities. Estimates of nutrient efflux by benthic invertebrates were determined in the spring and autumn from 2011 through 2013 and three times (spring, summer, and autumn) in 2015. This work extends UKL studies that began in 2006 to quantify the importance of benthic solute sources in the lake. In 2015, piezometers and thermistor sets were deployed to quantify potential groundwater exchange with the lake water column. Analysis of the 2013 soluble reactive phosphorus (SRP) benthic flux indicated no effect of location (lake region), habitat, or sampling period, and the average lakewide flux values were consistent with earlier studies that had been confined to the northern region of UKL and adjacent wetlands. The 2014 study therefore focused on estimating temporal trends at a site within Ball Bay. During both 2013 and 2014 field studies, fluxes of macronutrients (soluble reactive phosphorus (SRP) and ammonia) and micronutrients (iron [Fe] and manganese [Mn]) were consistently positive and increased prior to the initial AFA bloom, varied or lagged with water-column chlorophyll during the summer bloom period, then decreased after the cyanobacterial blooms, only to rebound toward pre-bloom conditions in the final weeks of sampling. These four solutes exhibited benthic loads greater than maximum riverine loads estimated during the spring and early summers of 2013 and 2014. However, consistently detectable concentrations for all four solutes provide no evidence that they consistently serve as the limiting nutrient for primary production in the lake. In contrast to the four solutes (SRP, ammonia, Fe, and Mn), benthic fluxes of dissolved arsenic (As) were both negative and positive (that is, the lakebed currently serves as both a source and a sink for dissolved As, depending on season). In a further contrast with SRP, ammonia, dissolved Fe, and Mn, dissolved-As riverine loads to UKL were of similar magnitude to benthic loads. A negative relationship between dissolved-As flux and water-column As over the 2014 temporal study provides a potential advantage for the management of water-quality in contrast to solutes, like SRP or ammonia, with consistently positive flux. The mean total benthic invertebrate density during 2013 was 12,610 individuals per square meter (n=63). Although benthic invertebrate density did not change over the study period, it was higher in littoral habitats than open-lake or trench habitats and higher in the northern region compared to the central or southern regions of UKL. Mean total benthic invertebrate density during 2014 was 19,726 individuals m −2 (n=27). Density during the pre-bloom and bloom periods of April 15 to August 13, 2014 (the first two thirds of the 2014 sampling period), were similar to 2013. However, benthic invertebrate density more than doubled during the latter one-third of the study, that is, the post-bloom period between August 20 to October 16, 2014. Oligochaeta, Chironomidae and Hirudinea represented well over 90 percent of the benthic fauna; Oligochaeta were twice as abundant as Chironomidae or Hirudinea, the latter two of which were similar in density. Benthic invertebrates may enhance dissolved-nutrient (or toxicant) transport across the sediment-water interface by (1) modifying diffusion-layer thicknesses and permeability through bioturbation, (2) enhancing advective flow across the interface through bioirrigation, and (3) excreting or expelling dissolved or particulate solutes directly into the overlying water column (Boudreau and Jorgensen, 2001). We evaluated SRP efflux via excretion for approximately 15 different major taxa in UKL. Once these measures were scaled, it was evident that benthic invertebrates potentially contribute approximately 1.5 times the amount of SRP to the water column of Upper Klamath Lake as diffusive SRP flux alone, measured in profiler deployments. Sets of piezometers and temperature loggers were deployed in UKL to obtain estimates of vertical advective solute flux. The pressure transducer installations, within the piezometers, did not perform as designed, rendering the head gradient data unreliable. However, in terms of future research, this field work did demonstrate the feasibility of collecting vertical gradient data with piezometer deployments. Advective flux estimates herein are based solely on heat-flow modeling based on temperature data from four lake sites, without use of transducer data. Given the magnitudes (both positive or negative) of the heat-transfer fluxes for SRP, relative to diffusive-flux and macroinvertebrate efflux measurements (all positive but spanning the same orders of magnitude), further examination of solute advective flux is recommended as a potential transport process to integrate into existing water-quality (for example, Total Maximum Daily Load [TMDL]) models. As a complement to the biogeochemical focus of this study, initial analyses of suspended-particle (floc) characteristics and settling velocities from the water column were derived near the surface and lakebed at two UKL sites. To better understand changing particle characteristics during the AFA-bloom period, suspended particles were examined in 2015 using a LabSFLOC (LF), which is a Laboratory Spectral Flocculation Characteristics version of an In-Situ Settling Velocity instrument (INSSEV-LF). Particle characteristics and settling velocities were analyzed from the water column near the surface (sample dp_10 ) and lakebed (sample dp_90 ) at two lake sites (open-lake site ML and littoral site LS01). The term “floc” refers herein to suspended particles that may aggregate or disaggregate to change in size, composition, and settling velocity. During pre-bloom (May) conditions, where maximum suspended particulate matter concentration (SPMC) was 140 milligrams per liter (mg L −1 ) was now observed at site LS01 in close proximity to the bed, where D mean peaked at 305 μm, and the corresponding Ws mean was 3.9 millimeters per second (mm s −1 ). The high near-bed SPMC (828 mg L −1 ) experienced during post-bloom October 2015 at LS01 formed a benthic nepheloid layer (BNL) above the lake’s bed. Numerous low density, fast settling macrofloc-sized organic aggregates (D >160 μm) were observed (some up to 1 mm in size) near bed at LS01 both during the bloom and post-bloom conditions; many of these flocs displayed fibrous organic structures. In terms of mass settling fluxes, the post-bloom BNL produced a total MSF of 4,139 milligrams per square meter per second (mg m −2 s −1 ) (92.1 percent of MSF credited to the macrofloc-sized organic aggregates/cyanobacterial colonies); that was nearly three times the corresponding near-bed settling flux observed during the July 2015 bloom and 360 times greater than the pre-bloom conditions from May 2015 (98.8 percent and 14 percent of MSF credited to the macrofloc-sized fractions for those respective months). Such changes in the near-bed settling flux demonstrate the highly significant seasonal effects that the AFA bloom has on the floc depositional fluxes in UKL and highlights the importance of seasonal monitoring of these conditions in order to correctly parameterize the wide range in depositional characteristics and floc properties measured throughout UKL. Collectively, floc populations observed within UKL demonstrated a wide range in settling velocity (Ws) for a given particle size, D. Similarly, a given settling velocity was not associated with a specific particle size. This variability in particle characteristics and properties indicates the influence of varying floc effective density and its effect on mass and mass settling fluxes (MSF). The use of instruments, such as the INSSEV-LF, enables measuring the variability of settling velocity and its relation to particle density and size.

