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USGS2025

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2023 through December 2023

We sampled juvenile wild Oncorhynchus mykiss (Steelhead Trout) in headwater streams of the Wind River, WA, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over twenty years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an inadequate adult ladder and contributed to increased water temperatures. Data from our study, and companion work by Washington Department of Fish and Wildlife, are contributing to the Columbia Basin Fish and Wildlife Program (2008) Research, Monitoring, and Evaluation (RM&E) Strategy of Fish Population Status Monitoring. Specifically, this work addresses the sub-strategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2023, we PIT-tagged 1,294 Steelhead Trout parr (age-0 and age-1), in the Trout Creek and upper Wind River watersheds. Age-0 parr were at high abundance due to a strong spawning run in 2023 (estimate of 814 adults from September snorkel survey compared to 22-year median of 450; Charlie Cochran, WDFW Fish Biologist, personal commun., 2022), but age-1 parr abundance was low following poor spawner numbers in 2022 (estimate of 159 adults from September snorkel survey). An additional 189 age-2 or older parr were tagged to provide fish for estimating detection efficiencies at PTISs. Steelhead Trout parr were recaptured and detected through repeat headwater sampling, smolt trapping, instream PTISs and Columbia River PIT-tag detection. We maintained and upgraded six instream PTISs to detect PIT-tagged Steelhead Trout parr, smolts, and adults, providing data for population assessments, and life-cycle research. Detection data from PIT-tagged adult Steelhead Trout at PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 99 percent during seven of the past nine years and have exceeded 97% at our primary PTIS in the Wind River during eight of the past nine years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek, where it had potential negative effects on Steelhead Trout populations due to hydrologic impairment, increased temperatures, and adult passage issues because of an inadequate fish ladder. Detections at the instream PTISs have shown trends of age-0 and age-1 Steelhead Trout parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. Our data suggest that often most fish from a cohort that migrate downstream will do so at age-1 for additional rearing downstream of their natal areas. It is unknown if this is ingrained behavior or a result of lack of habitat capacity. We have estimated that from 15 to 56% of parr tagged as age-0 fish in headwater areas make downstream migrations at age-1 for additional rearing. We have estimated that up to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall: this is especially pronounced in the upper Wind River portion of the watershed. These findings raise questions about preferred parr rearing habitat and whether migrations are density- or habitat-quality driven, and answers to such questions are part of the long-term goals of this study as active and passive habitat restoration actions occur. Repeat sampling at sites in the subbasin within and between years has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PIT-tagged parr during summer have been similar across the subbasin, though slightly lower in the Trout Creek watershed. Summer growth rates have been lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed. Yearly relative growth was similar across the subbasin for both age-0 and age-1 tagged parr. Non-native Salvelinus fontinalis (Brook Trout) are present in the subbasin, chiefly the Trout Creek watershed, and repeat sampling provides an index of their prevalence. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2024. Percent-of-catch and number of Brook Trout at the Trout Creek sites from 2011 through 2022, though variable, have generally declined. Evaluation and planning of habitat restoration efforts are critical to ensure efficient use of money and resources. Assessing Steelhead Trout life history variation in the Wind River subbasin informs research and tracking of many populations and habitat restoration and water allocation planning. Movement of Steelhead Trout parr from natal areas to other rearing areas raises questions regarding juvenile abundance, origin, and habitat use within watersheds. Improved PTISs and focused PIT-tagging of age-0 and age-1 Steelhead Trout parr allow investigation of such questions. Detailed viable salmonid population and life-history data, such as that provided by PIT-tagging and instream PTIS networks inform fisheries policy and management and enable assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek and proposed major instream habitat restoration in the upper Wind River.

