Linking Selenium Sources to Ecosystems: Local and Global Perspectives

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The sources, biogeochemistry, and ecotoxicology of selenium (Se) combine to produce a widespread potential for ecological risk such as deformities in birds and fish. Linking the understanding of source characteristics to a mechanistic, biodynamic dietary model of Se exposure on an ecosystem-scale improves the prediction of Se effects and its potential remediation.



Global map showing petroleum basins and phosphate deposits.

Figure 1. A predictive global map of latent risk for environmental Se loading indicates that ancient organic-rich depositional marine basins, unrestricted by age, are linked to the contemporary global distribution of Se source rocks. Given the geographic patterns, Se emerges as a contaminant within specific regions of the globe that may limit phosphate mining, oil refining, and drainage of agricultural lands because of potential ecological risks to vulnerable food webs. Selenium also may serve as a geochemical exploration tool that signals an ancient productive biological environment.

The sources and biogeochemistry of selenium (Se) combine to produce a widespread potential for ecological risk (Figure 1). Documented environmental effects across scientifically investigated sites include deformities in birds and fish, degraded fish communities, and exclusion of habitats for bird use (see Modeling and Irrigation pages).

The large geologic extent of Se sources is connected by human activities that include power generation, oil refining, irrigation drainage, and coal, phosphate, copper, and uranium mining (Figure 2). Study areas from the 1) San Joaquin Valley and San Francisco Bay-Delta Estuary, California, 2) watersheds of the Colorado River and other arid basins of the western US; 3) upper Blackfoot River watershed, Idaho; 4) upper Mud River watershed and other Appalachian basins, West Virginia; and 5) coal ash receiving basins such as Belews Lake in North Carolina include a range of processing activities that call attention to anthropogenic connections to the environment (e.g., production, storage, and disposal of subsurface irrigation drainage, oil refining effluents, and waste shales), in addition to surface processes (weathering, erosion, and runoff), that can ultimately mediate contamination.

The Se sources model components are:

  • oceanic depositional environments
  • organic carbon-rich marine sediments
  • anthropogenic activities that facilitate transfer to the environment
  • waste components and source waters and
  • affected receiving water bodies
Chart showing various anthropogenic activities that contribute to selenium exposure in the environment.

Figure 2. A selenium sources model that depicts anthropogenic activities that contribute to exposure in the environment.

The global distribution of organic-enriched sedimentary rocks (i.e., black shales, petroleum source rocks, phosphorites, and coals) (Figure 1) depends on the fundamental role of major and trace nutrients in determining primary productivity. Although black shales and their recoverable organic fractions as sources of trace elements are widely recognized, the implications of worldwide reservoirs, site-specific fluxes, and persistent biologic cycling of Se are not. Given the geographic distribution of these source rocks, Se emerges as a contaminant within specific regions of the globe that may limit mineral extraction and agricultural growth or exacerbate environmental toxicity.

Development of technologies for controlling Se pollution and predictive forecasts of ecological effects will become increasingly critical to commercial exploitation, as well as to faunal conservation. Based on our conceptual model, adoption of methodologies to protect fish and wildlife that recognize the full sequence of interacting processes from sources through food webs to vulnerable predators will advance risk management by including all considerations that cause systems to respond differently to Se contamination.

Flowchart showing ecosystem-scale selenium modeling methodology.

Figure 3.  Ecosystem-scale selenium modeling conceptualizes processes and parameters important for quantifying and understanding the effects of selenium in the environment. The model can be applied to forecast exposure and to evaluate the implications of management or regulatory choices. Kd = empirically determined environmental partitioning factor between water and particulate material; TTF = biodynamic food-web transfer factor between an animal and its food.

Development of an ecosystem-scale Se modeling methodology (see Modeling page) and its site-specific applications (e.g., San Francisco Bay-Delta Estuary, mountaintop coal mining areas) are examples of a new type of approach that predicts ecological Se effects based on dietary exposure and the major processes that determine how Se is processed through food webs to top fish and bird predator species.