Oregon

Assessing causes of mortality for endangered juvenile Lost River suckers (Deltistes luxatus) in mesocosms in Upper Klamath Lake, south-central Oregon, 2016

Executive Summary The recovery of endangered Lost River suckers ( Deltistes luxatus ) in Upper Klamath Lake, south-central Oregon, has been impeded because juveniles are not recruiting into adult spawning populations. Adult sucker populations spawn each spring but mortality of age-0 suckers during their first summer is excessively high, and recruitment of juveniles into adult populations does not occur in most years. The last significant year class to join spawning aggregations was hatched in 1991. Capture rates for age-0 Lost River suckers decrease so substantially each summer that it is thought that mortality is nearly 100 percent within the first year of life each year. Causes of mortality are not understood but poor water quality, parasites, disease, predation, and non-native species are suspected to contribute to mortality. Upper Klamath Lake is hypereutrophic and summer water-quality conditions have large diurnal and seasonal fluctuations. Photosynthesis of Aphanizomenon flos-aquae , the most abundant cyanobacterium in Upper Klamath Lake, is responsible for large fluctuations in dissolved-oxygen (DO) concentrations and pH. We introduced hatchery-raised, passive integrated transponder-tagged juvenile Lost River suckers into large mesocosms located at Fish Banks, Mid North, and Rattlesnake Point in Upper Klamath Lake, Oregon, to assess sucker mortality relative to water-quality conditions. We identified the date of death for each sucker by assessing movement patterns among vertically stratified antennas. We modeled daily mortality using known fate models relative to water-quality conditions measured by sondes. Histopathology was used to understand causes of eminent mortality for moribund suckers. Fish mortality, growth, health, and movement patterns varied among locations, but it was unclear whether this variation was due to water-quality or other factors. Seasonal mortality was 58.8 percent at Fish Banks, 27.4 percent at Mid North, and 11.5 percent at Rattlesnake Point. Growth over the 109-day study period was lowest at Fish Banks (34.5 ±10.0 millimeters [mm] standard length (SL); 18.6 ±7.7 grams [g]), intermediate at Mid North (57.5 ±13.6 mm SL; 40.1 ±15.4 g), and greatest at Rattlesnake Point (78.4 ±13.0 mm SL; 72.5 ±18.7 g). Our ability to assess causes of juvenile sucker mortality in mesocosms using our modelling approach was limited by low daily mortality. Zero to 3 mortalities occurred per day, except on July 30 at Fish Banks when 7 mortalities occurred. Relative to any other measured and tested water-quality condition, mortality was more likely to occur on days with large fluctuations in oxygen percent saturation. When we assessed the fit of the most parsimonious model, performance was poor, which suggested that other factors were contributing to mortality. Our ability to assess the relationship between seasonal patterns in water quality and fish mortality were limited by the absence of substantial differences in water quality among sites, inconsistency in the depth at which measurements were collected, and no clear pattern in conditions leading up to and during mortality events. Except for DO at Rattlesnake Point and diel temperature variations at Fish Banks, seasonally summarized water-quality factors were similar among sites. The locations of water-quality monitors within the water column likely explain the differences in DO at Rattlesnake Point and temperature variation at Fish Banks. Furthermore, DO concentrations and other water-quality factors occurring during and prior to mortality events were inconsistent. Microscopic assessments indicated severe gill hyperplasia, fusion of the secondary lamellae, and severe Ichthyobodo sp. infestations on the gills of most moribund suckers. Liver glycogen was usually depleted in suckers with severe Ichthyobodo sp. infestations. Ichthyobodo sp. infestations probably were the immediate cause of death and probably originated from the Klamath Tribes Fish Research Facility, although this parasite also is present in Upper Klamath Lake and severe water-quality conditions may have contributed to morbidity. As suckers in the mesocosms died, they were replaced with suckers from the Fish Research Facility that likely were heavily parasitized with Ichthyobodo sp. Therefore, it is possible that the gradient in mortality rate among sites was owing to site-varying differences in inadvertent increases in introduced parasite loads.

Oregon

Field comparison of five in situ turbidity sensors

Five commercially available turbidity sensors were field tested by the U.S. Geological Survey Hydrologic Instrumentation Facility for accuracy and data comparability. The tested sensors were the Xylem EXO (EXO), the Hach Solitax sc (Solitax), the In Situ Aqua TROLL sensor installed onto a TROLL 600 sonde (TROLL 600), the Campbell Scientific OBS501 (OBS501), and the Observator ANALITE NEP–5000 (NEP–5000). The sensors were deployed at Pearl River at National Space Technology Laboratories Station, Mississippi (U.S. Geological Survey site 02492620), and were serviced weekly. In addition to the five in situ turbidity sensors, corresponding discrete samples were collected and analyzed during the evaluation on a calibrated Hach 2100N benchtop turbidimeter. The OBS501 malfunctioned early in the evaluation and eventually failed, resulting in few data from the sensor. During this study, the four remaining sensors (minus the OBS501) changed similarly throughout the field test; however, sensor data from the EXO consistently demonstrated lower results than the Solitax, TROLL 600, and NEP–5000, possibly because of the variation in raw signal processing among manufacturers. Results from a single factor analysis of variance test and a Tukey Honestly Significant Difference test verified the low bias observed in the EXO data and indicated there was a significant difference between the EXO data and data from the Solitax, TROLL 600, and NEP–5000 but an insignificant difference among the data when the Solitax, TROLL 600, and NEP–5000 were compared to each other.