Washington↗

USGS2024

Assessing spatial variability of nutrients, phytoplankton, and related water-quality constituents in the California Sacramento–San Joaquin Delta at the landscape scale—2018 high resolution mapping surveys

Executive Summary This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suisun Bay, comprising three spatial surveys conducted in May, July, and October of 2018 that used continuous underway high frequency sampling and measurements onboard a high-speed boat to characterize spatial variation across the extent of the Delta. The method used involves simultaneously collecting information about the concentration and spatial distribution of all major nutrient forms with analogous information about the major classes of phytoplankton and associated water-quality conditions. The results showed substantial variation across space and time, providing an unprecedented snapshot of the dynamic environmental processes that shape the ways nutrients interact with and affect aquatic habitats in the Delta. The purposes of this study were to improve our understanding of how hydrodynamics, landscape features, and aquatic primary productivity interact to drive nutrient cycling and transport in the Delta and to provide insights into the underlying processes most directly responsible for the conditions at the time of this study, and thus into the range of conditions that may be expected following the wide array of prospective future changes to the Delta. One major anticipated change at the time of this study was the planned upgrade to the Sacramento Regional Wastewater Treatment Plant, but the study also informs our understanding of potential effects from other changes to the Delta, such as those caused by other nutrient-management actions, flow actions, large-scale wetland restoration, drought, flood, levee failure, and changes to water management. Nutrient loading is the primary driver of nutrient concentrations in the Delta, but several other major drivers interact to shape their distribution and effects: geomorphology, hydrodynamics, landscape features, and aquatic productivity. Hydrodynamics affect timescales of transport and dilution of nutrient loads in the Delta. During transit through the system, channel geometry, tidal mixing, and water exports affect hydrodynamics in diverse ways that influence water-residence and transport times, thereby markedly affecting the range of times during which natural internal cycling can alter nutrient concentrations and forms. Channel geometry and location shape tidal energy and river currents into these observed dynamics. Interactions with Delta aquatic landscapes such as herbaceous tidal marsh, submerged aquatic vegetation, and large expanses of intertidal or subtidal sediments (all highly productive landscapes) exert demand on available nutrient supplies but can also simultaneously transform and generate nutrients. Finally, while phytoplankton require nutrients to sustain production and thus are a potential nutrient sink, the amount and form of nutrients also can influence the occurrence of harmful algal blooms (HABs) that adversely affect aquatic organisms as well as affect the occurrence of beneficial algal blooms that result in production of algae that are favorable for imperiled Delta pelagic aquatic food webs. The surveys revealed a complex mosaic of spatial variation, with nutrient concentrations varying from near zero to well above concentrations considered eutrophic; nutrient concentrations were more often related to the extent of hydrologic transport and mixing than to specific geographic locations or to specific landscape features. Similarly, the surveys identified phytoplankton abundance ranging from near detection to the level of large phytoplankton blooms, with large variation in phytoplankton community composition. Although the study occurred during a period of low bloom activity, phytoplankton productivity appeared to be the strongest potential sink for inorganic nutrients in the Delta, indicating that it is a larger control on nutrient concentrations and distribution than previously understood. Cycling and transformation within the water column only appeared to substantially lower total nutrient concentrations at the longest estimated transport timescales. Contrary to expectations, we did not observe substantial nutrient depletion near landscape-scale features such as open-water habitats, submerged aquatic vegetation beds, extensive wetlands, or exposed sediments, indicating that these habitat types did not act as major sinks for nutrients in the Delta during these surveys. These results indicated that nutrient reduction efforts may have the greatest effect on pelagic phytoplankton productivity in the more productive reaches of the Delta and estuary, but these effects are unlikely to be magnified by changes to nutrient loss within the Delta over conceivable changes in flow conditions, Delta water management actions, or large-scale wetland restoration activities. Nevertheless, local processes were shown to cause substantial loss, and thus integrating of nutrient effects with other indicators of aquatic habitat conditions will help inform planning future actions at specific sites. Finally, we note that the primary contribution of this study was intended to be the survey data themselves. Aside from the results highlighted in this report, the surveys are a benchmark against which future environmental change may be evaluated, including changes to nutrient management or water exports, drought, large-scale wetland restoration, and climate change. Further, although we highlight some of the main findings from the surveys in this report, the necessarily limited scope precludes examination of many topics for which these surveys may be highly informative. To facilitate the utility of these data to stakeholders, managers, and researchers, we have released the data online (Bergamaschi and others, 2020) and created an online data exploration portal ( https://ca.water.usgs.gov/bay-delta/2018-delta-wide-mapping-surveys.html ) where users may query the surveys in a variety of ways to test hypotheses, examine relationships, assess spatial trends, and download data. The data exploration portal is intended to be an immersive experience that allows users to gain greater understanding of the complex interactions that shape Delta aquatic environments. This report is intended as a companion to the portal, allowing the reader to challenge and further explore the highlighted findings. This study was a collaboration between the U.S. Geological Survey and the Delta Regional Monitoring Program, with additional funding provided from U.S. Geological Survey Cooperative Matching Funds Program.

