This report summarizes findings from the third year of a 4-year-long field investigation to document selected baseline environmental conditions in 29 agricultural drains and ponds operated by the Imperial Irrigation District along the southern border of the Salton Sea. Routine water quality and fish species were measured at roughly quarterly intervals from April 2007 to January 2008. The water quality measurements included total suspended solids and total (particulate plus dissolved) selenium. In addition, during April and October 2007, water samples were collected from seven intensively monitored drains for measurement of particulate and dissolved selenium, including inorganic and organic fractions. In addition, sediment, aquatic food chain matrices (particulate organic detritus, filamentous algae, net plankton, and midge [chironomid] larvae), and two fish species (western mosquitofish, Gambusia affinis; and sailfin molly, Poecilia latipinna) were sampled from the seven drains for measurement of total selenium concentrations. The mosquitofish and mollies were intended to serve as surrogates for desert pupfish (Cyprinodon macularius), an endangered species that we were not permitted to take for selenium determinations. Water quality values were typical of surface waters in a hot desert climate. A few drains exhibited brackish, near anoxic conditions especially during the summer and fall when water temperatures occasionally exceeded 30°C. In general, total selenium concentrations in water varied directly with conductivity and inversely with pH. Although desert pupfish were found in several drains, sometimes in relatively high numbers, the fish faunas of most drains and ponds were dominated by nonnative species, especially red shiner (Cyprinella lutrensis), mosquitofish, and mollies. Dissolved selenium in water samples from the seven intensively monitored drains ranged from 0.700 to 24.1 µg/L, with selenate as the major constituent in all samples. Selenium concentrations in other matrices varied widely among drains and ponds, with at least one drain (for example, Trifolium 18) exhibiting especially high concentrations in food chain organisms (in detritus, 13.3–28.9 µg Se/g; in net plankton, 11.9–19.3 µg Se/g; in midge larvae, 12.7–15.4 µg Se/g) and fish (in mollies, 12.8-25.1 µg Se/g; in mosquitofish, 13.2-20.2 µg Se/g; all concentrations are dry weights). These elevated concentrations approached or exceeded average concentrations reported from flowing waters in seleniferous wetlands in the San Joaquin Valley.