Mississippi

Gazetteer of coal-mine lakes in southwestern Indiana

This gazetteer is a catalog of lakes formed by surface coal mining in southwestern Indiana that are 0.5 acre or larger and in nonactive mine areas. Approximately 1,000 of the lakes are listed by 7.5-minute quadrangle topographic-map name, lake-identification number, latitude and longitude, and county. Other data given are shape of lake, maximum length, mean width, length and development of shoreline, surface area, orientation, presence of a stream inlet or outlet, and geologic data (geologic formation of area surrounding the lake and the mined coal-bed member). Field data (sampling date, pH, specific conductance, apparent color of lake, and general vegetation along the shoreline) were collected for 287 of the lakes. Two hundred eighty-seven lakes were sampled once for pH and specific conductance. Vegetation along the shoreline and apparent color of each lake were identified at the same time. Although these data are not sufficient to quantify the water quality of the lakes, they do illustrate the variability of these characteristics. The pH of the 287 lakes ranged from 2.5 to 10.0; however, the pH of 80 percent of them ranged from 6 to 9. Specific conductance ranged from 99 to 3,800 micromhos per centimeter at 25? Celsius. Specific conductance for approximately 70 percent of the lakes in the Staunton and Brazil formations was less than 500 micromhos per centimeter at 25? Celsius, but for approximately 65 percent in the Dugger and Petersburg Formations it was greater than 1,000 micromhos per centimeter at 25? Celsius. The apparent colors of the lakes observed were varying shades of aqua, blue, brown, lime green, red, and green. Eighty percent of the lakes sampled were green. Lake sizes ranged from a chosen minimum of 0.5 acre to a maximum of 344 acres. Maximum length ranged from 0.1 to 2 miles, and the mean width was generally less than 0.8 mile.

Open-File Report

Water-quality conditions in Upper Klamath Lake, Oregon, 2002-04

Eleven (2002) to 14 (2003 and 2004) continuous water-quality monitors that measured pH, dissolved oxygen, temperature, and specific conductance, were placed in Upper Klamath Lake to support a telemetry tracking study of endangered adult shortnose and Lost River suckers. Samples for the analysis of chlorophyll a and nutrients were collected at a subset of the water-quality monitor sites in each year. The seasonal pattern in the occurrence of supersaturated dissolved oxygen concentrations and high pH associated with photosynthetic activity, as well as the undersaturated dissolved oxygen concentrations associated with oxygen demand through respiration and decay in excess of photosynthetic production, were well described by the dynamics of the massive blooms of Aphanizomenon flos aquae (AFA) that occur each year. Data from the continuous monitors provided a means to quantify the occurrence, duration, and spatial extent of water-quality conditions potentially harmful to fish (dissolved- oxygen concentration less than 4 milligrams per liter, pH greater than 9.7, and temperature greater than 28 degrees Celsius) in the northern part of the lake, where the preferred adult sucker habitat is found. There were few observations of temperature greater than 28 degrees Celsius, suggesting that temperature is not a significant source of chronic stress to fish, although its role in the spread of disease is harder to define. Observations of pH greater than 9.7 were common during times when the AFA bloom was growing rapidly, so pH may be a source of chronic stress to fish. Dissolved oxygen concentrations less than 4 milligrams per liter were common in all 3 years at the deeper sites, in the lower part of the water column and for short periods during the day. Less common were instances of widespread low dissolved oxygen, throughout the water column and persisting through the entire day, but this was the character of a severe low dissolved oxygen event (LDOE) that culminated in the start of a fish die-off in 2003. Documented evidence indicates that LDOEs played a role in three fish die-offs in the mid-1990s as well. In the historical context of 15 years of climate and water-quality data, 3 out of 4 of the recent fish die-off years, 1996, 1997, and 2003, were characterized by low winds and high temperatures in July or August coincident with the start of the die-off. High temperatures accelerate the oxygen demanding processes that lead to a LDOE. The role of low winds remains inconclusive, but it could include the development of stratification in the water column and/or the alteration of the wind-driven circulation pattern. At a site centrally located in the study area, die-off years could be successfully identified in the historical data by screening for water characterized by exceptionally low chlorophyll a concentration, exceptionally low dissolved oxygen concentration throughout the water column (not just near the bottom), and exceptionally high ammonia concentration and water temperature, just prior to or coincident with the start of a fish die-off. These conditions indicate that a severe decline in the AFA bloom and conversion of most of the organic matter into inorganic form had taken place.

Scientific Investigations Report

Relation Between Selected Water-Quality Variables, Climatic Factors, and Lake Levels in Upper Klamath and Agency Lakes, Oregon, 1990-2006