California↗

USGS2010

Methylmercury cycling, bioaccumulation, and export from agricultural and non-agricultural wetlands in the Yolo Bypass

This 18-month field study addresses the seasonal and spatial patterns and processes controlling methylmercury (MeHg) production, bioaccumulation, and export from natural and agricultural wetlands of the Yolo Bypass Wildlife Area (YBWA). The data were collected in conjuntion with a Proposition 40 grant from the State Water Resources Control Board in support of the development of Best Management Practices (BMP's) for reducing MeHg loading from agricultural lands in the wetland-dominated Yolo Bypass to the Sacramento-San Joaquin River Delta. The four managemenr-based questions addressed in this study were: 1. Is there a different among agricultural and managfed wetland types in terms of Me Hg dynamic (production, degradation, bioaccumulation, or export)? 2. Does water residence time influence MeHg dynamics? 3. Does the application of sulfate-based fertilizer impact MeHg production rates? 4. Does the presence (or absence) of vegetation influence MeHg production rates? Measurements of MeHg concentrations in sediment, water, and biota (plants, invertebrates, and fish) were made to assess management-level patterns in five wetland types, which included three type of shallowly-flooded agricultural wetlands (white rice, wild rice, and fallow) and two types of managed wetlands (permanently and seasonally flooded). To strengthen our understanding of the processes underlying the seasonal and spatial patterns of MeHg cycling, additional exploratory factors were measured including ancillary sediment and water quality parameters, stable isotope fractionation (oxygen, sulfur, carbon, and nitrogen), photodemethylation rates, and daily-integrated hydrologic budgets. Samples and field data were collected from May 2007 to July 2008, and nearly all sample analyses were completed by September 2008 as per the Quality Assurance Program Plan (QAPP) requirements. Although wetland type was a major factor that drove the study design, within-field hydrology also proved to be an important factor controlling aqueous MeHg and total mercury (THg) concentrations and export. Overall, agricultural wetlands exhibited higher MeHg concentrations in overlying water, sediment, and biota than did managed seasonal and permanent wetlands. This appears to be partly due to higher rates of sediment in microbial production of MeHg on agricultural wetlands during the fall through spring period. Both sulfate- and iron-reducing bacteria have been implicated in the MeHg production process, and both were demonstrably active in all wetlands studied; however, sulfate-reducing bacteria were not stimulated by the addition of sulfate-based fertilizer to agricultural wetlands, suggesting that easily-degraded (labile) organic matter, rather than sulfate, was limiting their activity in these field types. The data suggest that agriculturally-managed soils promoted MeHg production through 1) enhanced microbial activity via higher temperatures and larger pools of labile carbon, and 2) enhanced pools of microbially available inorganic divalent mercury (Hg(II)) resulting from a decrease in reduced-sulfur, solid-phase minerals under oxic or only mildly reducing conditions. MeHg mass balances were assessed by comparing filed-specific MeHg loads for inlets vs. outlet flows. The overall mass balance for MeHg in surface water during the summer irrigation period (June - September 2007) indicated little to no net MeHg export from the six agricultural wetlands taken as a whole. Of the six agricultural wetlands, there was net overall MeHg export from two fields (one fallow and one white rice) during August, and from four of the six fields (one fallow, one white rice, and two wild rice) during September) Over the entire summer irrigation period, two of the fields (one fallow and one wild rive) showed net MeHg export, and the other four fields showed wither net import or no significant change. Rates of measured photomethylation and exchange between sediment and water pools suggest that both processes may be responsible for the lack of MeHg export. Despite significant differences during winter months between fields in surface water concentrations of MeHg, MeHg loads were not calculated in mid-winter because flood waters had overtopped field boundaries and field fidelity could not be established. During the summer 2007 irrigation season, surface water out-flows from agricultural wetlands were 9%-36% of inlet flows, and evaporation rates explained most of this water loss, with infiltration likely accounting for the remainder. Unfiltered aqueous MeHg concentrations increased from <1 ng L -1 in source waters to up to 10 ng L -1 in agricultural wetland drains during the summer irrigation period. Increases in solute concentration caused by evapoconcentration were estimated by determining concentration factors (outflow/inflow) for chloride (a conservative dissolved constituent) and by measuring oxygen isotope ratios ( 18 O/ 16 O, expressed as δ 18 O) in water. Increases in MeHg concentration from inflows-to-outflows exceeded those caused by evapoconcentration on several fields during the summer irrigation season. This was especially true when initial surface water MeHg concentrations were