Recent investigation of Lake Koocanusa, a transboundary reservoir between Montana and British Columbia that receives effluent from coal mines in Canada, highlights this methodology (see Lake Koocanusa references below). The developed site- and species-specific model predicts protection of the reservoir’s ecosystems from selenium within a series of hydrodynamic source gradients and food-web exposure scenarios for a recreationally important community of fish. 


Links of Interest

U.S. Environmental Protection Agency

Lake Koocanusa References

San Francisco Bay-Delta, California

San Joaquin Valley, California

The Bureau of Reclamation is re-evaluating options for providing drainage service to the San Luis Unit of the Central Valley Project. The EIS evaluates seven action alternatives in addition to No Action: In-Valley Disposal, In-Valley/Groundwater Quality Land Retirement, In-Valley/Water Needs Land Retirement, In-Valley/Drainage-Impaired Area Land Retirement, Ocean Disposal, Delta-Chipps Island Disposal, and Delta-Carquinez Strait Disposal. All of the alternatives would include common elements: on-farm and in-district actions, drainwater collection systems, regional reuse facilities, the Firebaugh sumps, and land retirement of at least 44,106 acres. In addition to the common elements, the action alternatives (except Ocean Disposal) involve varying levels of drainwater treatment (reverse osmosis and/or biological selenium treatment) and/or additional land retirement before disposal.

The Grassland Bypass Project (GBP) is based upon an agreement between the U.S. Bureau of
Reclamation and the San Luis and Delta-Mendota Water Authority (Authority) to use a 28-mile segment
of the San Luis Drain. 

The western San Joaquin Valley is one of the most productive farming areas in the United States, but salt-buildup in soils and shallow groundwater aquifers threatens this area’s productivity. Elevated selenium concentrations in soils and groundwater complicate drainage management and salt disposal. In this document, we evaluate constraints on drainage management and implications of various approaches to management considered in: 

  • the San Luis Drainage Feature Re-Evaluation (SLDFRE) Environmental Impact Statement (EIS) (about 5,000 pages of documentation, including supporting technical reports and appendices)
  • recent conceptual plans put forward by the San Luis Unit (SLU) contractors (i.e., the SLU Plans) (about 6 pages of documentation); 
  • approaches recommended by the San Joaquin Valley Drainage Program (SJVDP) (1990a); and 
  • other U.S. Geological Survey (USGS) models and analysis relevant to the western San Joaquin Valley. 

Selenium Treatment Technologies

I. San Luis Unit Feature Re-evaluation Environmental Impact Statement, June 2006 
Final Appendix B: Pilot Studies 
B1: Reverse Osmosis 
B2: Selenium Treatment 
B3: Enhanced Evaporation 
B4: Bioaccumulation 
B5: References 
Attachment B-1: Pilot-Scale Evaluation of Biotreatment Technology 
II. San Luis Drainage Feature Re-evaluation Feasibility Report, March 2008 
Main Report 
Summary and Chapters 1–9 
A Feasibility Design Appendix 
B Appraisal Level Four-Account Analysis of the Environmental Quality Account and Other Social Effects Account Resources 
C Pump and Pipeline Design Data 
D Reverse Osmosis Analyses Reports 
E Selenium Biotreatment Pilot Reports 
F Geology Report 
G Technical Review of Field and Laboratory Permeability Testing 
H Evaluation of Enhanced Evaporation Technologies 
I Computer Modeling for Northerly Area Evaporation Basin 
J Comparison of Embankment Options for Evaporation Ponds 
K Mitigation 
L Economics 
M Record of Decision, San Luis Drainage Feature Re-evaluation 
III. San Luis Drainage Feature Reevaluation Implementation Demonstration Treatment Facility at Panoche Drainage District Draft Environmental Assessment and Finding of No Significant Impact, September, 2011

