Constructed evaporation basins are an important and economical disposal option for subsurface drainage water to sustain irrigated agriculture in the hydrologically closed basin portion of the San Joaquin Valley of California. The subsurface drainwaters flowing into the evaporation basins contained elevated concentrations of trace elements from geological settings. The trace element of most concern is selenium (Se) due to its potential toxicity in the aquatic food chain to waterbirds. We investigated Se speciation and accumulation in an evaporation basin facility consisting of ten cells covering a surface area of 726 ha. Water is serially transported from Cell 1 to Cell 10. The ten cells represented a wide range of water salinity and redox condition. The serial entrance of solutes and organic matter into the cells led to the accumulation of solutes from evapoconcentration and the development of reduced environments as the organic matter, mainly algae, is microbially degraded. Aqueous Se speciation was determined for both inorganic [Se(VI) and Se(IV)] and organic species (org-Se) at representative sites within the cells. Sequential extraction of sediment samples was used to identify the fractionation of Se associated with soluble, adsorbed, carbonate, and organic matter at representative sites. Selenium concentrations in surface waters generally decreased from the drainage water and Se accumulated mostly in surface sediments. Percentage of reduced species increased following the water flow. The redox environment in the evaporation pond waters was evaluated using platinum electrode (Eh) measurement and oxidation capacity (OXC), which was determined by the major dissolved redox species (oxygen, nitrate, Mn(II), Fe(III)/(II), sulfate, sulfide, and DOC). Presence of nitrate was inhibiting selenate reduction in the initial receiving cell. Major redox sensitive components in the solid-phase (extractable Fe/Mn, TOC) were also determined. Overall, reducing environment in the evaporation basins led to immobilization of Se into the sediments.