low, as seen in the southern block of fields receiving irrigation water directly from the Toe Drain. The northern block of fields received irrigation water from Greens Lake, which included Toe Drain water plus recirculated drain water from other agricultural fields within the Yolo Bypass and west of the Yolo Bypass; as such, the northern fields showed a smaller percentage increase in MeHg concentration because initial MeHg concentrations in surface water inflows were greater than in inputs to the southern fields. Mercury concentrations in fish were greater in agricultural wetlands white rice and wild rice) than in the two permanently flooded wetlands. Additionally, Hg concentrations in biota showed a general increase from inlets to outlets withing agricultural wetlands, but not within permanent wetlands. This was particular evident in white rice fields where caged western mosquitofish at the outlets had Hg concentrations that were more than 4 times higher than in caged fish held at the inlets. Similar spatial patterns in Hg bioaccumulation in agricultural and permanent wetlands were seen for wild populations of western mosquitofish and Mississippi silversides. In contrast to fish, invertebrates, such as water-boatman (Corixidae) and back swimmers (Notonectidae), had greater Hg concentrations in permanent wetlands than in tempoarirly flooded agricultural wetlands, Fish THg concentrations were weakly correlated with water MeHg,a and not correlated with sediment MeHg. In contrast, invertebrate MeHg concentrations were more strongly correlated with sediment MeHg than with water MeHg concentrations. These results illustrate the complexity of MeHg bioaccumulation through food webs and indicate the importance of simultaneously using multiple biosentinels when monitoring MeHg production and bioaccumulation. Despite high sediment production rates and water concentrations in agricultural wetlands, MeHg export was physically limited by hydrologic export for all wetlands studied. We suggest that load reduction is maximized by limiting water throughout, but that on-site biota exposure is maximized by this loner water residence time. While field-specific hydrologic loads could not be fully quantified during flood conditions in February 2008, we suggest that the primary period of MeHg export from Yolo Bypass Wildlife Area is during those winter flooding periods when overall microbial activity and MeHg production in agricultural soils is fueled by the decomposition of rice straw, and when hydrologic flowthrough is maximal. Local stakeholders participated in two workshops related to this study, demonstrating an interest in understanding factors controlling MeHg production, export, and bioaccumulation. The results of this field study show that permanently flooded, naturally vegetated wetlands are unlikely to a large source of MeHg production within the YBWA, in contrast with agriculturally-managed wetlands. MeHg loading to Toe Drain waters of the Yolo Bypass may be reduced by lowering rated of hydrologic export from agricultural wetlands during the growing season and especially during rice harvest, However, under these water-holding conditions, biota living within agricultural wetlands may thus be exposed to higher MeHg concentrations in surface water, As observed in this study, rapid bioacculumaltion over a 2-month period led to MeHg concentrations in invertebrates and fish more than 6 and 11 times higher, respectively, than proposed TMDL target values to protect wildlife (0.03 ppm ww). The results of this field study, together with the information from YBWA stakeholders, provide a more definitive understanding of how MeHg cycling and bioaccumulation respond to habitat differences and specific management practices. These results directly address 4 core components of CBDA's Mercury Strategy for the Bay-Delta Ecosystem (Wiener et al., 2003a): a) Quantification and evaluation of THg and MeHg sources, b) Quantification of effects of ecosystem restoration on MeHg exposure, c) Assessment of ecological risk, and d) Identification and testing of potential management approaches for reducing MeHg contamination. In addition, the quantitative results reported here assess the effect of current land use practices in the Yolo Bypass MeHg production, bioaccumulation and export, and provide process-based advice towards achieving current goals of the RWQCB-CVR's Sacramento -- San Joaquin Delta Estuary TMDL for Methyl & Total Mercury (Wood et al., 2010b). Further work is necessary to evaluate biotic exposure in the Yolo Bypass Wildlife Area at higher trophic levels (e.g. birds), to quantify winter hydrologic flux of MeHg to the larger Delta ecosystem, and to evaluate rice straw management options to limit labile carbon supplies to surface sediment during winter months. In summary, agricultural management of rice fields -- specifically the periodic flooding and production of easily degraded organic matter -- promotes the production of MeHg beyond rates seen in naturally vegetated wetlands, whether seasonally or permanently flooded., The exported load from MeHg from these agricultural wetlands may be controlled by limiting hydrologic export from fields to enhance on-site MeHg removal processes, but the tradeoff is that this impoundement increases Me Hg exposure to resident organisms.