Growth and decomposition of dense blooms of Aphanizomenon flos-aquae in Upper Klamath Lake frequently cause extreme water-quality conditions that have led to critical fishery concerns for the region, including the listing of two species of endemic suckers as endangered. The Bureau of Reclamation has asked the U.S. Geological Survey (USGS) to examine water-quality data collected by the Klamath Tribes for relations with lake level. This analysis evaluates a 17-year dataset (1990-2006) and updates a previous USGS analysis of a 5-year dataset (1990-94). Both univariate hypothesis testing and multivariable analyses evaluated using an information-theoretic approach revealed the same results-no one overarching factor emerged from the data. No single factor could be relegated from consideration either. The lack of statistically significant, strong correlations between water-quality conditions, lake level, and climatic factors does not necessarily show that these factors do not influence water-quality conditions; it is more likely that these conditions work in conjunction with each other to affect water quality. A few different conclusions could be drawn from the larger dataset than from the smaller dataset examined in 1996, but for the most part, the outcome was the same. Using an observational dataset that may not capture all variation in water-quality conditions (samples were collected on a two-week interval) and that has a limited range of conditions for evaluation (confined to the operation of lake) may have confounded the exploration of explanatory factors. In the end, all years experienced some variation in poor water-quality conditions, either in timing of occurrence of the poor conditions or in their duration. The dataset of 17 years simply provided 17 different patterns of lake level, cumulative degree-days, timing of the bloom onset, and poor water-quality conditions, with no overriding causal factor emerging from the variations. Water-quality conditions were evaluated for their potential to be harmful to the endangered sucker species on the basis of high-stress thresholds-water temperature values greater than 28 degrees Celsius, dissolved-oxygen concentrations less than 4 milligrams per liter, and pH values greater than 9.7. Few water temperatures were greater than 28 degrees Celsius, and dissolved-oxygen concentrations less than 4 milligrams per liter generally were recorded in mid to late summer. In contrast, high pH values were more frequent, occurring earlier in the season and parallel with growth in the algal bloom. The 10 hypotheses relating water-quality variables, lake level, and climatic factors from the earlier USGS study were tested in this analysis for the larger 1990-2006 dataset. These hypotheses proposed relations between lake level and chlorophyll-a, pH, dissolved oxygen, total phosphorus, and water temperature. As in the previous study, no evidence was found in the larger dataset for any of these relations based on a seasonal (May-October) distribution. When analyzing only the June data, the previous 5-year study did find evidence for three hypotheses relating lake level to the onset of the bloom, chlorophyll-a concentrations, and the frequency of high pH values in June. These hypotheses were not supported by the 1990-2006 dataset, but the two hypotheses related to cumulative degree-days from the previous study were: chlorophyll-a concentrations were lower and onset of the algal bloom was delayed when spring air temperatures were cooler. Other relations between water-quality variables and cumulative degree-days were not significant. In an attempt to identify interrelations among variables not detected by univariate analysis, multiple regressions were performed between lakewide measures of low dissolved-oxygen concentrations or high pH values in July and August and six physical and biological variables (peak chlorophyll-a concentrations, degree-days, water temperature, median October-May discharg

Scientific Investigations Report

Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2005

During June-October 2005, water quality data were collected from Upper Klamath and Agency Lakes in Oregon, and meteorological data were collected around and within Upper Klamath Lake. Data recorded at two continuous water quality monitors in Agency Lake showed similar temperature patterns throughout the field season, but data recorded at the northern site showed more day-to-day variability for dissolved oxygen concentration and saturation after late June and more day-to-day variability for pH and specific conductance values after mid-July. Data recorded from the northern and southern parts of Agency Lake showed more comparable day-to-day variability in dissolved oxygen concentrations and pH from September through the end of the monitoring period. For Upper Klamath Lake, seasonal (late July through early August) lows of dissolved oxygen concentrations and saturation were coincident with a seasonal low of pH values and seasonal highs of ammonia and orthophosphate concentrations, specific conductance values, and water temperatures. Patterns in these parameters, excluding water temperature, were associated with bloom dynamics of the cyanobacterium (blue-green alga) Aphanizomenon flos-aquae in Upper Klamath Lake. In Upper Klamath Lake, water temperature in excess of 28 degrees Celsius (a high stress threshold for Upper Klamath Lake suckers) was recorded only once at one site during the field season. Large areas of Upper Klamath Lake had periods of dissolved oxygen concentration of less than 4 milligrams per liter and pH value greater than 9.7, but these conditions were not persistent throughout days at most sites. Dissolved oxygen concentrations in Upper Klamath Lake on time scales of days and months appeared to be influenced, in part, by bathymetry and prevailing current flow patterns. Diel patterns of water column stratification were evident, even at the deepest sites. This diel pattern of stratification was attributable to diel wind speed patterns and the shallow nature of most of Upper Klamath Lake. Timing of the daily extreme values of dissolved oxygen concentration, pH, and water temperature was less distinct with increased water column depth. Chlorophyll a concentrations varied spatially and temporally throughout Upper Klamath Lake. Location greatly affected algal concentrations, in turn affecting nutrient and dissolved oxygen concentrations - some of the highest chlorophyll a concentrations were associated with the lowest dissolved oxygen concentrations and the highest un-ionized ammonia concentrations. The occurrence of the low dissolved oxygen and high un-ionized ammonia concentrations coincided with a decline in algae resulting from cell death, as measured by concentrations of chlorophyll a. Dissolved oxygen production rates in experiments were as high as 1.47 milligrams of oxygen per liter per hour, and consumption rates were as much as -0.73 milligrams of oxygen per liter per hour. Dissolved oxygen consumption rates measured in this study were comparable to those measured in a 2002 Upper Klamath Lake study, and a higher rate of dissolved oxygen consumption was recorded in dark bottles positioned higher in the water column. Data, though inconclusive, indicated that a decreasing trend of dissolved oxygen productivity through July could have contributed to the decreasing dissolved oxygen concentrations and percent saturation recorded in Upper Klamath Lake during this time. Phytoplankton self-shading was evident from a general inverse relation between depth of photic zone and chlorophyll a concentrations. This shading caused net dissolved oxygen consumption during daylight hours in lower parts of the water column that would otherwise have been in the photic zone. Meteorological data collected in and around Upper Klamath Lake showed that winds were likely to come from a broad range of westerly directions in the northern one-third of the lake, but tended to come from a narrow range of northwesterly directions

