This report presents raw data on selenium concentrations in samples of water, sediment, detritus, and selected food-chain matrices collected from selected agricultural drains in the southern portion of the Salton Sea during October 2006 and January 2007. Total selenium and selenium species were determined in water samples, whereas total selenium was determined in sediment, detritus, algae, plankton, midge larvae (Family Chironomidae), and two fish species (western mosquitofish, Gambusia affinis, and sailfin molly, Poecilia latipinna).