Phosphate Mining

  • Real-time stream gauging data for the Blackfoot River above the Blackfoot Reservoir (USGS station 13063000) is available:
  • For a complete description of the book entitled Life Cycle of the Phosphoria Formation: From Deposition to the Post-Mining Environment published by Elsevier, New York, containing USGS research on the Phosphoria Formation, go to the site now.
  • Chemical Composition of Samples Collected from Waste Rock Dumps and Other Mining-Related Features at Selected Phosphate Mines in Southeastern Idaho, Western Wyoming, and Northern Utah By: Phillip R. Moyle1 and J. Douglas Causey1 Western U.S. Phosphate Project2 Open-File Report 01-41, 2001
  • Digital database of mining-related features at selected historic and active phosphate mines, Bannock, Bear Lake, Bingham, and Caribou Counties, Idaho  B y: J. Douglas Causey1 and Phillip R. Moyle1 Western U.S. Phosphate Project2 U.S. Geological Survey Open-File Report 01-142 Digital Database, Online version 1.0, 2001
  • An upwelling model for the Phosphoria sea: A Permian, ocean-margin sea in the northwest United States David Z. Piper and Paul Karl Link AAPG Bulletin, v. 86, no. 7 (July 2002), pp. 1217–1235
  • Geochemistry of Permian Rocks from the Margins of the Phosphoria Basin: Lakeridge Core, Western Wyoming By Robert B. Perkins, Brandie McIntyre, James R. Hein, and David Z. Piper USGS Open-File Report 03-21
  • Chemical composition of weathered and unweathered strata of the Meade Peak Phosphatic Shale Member of the Permian Phosphoria Formation--A; Measured sections A and B, central part of Rasmussen Ridge, Caribou County, Idaho By Herring, J.R., Desborough, G.A., Wilson, S.A., Tysdal, R.G., Grauch, R.I., and Gunter, M.E. 1999 USGS Open-File Report 99-147-A, 24 p.
  • Herring, J.R., Grauch, R.I., Siems, D.F., Tysdal, R.G., Johnson, E.A., Zielinski, R.A., Desborough, G.A., Knudsen, A.C., and Gunter, M.E. 2001 USGS Open-File Report 01-195, 72 p.

Coal Mining

  • West Virginia Water Science Center, Water Resources of West Virginia, Coal Topics, Databases, and Related Information:
  • U.S. Geological Survey Open-File Report 2005-1330: Spatial Trends in Ash Yield, Sulfur, Selenium, and Other Selected Trace Element Concentrations in Coal Beds of the Appalachian Plateau Region, U.S.A. Published 2005, Version 1.0, Online only Sandra G. Neuzil, Frank T. Dulong, and C. Blaine Cecil
  • National Coal Resources Data System, US Coal Quality Database
  • West Virginia Geological and Economic Survey. Trace Elements in West Virginia Coals.  These pages explore the geologic, environmental and economic aspects of trace elements in West Virginia coals.
  • Mountaintop Mining / Valley Fills in Appalachia: Final Programmatic Environmental Impact Statement (Final PEIS) October, 2005. In October 2005, the U.S. Army Corps of Engineers, US Environmental Protection Agency (EPA), US Fish and Wildlife Service, US Office of Surface Mining, and West Virginia Department of Environmental Protection completed their review and evaluation of all comments received on the Draft PEIS and jointly prepared the Final PEIS on mountaintop coal mining and associated valley fills in Appalachia. On October 28, 2005, the agencies announced the availability of the Final PEIS in a Federal Register notice and in a multi-agency press release widely distributed to local and national media. Please use these highlighted links to view these documents and any attachments.


Presser, T.S., Piper, D.Z., Bird, K.J., Skorupa, J.P., Hamilton, S.J., Detwiler, S.J. and Huebner, M.A., 2004, The Phosphoria Formation: a model for forecasting global selenium sources to the environment, in J. Hein, ed., Life Cycle of the Phosphoria Formation: From Deposition to the Post-Mining Environment: Elsevier, New York, p. 299-319.

Presser, T.S., Hardy, M.A., Huebner, M.A., and Lamothe, P., 2004, Selenium loading through the Blackfoot River watershed: linking sources to ecosystems: in J. Hein, ed., Life Cycle of the Phosphoria Formation, From Deposition to the Post-Mining Environment: Elsevier, New York, p. 437-466.