Scientific Investigations Report

Water Quality Conditions in Upper Klamath and Agency Lakes, Oregon, 2006

The U.S. Geological Survey Upper Klamath Lake water quality monitoring program gathered information from multiparameter continuous water quality monitors, physical water samples, dissolved oxygen production and consumption experiments, and meteorological stations during the June-October 2006 field season. The 2006 study area included Agency Lake and all of Upper Klamath Lake. Seasonal patterns in water quality were similar to those observed in 2005, the first year of the monitoring program, and were closely related to bloom dynamics of the cyanobacterium (blue-green alga) Aphanizomenon flos-aquae (AFA) in the two lakes. High dissolved oxygen and pH conditions in both lakes before the bloom declined in July, which coincided with seasonal high temperatures and resulted in seasonal lows in dissolved oxygen and decreased pH. Dissolved oxygen and pH in Upper Klamath and Agency Lakes increased again after the bloom recovered. Seasonal low dissolved oxygen and decreased pH coincided with seasonal highs in ammonia and orthophosphate concentrations. Seasonal maximum daily average temperatures were higher and minimum dissolved oxygen concentrations were lower in 2006 than in 2005. Conditions potentially harmful to fish were influenced by seasonal patterns in bloom dynamics and bathymetry. Potentially harmful low dissolved oxygen and high un-ionized ammonia concentrations occurred mostly at the deepest sites in the Upper Klamath Lake during late July, coincident with a bloom decline. Potentially harmful pH conditions occurred mostly at sites outside the deepest parts of the lake in July and September, coincident with a heavy bloom. Instances of possible gas bubble formation, inferred from dissolved oxygen data, were estimated to occur frequently in shallow areas of Upper Klamath and Agency Lakes simultaneously with potentially harmful pH conditions. Comparison of the data from monitors in nearshore areas and monitors near the surface of the water column in the open waters of Upper Klamath Lake revealed few differences in water quality dynamics. Median daily temperatures were higher in nearshore areas, and dissolved oxygen concentrations were periodically higher as well during periods of high AFA bloom. Differences between the two areas in water quality conditions potentially harmful to fish were not statistically significant (p < 0.05). Chlorophyll a concentrations varied temporally and spatially throughout Upper Klamath Lake. Chlorophyll a concentrations indicated an algal bloom in late June and early July that was followed by an algae bloom decline in late July and early August and a subsequent recovery in mid-August. Sites in the deepest part of the lake, where some of the highest chlorophyll a concentrations were observed, were the same sites where the lowest dissolved oxygen concentrations and the highest un-ionized ammonia concentrations were recorded during the bloom decline, indicating cell senescence. Total phosphorus concentrations limited the initial algal bloom in late June and early July. The rate of net dissolved oxygen production (that is, production in excess of community respiration) and consumption (due to community respiration) in the lake water column as measured in light and dark bottles, respectively, ranged from 2.79 to -2.14 milligrams of oxygen per liter per hour. Net production rate generally correlated positively with chlorophyll a concentration, except episodically at a few sites where high chlorophyll a concentrations resulted in self-shading that inhibited photosynthesis. The depth of photic zone was inversely correlated with chlorophyll a concentration. Calculations of a 24-hour change in dissolved oxygen concentration indicated that oxygen-consuming processes predominated at the deep trench sites and oxygen-producing processes predominated at the shallow sites. In addition, calculations of the 24-hour change in dissolved oxygen indicate that oxygen-consuming processes in the water column di

Scientific Investigations Report

Methods for Estimating Water Withdrawals for Aquaculture in the United States, 2005

Aquaculture water use is associated with raising organisms that live in water - such as finfish and shellfish - for food, restoration, conservation, or sport. Aquaculture production occurs under controlled feeding, sanitation, and harvesting procedures primarily in ponds, flow-through raceways, and, to a lesser extent, cages, net pens, and tanks. Aquaculture ponds, raceways, and tanks usually require the withdrawal or diversion of water from a ground or surface source. Most water withdrawn or diverted for aquaculture production is used to maintain pond levels and/or water quality. Water typically is added for maintenance of levels, oxygenation, temperature control, and flushing of wastes. This report documents methods used to estimate withdrawals of fresh ground water and surface water for aqua-culture in 2005 for each county and county-equivalent in the United States, Puerto Rico, and the U.S. Virgin Islands by using aquaculture statistics and estimated water-use coefficients and water-replacement rates. County-level data for commercial and noncommercial operations compiled for the 2005 Census of Aquaculture were obtained from the National Agricultural Statistics Service. Withdrawals of water used at commercial and noncommercial operations for aquaculture ponds, raceways, tanks, egg incubators, and pens and cages for alligators were estimated and totaled by ground-water or surface-water source for each county and county equivalent. Use of the methods described in this report, when measured or reported data are unavailable, could result in more consistent water-withdrawal estimates for aquaculture that can be used by water managers and planners to determine water needs and trends across the United States. The results of this study were distributed to U.S. Geological Survey water-use personnel in each State during 2007. Water-use personnel are required to submit estimated withdrawals for all categories of use in their State to the U.S. Geological Survey National Water-Use Information Program for inclusion in a national report describing water use in the United States during 2005. Water-use personnel had the option of submitting the estimates determined by using the methods described in this report, a modified version of these estimates, their own set of estimates, or reported data for the aquaculture category. Estimated withdrawals resulting from the method described in this report are not presented herein to avoid potential inconsistencies with estimated withdrawals for aquaculture that will be presented in the national report, as different methods used by water-use personnel may result in different withdrawal estimates. Estimated withdrawals also are not presented to avoid potential disclosure of confidential information for individual aquaculture operations.

Scientific Investigations Report

Modeling hydrodynamics, water temperature, and water quality in the Klamath River upstream of Keno Dam, Oregon, 2006-09