California↗

USGS2018

Evaluation of the Source and Transport of High Nitrate Concentrations in Ground Water, Warren Subbasin, California

Ground water historically has been the sole source of water supply for the Town of Yucca Valley in the Warren subbasin of the Morongo ground-water basin, California. An imbalance between ground-water recharge and pumpage caused ground-water levels in the subbasin to decline by as much as 300 feet from the late 1940s through 1994. In response, the local water district, Hi-Desert Water District, instituted an artificial recharge program in February 1995 using imported surface water to replenish the ground water. The artificial recharge program resulted in water-level recoveries of as much as 250 feet in the vicinity of the recharge ponds between February 1995 and December 2001; however, nitrate concentrations in some wells also increased from a background concentration of 10 milligrams per liter to more than the U.S. Environmental Protection Agency (USEPA) maximum contaminant level (MCL) of 44 milligrams per liter (10 milligrams per liter as nitrogen). The objectives of this study were to: (1) evaluate the sources of the high-nitrate concentrations that occurred after the start of the artificial-recharge program, (2) develop a ground-water flow and solute-transport model to better understand the source and transport of nitrates in the aquifer system, and (3) utilize the calibrated models to evaluate the possible effect of a proposed conjunctive-use project. These objectives were accomplished by collecting water-level and water-quality data for the subbasin and assessing changes that have occurred since artificial recharge began. Collected data were used to calibrate the ground-water flow and solute-transport models. Data collected for this study indicate that the areal extent of the water-bearing deposits is much smaller (about 5.5 square miles versus 19 square miles) than that of the subbasin. These water-bearing deposits are referred to in this report as the Warren ground-water basin. Faults separate the ground-water basin into five hydrogeologic units: the west, the midwest, the mideast, the east and the northeast hydrogeologic units. Water-quality analyses indicate that septage from septic tanks is the primary source of the high-nitrate concentrations measured in the Warren ground-water basin. Water-quality and stable-isotope data, collected after the start of the artificial recharge program, indicate that mixing occurs between imported water and native ground water, with the highest recorded nitrate concentrations in the midwest and the mideast hydrogeologic units. In general, the timing of the increase in measured nitrate concentrations in the midwest hydrogeologic unit is directly related to the distance of the monitoring well from a recharge site, indicating that the increase in nitrate concentrations is related to the artificial recharge program. Nitrate-to-chloride and nitrogen-isotope data indicate that septage is the source of the measured increase in nitrate concentrations in the midwest and the mideast hydrogeologic units. Samples from four wells in the Warren ground-water basin were analyzed for caffeine and selected human pharmaceutical products; these analyses suggest that septage is reaching the water table. There are two possible conceptual models that explain how high-nitrate septage reaches the water table: (1) the continued downward migration of septage through the unsaturated zone to the water table and (2) rising water levels, a result of the artificial recharge program, entraining septage in the unsaturated