Skorupa, J.P., Detwiler, S., and Brassfield, R., 2002, Reconnaissance Survey of Selenium in Water and Avian Eggs at Selected Sites Within the Phosphate Mining Region Near Soda Springs, Idaho, May-June, 1999: U.S. Fish and Wildlife Report, U.S. Fish and Wildlife Service, Sacramento, California, 95 p.

Piper, D.Z., Skorupa, J.P., Presser, T.S., Hardy, M.A., Hamilton, S.J., Huebner, M.A., and Gulbrandsen, R.A., 2000, The Phosphoria Formation at the Hot Springs Mine in southeast Idaho: a source of trace elements to ground water, surface water, and biota: U. S. Geological Survey Open-File Report 00-050, 73 p.


Ecosystem-scale selenium modeling methodology:

Chapman, P.M., Adams, W.J., Brooks, M.L., Delos, C.G., Luoma, S.N., Maher, W.A., Ohlendorf, H.M., Presser, T.S., and Shaw, D.P., eds., 2010, Ecological Assessment of Selenium in the Aquatic Environment: Society of Environmental Toxicology and Chemistry (SETAC) Press, Pensacola Florida, 339 p.

Presser, T.S., and Luoma, S.N., 2010, A Methodology for ecosystem-scale modeling of selenium: Integrated Environmental Assessment and Management, v. 6, no. 4, p. 685-710.

Luoma, S.N., and Presser, T.S., 2009, Emerging opportunities in management of selenium contamination: Environmental Science and Technology, v. 43, no. 22, p. 8483-8487.

Luoma, S.N., and Rainbow, P.S., 2005, Why is metal bioaccumulation so variable? Biodynamics as a unifying concept: Environmental Science and Technology, 39:1925–1931.


In-depth publications for site-specific application of ecosystem-scale selenium modeling:

Luoma, S.N., and Presser, T.S., 2018, Status of selenium in south San Francisco Bay—A basis for modeling potential guidelines to meet National tissue criteria for fish and a proposed wildlife criterion for birds: U.S. Geological Survey Open-File Report 2018–1105, 75 p.

Presser, T.S., and Naftz, D.L., 2018, USGS Measurements of Dissolved and Suspended Particulate Material Selenium in Lake Koocanusa in the Vicinity of Libby Dam (MT), 2015-2017 (update): U.S. Geological Survey data release.

Presser, T.S., and Naftz, D.L., 2017, USGS Measurements of Dissolved and Suspended Particulate Material Selenium in Lake Koocanusa in the Vicinity of Libby Dam (MT), 2015-2016: U.S. Geological Survey data release.

Jenni, K.E., Naftz, D.L., Naftz, Presser, T.S., 2017, Conceptual Modeling Framework to Support Development of Site-Specific Selenium Criteria for Lake Koocanusa, Montana, U.S.A., and British Columbia, Canada: U.S. Geological Survey Open-File Report 2017-1130, 14 p.

Presser, T.S., 2013, Selenium in Ecosystems within the Mountaintop Coal Mining and Valley-Fill Region of Southern West Virginia-Assessment and Ecosystem-Scale Modeling, U.S. Geological Survey Professional Paper 1803, 86 p.

Presser, T.S., and Luoma, S.N., 2013, Ecosystem-scale selenium model for the San Francisco Bay-Delta Regional Ecosystem Restoration Implementation Plan (DRERIP): San Francisco Estuary and Watershed Science, v. 11, no. 1, p. 1-39.

Presser, T.S., and Luoma, S.N., 2010, Ecosystem-scale selenium modeling in support of fish and wildlife selenium criteria development for the San Francisco Bay-Delta Estuary, California: U.S. Geological Survey Administrative Report, 101 p. and Appendices A-D. [Published 12/14/2010; released by USEPA (Region 9, San Francisco, California) 8/29/2011]

Presser, T.S., and Luoma, S.N., 2009, Modeling of selenium for the San Diego Creek watershed and Newport Bay, California: U.S. Geological Survey Open-File Report 2009-1114, 48 p.