A hydrodynamic, water temperature, and water-quality model was constructed for a 20-mile reach of the Klamath River downstream of Upper Klamath Lake, from Link River to Keno Dam, for calendar years 2006-09. The two-dimensional, laterally averaged model CE-QUAL-W2 was used to simulate water velocity, ice cover, water temperature, specific conductance, dissolved and suspended solids, dissolved oxygen, total nitrogen, ammonia, nitrate, total phosphorus, orthophosphate, dissolved and particulate organic matter, and three algal groups. The Link-Keno model successfully simulated the most important spatial and temporal patterns in the measured data for this 4-year time period. The model calibration process provided critical insights into water-quality processes and the nature of those inputs and processes that drive water quality in this reach. The model was used not only to reproduce and better understand water-quality conditions that occurred in 2006-09, but also to test several load-reduction scenarios that have implications for future water-resources management in the river basin. The model construction and calibration process provided results concerning water quality and transport in the Link-Keno reach of the Klamath River, ranging from interesting circulation patterns in the Lake Ewauna area to the nature and importance of organic matter and algae. These insights and results include: * Modeled segment-average water velocities ranged from near 0.0 to 3.0 ft/s in 2006 through 2009. Travel time through the model reach was about 4 days at 2,000 ft 3 /s and 12 days at 700 ft3/s flow. Flow direction was aligned with the upstream-downstream channel axis for most of the Link-Keno reach, except for Lake Ewauna. Wind effects were pronounced at Lake Ewauna during low-flow conditions, often with circulation in the form of a gyre that rotated in a clockwise direction when winds were towards the southeast and in a counterclockwise direction when winds were towards the northwest. * Water temperatures ranged from near freezing in winter to near 30 degrees C at some locations and periods in summer; seasonal water temperature patterns were similar at the inflow and outflow. Although vertical temperature stratification was not present at most times and locations, weak stratification could persist for periods up to 1-2 weeks, especially in the downstream parts of the reach. Thermal stratification was important in controlling vertical variations in water quality. * The specific conductance, and thus density, of tributaries within the reach usually was higher than that of the river itself, so that inflows tended to sink below the river surface. This was especially notable for inflows from the Klamath Straits Drain, which tended to sink to the bottom of the Klamath River at its confluence and not mix vertically for several miles downstream. * The model was able to capture most of the seasonal changes in the algal population by modeling that population with three algal groups: blue-green algae, diatoms, and other algae. The blooms of blue-green algae, consisting mostly of Aphanizomenon flos aquae that entered from Upper Klamath Lake, were dominant, dwarfing the populations of the other two algae groups in summer. A large part of the blue-green algae population that entered this reach from upstream tended to settle out, die, and decompose, especially in the upper part of the Link-Keno reach. Diatoms reached a maximum in spring and other algae in midsummer. * Organic matter, occurring in both dissolved and particulate forms, was critical to the water quality of this reach of the Klamath River, and was strongly tied to nutrient and dissolved-oxygen dynamics. Dissolved and particulate organic matter were subdivided into labile (quickly decaying) and refractory (slowing decaying) groups for modeling purposes. The particulate matter in summer, consisting largely of dead blue-green algae, decayed quickly. Consequently, this particulate matt

Oregon

Distribution and variation of arsenic in Wisconsin surface soils, with data on other trace elements

A total of 664 soil samples distributed among different geographic regions and soil types were collected across Wisconsin to describe the distribution of arsenic relative to parent material, soil texture, and drainage class. Soils from 6 inches in depth were composited, digested in aqua regia, and analyzed for 17 trace elements. Observed soil arsenic concentrations range from a high of 39 milligrams per kilogram (mg/kg) to less than the laboratory detection limit of 1 mg/kg. Ten samples with soil arsenic concentrations greater than 8.5 mg/kg were determined to be significantly separate from the main cluster of the dataset. With these outliers removed, overall soil arsenic concentrations in Wisconsin have a median value of 1.8 mg/kg, and the 95-percent upper confidence limit of the mean is 2.4 mg/kg. Soils with sandy glacial outwash as a parent material have a lower median arsenic concentration (1.0 mg/kg) than soils forming in other parent materials (1.5 to 3.0 mg/kg). Soil texture and drainage category also influence median arsenic concentration. Finer grained soils have a higher observed range of concentrations. For loamy and loess-dominated soil groups, drainage category influences the median arsenic concentration and observed range of values, but a consistent relationship within the data is not apparent. Statistical analysis of the 16 other elements are presented in this report, but the relationships of concentrations to soil properties or geographic areas were not examined.

Wisconsin

Upstream factors affecting Tualatin River algae—Tracking the 2008 Anabaena algae bloom to Wapato Lake, Oregon

Significant Findings A large bloom that included floating mats of the blue-green algae Anabaena flos-aquae occurred in the lower 20 miles of the Tualatin River in northwestern Oregon between July 7 and July 17, 2008. The floating bloom was deemed a hazard to recreational users of the river due to the potential production of algal toxins (anatoxin- a and microcystin), and a public health advisory was posted for the lower 10.8 miles of the river by the Oregon Department of Human Services for July 12&ndash;25, 2008. The bloom caused nuisance taste and odor issues and required modified drinking-water treatment techniques where water was withdrawn for municipal uses in the upper reaches of the Tualatin River, some 46 miles upstream of the worst algae problems. Using water sample data from Clean Water Services and the Joint Water Commission, and continuous and discrete monitoring data from the U.S. Geological Survey, the source of the anomalous water-quality conditions and the likely source of the Anabaena bloom was traced upstream to discharges from the Wapato Lake agricultural area near Gaston, Oregon, in the upper part of the watershed near river mile 60. The Wapato Lake algae bloom occurred as standing water remained on the lakebed far longer than normal&mdash;into early summer. A failure of the levee on the edge of Wapato Lake in December 2007 caused by heavy rainfall and high water in the canal outside the levee inundated the lakebed to a depth of 7&ndash;9 feet, storing thousands of acre-feet more water than its normal winter volume. The water could not be pumped out until the levee was repaired or river levels receded, thus delaying drainage of the lake until summer and facilitating the bloom. In normal summers, the lower Tualatin River grows a moderate crop of algae that responds strongly to streamflow (residence time), light available for photosynthesis, and phosphorus concentrations. In 2008, however, inoculation of the river with phytoplankton and zooplankton discharged from Wapato Lake some 30 miles upstream of the lower, pooled reach of the river demonstrated the importance of upstream factors on plankton communities and water-quality conditions in the Tualatin River. The Wapato Lake algae bloom of July 2008 provided useful information and lessons for agencies managing public health, wetlands, agricultural activities, and water quality in the Tualatin River basin and similar river basins elsewhere. The results and insights derived from this study can be used to enhance future monitoring and data collection strategies designed to improve water quality and plankton models and better predict dissolved-oxygen concentrations in the lower Tualatin River.

Oregon

Methods for the preparation and analysis of solids and suspended solids for total mercury

The methods documented in this report are utilized by the Wisconsin District Mercury Lab for analysis of total mercury in solids (soils and sediments) and suspended solids (isolated on filters). Separate procedures are required for the different sample types. For solids, samples are prepared by room-temperature acid digestion and oxidation with aqua regia. The samples are brought up to volume with a 5 percent bromine monochloride solution to ensure complete oxidation and heated at 50C in an oven overnight. Samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. A method detection limit of 0.3 ng of mercury per digestion bomb was established using multiple analyses of an environmental sample. Based on the range of masses processed, the minimum sample reporting limit varies from 0.6 ng/g to 6 ng/g. Suspended solids samples are oxidized with a 5 percent bromine monochloride solution and held at 50?C in an oven for 5 days. The samples are then analyzed with an automated flow injection system incorporating a cold vapor atomic fluorescence spectrometer. Using a certified reference material as a surrogate for an environmental sample, a method detection limit of 0.059 ng of mercury per filter was established. The minimum sample reporting limit varies from 0.059 ng/L to 1.18 ng/L, depending on the volume of water filtered.

