Evaporation basins (or ponds) are the most commonly used facilities for disposal of selenium-laden saline agricultural drainage in the closed hydrologic basin portion of the San Joaquin Valley, California. However concerns remain for potential risk from selenium (Se) toxicity to water fowl in these evaporation basins. In this study, we examined the chemical status of Se in both waters and sediments in two currently operating evaporation pond facilities in the Tulare Lake Drainage District. Some of the saline ponds have been colonized by brine-shrimp (Artemia), which have been harvested since 2001. We evaluated Se concentration and speciation, including selenate [Se(VI)], selenite [Se(IV)], and organic Se [org-Se or Se(-II)] in waters and sediment extracts, and fractionation (soluble, adsorbed, organic matter (OM)-associated, and Se(0) and other resistant forms) in sediments and organic-rich surface detrital layers from the decay of algal blooms. Selenium in ponds without vascular plants exhibited similar behavior to wetlands with vascular plant present, indicating that similar Se transformation processes and mechanisms had resulted in Se immobilization and an increase of reduced Se species [Se(IV), org-Se, and Se(0)] from Se(VI)-dominated input waters. Selenium concentrations in most pond waters were significantly lower than the influent drainage water. This decrease of dissolved Se concentration was accompanied by the increase of reduced Se species. Selenium accumulated preferentially in sediments of the initial pond cell receiving drainage water. Brine-shrimp harvesting activities did not affect Se speciation but may have reduced Se accumulation in surface detrital and sediments.