Closed-system microcosms were used to study factors affecting the fate of selenium (Se) in aquatic systems. Distribution and bioaccumulation of Se varied among sediment types and Se species. A mixture of dissolved ⁷⁵Se species (selenate, selenite and selenomethionine) was sorbed more rapidly to fine-textured, highly organic pond sediments than to sandy riverine sediments. Sulfate did not affect the distribution and bioaccumulation of ⁷⁵Se over the range 80–180 mg SO₄ liter⁻¹. When each Se species was labeled separately, selenomethionine was lost from the water column more rapidly than selenate or selenite. Selenium lost from the water column accumulated primarily in sediments, but volatilization was also an important pathway for loss of Se added as selenomethionine. Loss rates of dissolved Se residues were more rapid than rates reported from mesocosm and field studies, suggesting that sediment: water interactions are more important in microcosms than in larger test systems. Daphnids accumulated highest concentrations of Se, followed by periphyton and macrophytes. Selenium added as selenomethionine was bioaccumulated preferentially compared to that added as selenite or selenate. Organoselenium compounds such as selenomethione may thus contribute disproportionately to Se bioaccumulation and toxicity in aquatic organisms.