Techniques and Methods

Nitrogen and phosphorus loading from drained wetlands adjacent to Upper Klamath and Agency lakes, Oregon

Upper Klamath Lake and the connecting Agency Lake constitute a large, shallow lake in south-central Oregon that the historical record indicates has likely been eutrophic since its discovery by non-Native Americans. In recent decades, however, the lake has had annual occurrences of near-monoculture blooms of the blue-green alga Aphanizomenon flos-aquae that are thought to be a result of accelerated eutrophication. In 1988, two sucker species endemic to the lake, the Lost River sucker ( Deltistes luxatus ) and the shortnose sucker ( Chasmistes brevirostris ), were listed as endangered by the U.S. Fish and Wildlife Service, and it has been proposed that their decline is due to the poor water quality associated with extremely long and productive algal blooms. It has also been proposed that the effluent drained from wetlands has contributed to accelerated eutrophication. Since the turn of century, most of the wetlands adjacent to Upper Klamath Lake have been drained for agriculture--cultivation of crops and grazing of cattle. Wetland areas were reclaimed from the lake by building dikes to isolate them from the lake, constructing a series of drainage ditches, and installing pumps to drain the water and maintain a lowered water table. A consequence of lowering the water table is the increased ability of air and oxygenated water to move through the subsurface and facilitate the rapid aerobic decomposition of the peat soils. Nutrients, nitrogen and phosphorus, are then liberated, leach into adjacent ditches, and are subsequently pumped to the lake or its tributaries. The rate of peat decomposition may be related to the time since drainage and the type of agricultural land use. On lands cultivated for crops, farming practices, such as disking and furrowing, could enhance the movement of air and oxygenated water, resulting in a rapid rate of decomposition. In contrast, on grazed lands, the compaction of soils by cattle probably inhibits the movement of air and oxygenated water and results in a slower rate of decomposition relative to drained wetlands used for the cultivation of crops. This report presents the results of a cooperative study between the U.S. Geological Survey and the Bureau of Reclamation whose overall objective was to determine the nutrient loading to Upper Klamath Lake from adjacent drained wetlands. Nutrient loading from drained wetlands was estimated using two independent techniques. The first method involved the measurement of the quantity and quality of water discharged by pumps draining the wetlands. The second method was used to estimate the initial (before drainage) and present-day nutrient mass of the organic soils within the drained wetlands and to calculate the change (or loss) in nutrient mass. In an effort to estimate the nutrient contributions from the water pumped off selected drained wetlands adjacent to Upper Klamath Lake, annual loads and yields of total nitrogen and total phosphorus were estimated from concentration data and the volume of water pumped during the water year. In general, there was little variation among sites or among years in the annual total nitrogen (median load of about 18 tons per year and median yield of about 8 pounds per acre per year) or the annual total phosphorus (median load of about 3 tons per year and median yield of about 2 pounds per acre per year) contributions. The sum of the annual loads of nitrogen and phosphorus calculated for each of the pumping stations in 1995 was 80 tons per year and 15 tons per year, respectively. In 1995, soil-coring activities were undertaken to ascertain the nature and extent of the organic soils in the drained and undrained wetlands. The present-day nutrient mass was calculated for each drained wetland using the nutrient content (concentration) and the present-day peat mass. The initial nutrient mass prior to drainage was estimated for each drained wetland by using the initial nutrient content (assumed to be equal to the nutrient content of the undrained wetlands) and the initial peat mass as determined using the amount of accumulated decomposition residue. The cumulative loss of nutrient mass since drainage was calculated as the change between initial and present-day nutrient mass for each drained area. The cumulative yield of total nitrogen and total phosphorus loss from the organic soils of individual wetlands since drainage ranged from 3,000 to 70,000 pounds per acre and from 0 to 1,300 pounds per acre, respectively. For all the drained wetlands sampled, the cumulative nitrogen and phosphorus loss since drainage totaled 250,000 tons and 4,300 tons, respectively. This represents about 30 percent and 22 percent of the mass of nitrogen and phosphorus, respectively, that initially existed in the organic soils. The loss of nutrients from the drained wetlands is considered to be a maximum estimate of the possible contribution of nutrients to Upper Klamath Lake from the peat soils of the drained wetlands sampled. However, not all the nutrients released by the soils are discharged to the lake. Nutrients lost from the peat soils of the drained wetlands may have been taken up by crops and harvested or consumed by grazing cattle. In addition, nitrogen can be lost to the atmosphere by denitrification and the volatilization of ammonia; phosphorus may be bound to adjacent soil layers by adsorption. The annual nutrient loss for the period 1994&ndash;95 was calculated using a first-order rate law to describe nutrient loss since drainage began. For individual drained wetlands, the yield of nitrogen and phosphorus lost from the organic soils for the period 1994&ndash;95 ranged from 27 to 540 pounds per acre per year and from 0 to 15 pounds per acre per year, respectively. The total mass of nitrogen and phosphorus loss during this period was 3,000 tons per year and 60 tons per year, respectively, for all drained wetlands that were sampled. The yield and mass of nutrient loss determined in this fashion reflect what might be expected on the basis of time-averaged or longterm contributions of nutrients to the lake and do not reflect the specific conditions existing during the period 1994&ndash;95. The results of this study could be useful in helping to prioritize which drained wetlands may provide the greatest benefits with regard to reducing nutrient loads to the lake if restoration or land-use modifications are instituted. Recent acquisition and planned restoration of drained wetland areas at the Wood River and Williamson River North properties may produce significant reduction in the quantity of nutrients released by the decomposition of peat soils of these areas. If the water table rises to predrainage levels, the peats soils may become inundated most of the year, resulting in the continued long-term storage of nutrients within the peat soils by reducing aerobic decomposition. The maximum benefit, in terms of decreasing potential nutrient loss due to peat decomposition, could be the reduction of total nitrogen and total phosphorus loss to about one-half that of the 1994&ndash;95 annual loss estimated for all the drained wetlands sampled for this study.

