Estuaries provide critical habitat for a vast array of fish and wildlife but are also a nexus for core economic activities that mobilize and concentrate contaminants that can threaten aquatic species. Selenium (Se), an essential element and potent reproductive toxin, is enriched in parts of the San Francisco Estuary (SFE) to levels known to cause toxicity, yet the risk of Se to species that inhabit the SFE is not well understood. We quantified Se concentrations in muscle, liver, and ovary of the demersal cyprinid Sacramento Splittail from six regions in the SFE at three time points (fall 2010-11, spring 2017) to evaluate Se exposure risk. Here we report fish morphological attributes, total selenium concentrations in fish boneless skinless muscle, liver, and ovary, as well as carbon, nitrogen and sulfur stable isotope values and elemental mass concentrations in fish muscle.

In response to the rapidly evolving conditions at the Salton Sea, with the emergence of both newly formed wetland habitat and increasing hazards to wildlife, the U.S. Bureau of Reclamation and U.S. Geological Survey have funded a re-evaluation of data gaps regarding selenium concentrations in biota the region. As part of this work, selenium concentrations in biological tissue samples were compiled from published reports, public databases, and unpublished archives into a tabulated spreadsheet. Since the California Department of Water Resources summarized selenium biological data in 2005, our compilation efforts focused on the 2005 through 2020 range. The resulting dataset encompasses all records available to us from 1984 to 2020, although we did not find any selenium records after 2017.

Due to declining water levels and increasing salinity in the Salton Sea which may increase the hazards to wildlife, the U.S. Geological Survey and U.S. Bureau of Reclamation are re-evaluating selenium concentrations in the region. As part of this work, selenium concentrations in water and sediment samples and selected other inorganic constituents were compiled from published reports, public databases, and unpublished archives into a tabulated spreadsheet. This spreadsheet represents a rapid synthesis of available data on selenium concentrations in water and sediment in the region surrounding the Salton Sea, however it does not include all data ever published in the region. Additionally, the data compilation was done with an emphasis on selenium concentrations measured after 2005, therefore earlier selenium data may be under-represented.

Working in cooperation with EPA, the USGS coordinated the collection of fish tissue for processing and analyses by the EPA Region 10 Manchester Environmental Laboratory located in Port Orchard, WA. This effort was being tied to existing operations work performed by state wildlife agencies in Idaho and Montana (Ross et al. 2018). Annually, in late August and September, the Idaho Department of Fish and Game (IDFG), the Montana Department of Fish, Wildlife and Parks (MTFWP), and the Kootenai Tribe of Idaho conduct population surveys on the Kootenai River. During the 2018 electrofishing population surveys, state wildlife agency personnel also retained collected fish for this effort. The following were key design components of fish collection in the Kootenai River: (1) Fish were caught and analyzed for selenium and mercury in multiple tissues (filet, whole body, and/or egg/ovaries) as available to assess baseline contamination/bioaccumulation in fish species between Libby Dam and downstream of Bonners Ferry, ID. (2) Fish were caught from the mainstem Kootenai River in early September 2018 and analyzed for selenium and mercury from immediately downstream of Libby Dam (tailwater), downstream of Troy, MT, downstream of the ID/MT border, and in the proximity of Shorty’s Island downstream of Bonner’s Ferry. (3) The EPA Region 10 laboratory provided in-kind support for selenium and mercury analyses for the 142 fish samples collected. EPA Region 10 also provided data and sample management support via the Scribe Project Manager (RSCC). More details of the study design are given by USEPA and USGS (2018). Results: A total of 142 fish representing 13 species were retained for tissue analysis. Eggs were obtained from two species, kokanee salmon and mountain whitefish. In kokanee salmon, eggs were found in two fish from only site KR13 (Kootenai River below Libby Dam) and ranged from 4.17 to 5.01 mg/kg selenium as dry weight (dw). Eggs were found in mountain whitefish from all sites except the most downstream site sampled, KR4 (Kootenai River near Shorty’s Island). Selenium concentrations in mountain whitefish eggs ranged from 11.6 to 24.8 mg/kg (dw). An objective of the study was to compare selenium concentrations in fish and water to USEPA nationally recommended water quality criteria for selenium. The national criteria recommend that concentrations in fish eggs not exceed 15.1 mg/kg (dw), concentrations in whole-body of fish not exceed 8.5 mg/kg dry weight, or (b) concentrations in muscle tissue not exceed 11.3 mg/kg dry weight (USEPA 2016). For eggs, 6 of the 8 mountain whitefish egg samples exceeded EPA’s recommended value. No samples exceeded the whole-body criterion component of 8.5 mg/kg dry weight and no samples exceeded the muscle criterion component of 11.3 mg/kg dry weight. References: Ross, T.J., K. McDonnell, R. Hardy, and S. Stephenson. 2018. Kootenai River resident fish mitigation: white sturgeon, burbot, native salmonid monitoring and evaluation (Annual Progress Report May 1, 2016 — April 31, 2017). BPA Project # 1988-065-00, Idaho Department of Fish and Game. Report to the Bonneville Power Administration, Environment, Fish and Wildlife, Portland, OR. 118 pp. https://www.cbfish.org. USEPA. 2016. Aquatic Life Ambient Water Quality Criterion for Selenium – Freshwater 2016. 822-R-16-006, U.S. Environmental Protection Agency. 807 pp. https://www.epa.gov/wqc/aquatic-life-criterion-selenium [Accessed February 21, 2018]. USEPA and USGS. 2018. Kootenai River Fish Tissue Study Quality Assurance Project Plan. Prepared by U.S. Environmental Protection Agency, Regions 8 and 10, and U.S. Geological Survey, Idaho Water Science Center. 28 August 2018 (Revised 01 October 2018). 41 pp.