zone. The observations that nitrate concentrations increase in ground-water samples from wells soon after the start of the artificial recharge program in 1995 and that the largest increase in nitrate concentrations occur in the midwest and mideast hydrogeologic units where the largest increase in water levels occur indicate the validity of the second conceptual model (rising water levels). The potential nitrate concentration resulting from a water-level rise in the midwest and mideast hydrogeologic units was estimated using a simple mixing-cell model. The estimated value is within the range of concentrations measured in samples from wells, further indicating the validity of the second conceptual model. A ground-water flow model and a solute-transport model were developed for the Warren ground-water basin for the period 1956-2001. MODFLOW-96 was used for the ground-water flow model and MOC3D was used for the solute-transport model. The model cell size is about 500 feet by 500 feet and the models were discretized vertically into three layers. The models were calibrated using a trial-and-error approach using water-level and nitrate-concentration data collected between 1956-2001. In order to better match the measured data, low fault hydraulic characteristic values were required, thereby compartmentalizing the ground-water basin. In addition, it was necessary to parameterize the specific yield distribution for the top model layer where unconfined ground-water conditions occur into three homogeneous zones. Separate sets of specific- yield values were needed to simulate the drawdown and subsequent water-level recovery. In addition, the calibrated natural recharge was about 83 acre-feet per year. The entrainment of unsaturated-zone septage was simulated as recharge having an associated nitrate concentration. The volume of recharge was a function of the measured water-level rise between 1994-98 and the moisture content of the unsaturated zone. The nitrate concentration of the recharge water was a weighted function of the assumed nitrate concentration in the infiltrating water associated with the overlying land use. The simulated hydraulic head and nitrate concentration results were in good agreement with the measured data indicating that the mechanism for the increase in nitrate concentrations was rising water levels entraining high-nitrate septage in the unsaturated-zone. The calibrated models were used to simulate the possible effects of a planned conjunctive-use project in the western part of the ground-water basin. The simulated project included the addition of a new recharge pond and a new extraction well. In addition, recharge at two existing recharge ponds was increased and three existing production wells were pumped, treated in a nitrate-removal facility, and used for water supply. The simulated hydraulic heads increased in the west, the mideast, and parts of the east hydrogeologic units; however, the simulated hydraulic heads decreased in the midwest and northeast hydrogeologic units. The simulated nitrate concentrations increased to above the MCL of 44 milligrams per liter (10 milligrams per liter as nitrogen) in parts of the west as a result of the increase in simulated hydraulic head. The simulated nitrate concentrations decreased in part of the midwest hydrogeologic unit as a result of the artificial recharge and pumping from the nitrate-removal wells. The simulated nitrate concentrations increased to above the MCL of 44 milligrams per liter in part of the mideast and parts of the east hydrogeologic units beneath commercial land-use areas.

California↗