Oregon

Prototype downscaling algorithm for MODIS Satellite 1 km daytime active fire detections

This work presents development of an algorithm to reduce the spatial uncertainty of active fire locations within the 1 km MODerate resolution Imaging Spectroradiometer (MODIS Aqua and Terra) daytime detection footprint. The algorithm is developed using the finer 500 m reflective bands by leveraging on the increase in 2.13 μm shortwave infrared reflectance due to the burning components as compared to the non-burning neighborhood components. Active fire presence probability class for each of the 500 m pixels within the 1 km footprint is assigned by locally adaptive contextual tests against its surrounding neighborhood pixels. Accuracy is assessed using gas flares and wildfires in conjunction with available high-resolution imagery. Proof of concept results using MODIS observations over two sites show that under clear sky conditions, over 84% of the 500 m locations that had active fires were correctly assigned to high to medium probabilities, and correspondingly low to poor probabilities were assigned to locations with no visible flaming fronts. Factors limiting the algorithm performance include fire size/temperature distributions, cloud and smoke obscuration, sensor point spread functions, and geolocation errors. Despite these limitations, the resulting finer spatial scale of active fire detections will not only help first responders and managers to locate actively burning fire fronts more precisely but will also be useful for the fire science community.

Fire

A land product characterization system for comparative analysis of satellite data and products

A Land Product Characterization System (LPCS) has been developed to provide land data and products to the community of individuals interested in validating space-based land products by comparing them with similar products available from other sensors or surface-based observations. The LPCS facilitates the application of global multi-satellite and in situ data for characterization and validation of higher-level, satellite-derived, land surface products (e.g., surface reflectance, normalized difference vegetation index, and land surface temperature). The LPCS includes data search, inventory, access, and analysis functions that will permit data to be easily identified, retrieved, co-registered, and compared statistically through a single interface. The system currently includes data and products available from Landsat 4 through 8, Moderate Resolution Imaging Spectroradiometer (MODIS) Terra and Aqua, Suomi National Polar-Orbiting Partnership (S-NPP)/Joint Polar Satellite System (JPSS) Visible Infrared Imaging Radiometer Suite (VIIRS), and simulated data for the Geostationary Operational Environmental Satellite (GOES)-16 Advanced Baseline Imager (ABI). In addition to the future inclusion of in situ data, higher-level land products from the European Space Agency (ESA) Sentinel-2 and -3 series of satellites, and other high and medium resolution spatial sensors, will be included as available. When fully implemented, any of the sensor data or products included in the LPCS would be available for comparative analysis.

Remote Sensing

Exploring VIIRS continuity with MODIS in an expedited capability for monitoring drought-related vegetation conditions

Vegetation has been effectively monitored using remote sensing time-series vegetation index (VI) data for several decades. Drought monitoring has been a common application with algorithms tuned to capturing anomalous temporal and spatial vegetation patterns. Drought stress models, such as the Vegetation Drought Response Index (VegDRI), often use VIs like the Normalized Difference Vegetation Index (NDVI). The EROS expedited Moderate Resolution Imaging Spectroradiometer (eMODIS)-based, 7-day NDVI composites are integral to the VegDRI. As MODIS satellite platforms (Terra and Aqua) approach mission end, the Visible Infrared Imaging Radiometer Suite (VIIRS) presents an alternate NDVI source, with daily collection, similar band passes, and moderate spatial resolution. This study provides a statistical comparison between EROS expedited VIIRS (eVIIRS) 375-m and eMODIS 250-m and tests the suitability of replacing MODIS NDVI with VIIRS NDVI for drought monitoring and vegetation anomaly detection. For continuity with MODIS NDVI, we calculated a geometric mean regression adjustment algorithm using 375-m resolution for an eMODIS-like NDVI (eVIIRS’) eVIIRS’ = 0.9887 × eVIIRS − 0.0398. The resulting statistical comparisons (eVIIRS’ vs. eMODIS NDVI) showed correlations consistently greater than 0.84 throughout the three years studied. The eVIIRS’ VegDRI results characterized similar drought patterns and hotspots to the eMODIS-based VegDRI, with near zero bias.

Kansas

Application and comparison of the MODIS-Derived Enhanced Vegetation Index (EVI) to VIIRS, Landsat 5 TM, and Landsat 8 OLI platforms: A case study in the arid Colorado River Delta, Mexico

The Enhanced Vegetation Index (EVI) is a key Earth science parameter used to assess vegetation, originally developed and calibrated for the Moderate Resolution Imaging Spectroradiometer (MODIS) aboard the Terra and Aqua satellites. With the impending decommissioning of the MODIS sensors by the year 2020/2022, alternative platforms will need to be used to estimate EVI. We compared Landsat 5 (2000–2011), 8 (2013–2016) and the Visible Infrared Imaging Radiometer Suite (VIIRS; 2013–2016) to MODIS EVI (2000–2016) over a 420,083-ha area of the arid lower Colorado River Delta in Mexico. Over large areas with mixed land cover or agricultural fields, we found high correspondence between Landsat and MODIS EVI (R 2 = 0.93 for the entire area studied and 0.97 for agricultural fields), but the relationship was weak over bare soil (R 2 = 0.27) and riparian vegetation (R 2 = 0.48). The correlation between MODIS and Landsat EVI was higher over large, homogeneous areas and was generally lower in narrow riparian areas. VIIRS and MODIS EVI were highly similar (R 2 = 0.99 for the entire area studied) and did not show the same decrease in performance in smaller, narrower regions as Landsat. Landsat and VIIRS provide EVI estimates of similar quality and characteristics to MODIS, but scale, seasonality and land cover type(s) should be considered before implementing Landsat EVI in a particular area.

Colorado River Delta