These data were compiled to study mercury and selenium concentrations in fish species and assemblages in lotic waterbodies across the Upper Colorado River Basin. Data were compiled from State and Federal agencies. This data table contains raw concentration data, as well as standardized concentrations corrected for differences based on sample type (i.e., tissue type), species-specific bioaccumulation rates (Table S1), and fish size (Table S2). The data were used in linear mixed effects models to estimate average mercury and selenium concentration in fish species and in fish assemblages, including fish total length (cm), sampling location (Sub basin name and GPS coordinates), and sampling year (Figures 2,3, and 4 from manuscript).

Birds (Clark’s grebe , Aechmophorus clarkii; Forster’s Tern, Sterna forsteri), fish (Peacock bass, Cichla temensis, Cichla monoculus; Pescada, Plagioscion squamosissimus) and earthworms were analyzed for selenium, total mercury, and methyl mercury c oncentration and mercury speciation. A Clark’s grebe was collected from Lake Berryessa (California, United States) in September 2012. A Forster’s Tern was collected from the San Francisco Bay Estuary (California, United States) in June 2018. Bird necropsies were performed at the U.S. Geological Survey (Dixon, CA) to obtain the following tissues: head feather, breast feather, brain, skeletal muscle, kidney, and liver. Fishes were collected in September 2018 from the Tapajós River (Brazil), which is close to artisanal gold mining areas where liquid elemental mercury is used. Fish necropsies were performed to obtain muscle and liver. Earthworms were collected in 2017-2018 from two soils (Site S1 Champ-sur-Drac, Site S2 Champ-sur-Drac; France) near the chlor-alkali plant of Champ-sur-Drac. Five endogeic and one anecic earthworm were sampled at Site S1 and five endogeic and two anecic at Site S2. Chemical analyses for total mercury and methylmercury were made at the U.S. Geological Survey Mercury Research Laboratory (Middleton, Wisconsin). Chemical analyses for total selenium were made at the U.S. Geological Survey (Menlo Park, California) and University of La Rochelle (La Rochelle, France). Mercury speciation was measured by high energy-resolution X-ray absorption fine structure (HR-XANES) and extended X-ray absorption fine structure (EXAFS) spectroscopy at beamline ID26 at the European Synchrotron Radiation Facility. The screening of selenium and mercury associated with protein extracts was measured by double affinity (AF) high performance liquid chromatography-inductively coupled plasma mass spectrometry (AF-HPLC-ICPM) at the LGC Group (Teddington, United Kingdom). ORCA, a geometry optimization platform, was used to predict the structures of mercury bound to selenium in two configurations: Hg(selenoeine)4 and Hg10(methaneselenolate)20 (Hg10(SeMe)20). There are 7 files (*.csv) provided in this product: 1) site descriptions 2) analysis descriptions, 3) HR-XANES results and chemical analyses, 4) HR-XANES spectra, 5) EXAFS data, 6) EXAFS spectrum, and 7) modeled cartesian coordinates of the mercury-selenium clusters.

