Most of the agricultural products produced in the western United States would not be possible without the use of irrigation. In semi-arid areas of the West excess water is applied to fields to flush out salts leached onto the surface soils. This excess water (drainwater or return flow) either infiltrates into the soil or runs off into nearby basins, ponds, or streams. Pesticides applied to the irrigated crops can be mobilized and transported by drainwater and return flows to surface waters. Irrigation water applied to soils containing soluble trace elements can leach trace elements, such as selenium, and arsenic from the soil. Generally, soils derived from marine Cretaceous shales can contain elevated concentrations of selenium and other trace elements. Irrigation projects with a high risk of selenium toxicity to fish and wildlife have the following characteristics:

• wetlands located on upper Cretaceous marine shales;
• soils derived from upper Cretaceous marine shales;
• a high evaporation index (>2.5);
• terminal lakes & ponds; or
• they are located downstream from a major selenium source(s).

High evaporation rates can concentrate these trace elements to levels that are toxic to fish and sensitive bird species. Selenium is typically the trace element of particular concern. Although small concentrations of selenium are necessary in the diet of most animals, high concentrations are toxic to sensitive species of fish and birds. Waterfowl or fish can ingest large concentrations of selenium when they consume plants and insects from ponds that receive selenium-contaminated irrigation runoff or drainwater. The effects of selenium toxicity to fish and birds include impaired reproduction and deformed embryos.

Selenium and other trace elements as well as salts in irrigation drainwater and return flows can cause farmland to become non-productive and can pollute groundwater. Irrigation systems, such as surge and sprinkler systems, create less runoff and reduce deep percolation consequently reducing the problems associated with irrigation drainwater and return flows.