Yuma Ridgway’s rail (Rallus obsoletus yumanensis, hereafter, rail) are an endangered species for which patches of emergent marsh within the Salton Sea watershed comprise a substantial portion of habitat for the species’ disjointed range in the southwestern United States. These areas of emergent marsh include: 1) marshes managed by federal (particularly the U.S. Fish and Wildlife Service’s Sonny Bono Salton Sea National Wildlife Refuge (SBSSNWR), state (California Department of Fish and Wildlife), and local (Imperial Irrigation District) resource agencies that are sustained by direct deliveries of Colorado River water; and 2) unmanaged marshes sustained by agricultural drainage water. Management of rail habitat in this arid environment is complicated by increasingly limited availability of unimpaired freshwater owing by recent water management decisions associated with the Quantification Settlement Agreement, and risks posed by potentially harmful concentrations of selenium (Se) found in agricultural drainage water that can readily bioaccumulate in aquatic food webs. To provide timely science for managers, the selenium concentrations in this data release are the basis for summary statistics reported in Ricca et al. 2022. These data comprise selenium concentrations and associated locations and dates of the following matrices sampled to describe pathways of selenium exposure to rails occupying managed and unmanaged marshes: 1) unfiltered surface water, midge larvae (Chironomidae), water boatmen (Corixidae), mosquitofish (Gambusia spp.) and crayfish (Astacidae). Selenium samples were collected from 15 fixed sampling points each in managed and unmanaged marshes during late February, April, and June of 2016, which corresponded to rail pre-nesting, nesting, and fledgling reproductive life-stages, respectively. Two areas within the two treatment types (managed vs. unmanaged marsh) were of particular interest to help assess risks associated with changing Sea dynamics and different water management strategies: 1) a large unmanaged marsh (Morton Bay) unintentionally created in approximately 2008 when it became separated from the Salton Sea as water inflows began to drop and a berm formed from accumulated sediment; and 2) a restored marsh (HZ-9A) managed by the SBSSNWR, which is currently supplied with Colorado River water, but may be sustained in the future by a blend of clean (that is, low Se) Colorado River and agricultural drainage water with higher Se from the Alamo River.

The trace element selenium is an essential element with a narrow window between concentrations needed to support life and those that cause toxicity to egg laying organisms. Selenium bioaccumulation in aquatic organisms is primarily the result of trophic transfer through food webs and is poorly predicted by dissolved concentrations in freshwater bodies. To better understand the hydrologic and biological dynamics that control selenium accumulation into fishes of the Lower Gunnison River Basin (Colorado), ecosystem scale selenium accumulation models were developed from data collected between June 2015 and October 2016.

The U.S. Geological Survey (USGS), in cooperation with the Bureau of Reclamation, completed a review of dissolved selenium data collected from the Selenium Management Program network during each water year (WY) in the lower Gunnison River Basin, in western Colorado. The data tables include dissolved-selenium concentrations, selected streamflow data, and computed loads as well as dissolved-selenium regression model calibration and output tables. Concentration and streamflow data are compiled from the USGS National Water Information System database. Tables include monitoring location identification information, data collection time frames, concentration data, as well as calculations of mean, median, select percentiles, and percentage reduction in loads. Tables are organized by each year, with a zipped folder for WY 2018 (October 1, 2017 through September 30, 2018), WY 2019 (October 1, 2018 through September 30, 2019), WY 2020 (October 1, 2019 through September 30, 2020), WY 2021 (October 1, 2020 through September 30, 2021), and WY 2022 (October 1, 2021 through September 30, 2022). Within each zipped folder is a metadata .xml file describing each comma-separated value (.csv) data file contained therein. The methods used to complete this review are available in Henneberg (2018) and Mayo and Leib (2012). Version 3.0 contains additional zipped folders for WY 2021 and 2022, which were not included in the original data release. While previous versions are available from the author, all records in previous versions can be found in version 3.0. First posted - April 23, 2021 (available from author) Revised - June, 2022 (version 2.0) Revised - July, 2023 (version 3.0)

This data release and accompanying spreadsheet illustrate the ecosystem scale selenium model for Lake Koocanusa described in USGS Open-File Report 2020-xxxx, "Understanding and Documenting the Scientific Basis of Selenium Ecological Protection in Support of Site-Specific Guidelines Development for Lake Koocanusa, Montana, U.S.A., and British Columbia, Canada." All report sections, equations, and tables referenced in this data release and spreadsheet are from that report, referred to hereafter as “the OFR.” Two models are described in the OFR. Results for several different “runs” of this model with different model input parameters and assumptions are included in this data release. The spreadsheet calculations that produced those results are also included with this data release. Model 1, IFM = Insect-to-fish model, summarized by Eq. 11: protective C(Se)dissolved = tissue guideline/TTFfish /[(TTFinvert1*invert fraction1) + (TTFinvert2*invert fraction2)]/SPM bioavailability fraction/(Kd/1,000). Model2, TFM = Trophic-fish model, summarized by Eq. 12: protective C(Se)dissolved = tissue guideline/TTFfishTL4/TTFfishTL3/[(TTFinvert1*invert fraction1) + (TTFinvert2*invert fraction2)]/SPM bioavailability fraction/(Kd/1,000). Model results are presented for the four representative IFM food webs described in Table 6 of the OFR, and for three representative TFM food webs described in Table 7 of the OFR. “Generic” IFM and TMF modeling spreadsheets (consistent with Tables 8 and 9 of the OFR) are provided that implement the two models such that a user can establish their own modeling assumptions and view the results of the models with those assumptions.Finally, four alternative modeling scenarios and results specifically requested by the Montana Department of Environmental Quality, the cooperator in this work, are also presented here.