This report summarizes comprehensive findings from a 4-year-long field investigation to document 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 collections and fish community assessments were conducted on as many as 16 sampling dates at roughly quarterly intervals from July 2005 to April 2009. The water-quality measurements included total suspended solids and total (particulate plus dissolved) selenium. With one exception, fish were surveyed with baited minnow traps at quarterly intervals during the same time period. However, in July 2007, fish surveys were not conducted because we lacked permission from the California Department of Fish and Game for incidental take of desert pupfish (Cyprinodon macularius), an endangered species. During April and October 2006–08, water samples also were collected from seven intensively monitored drains (which were selected from the 29 total 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 pupfish, which we were not permitted to sacrifice for selenium determinations. Water quality (temperature, dissolved oxygen, pH, specific conductance, and turbidity) values were typical of surface waters in a hot, arid climate. A few drains exhibited brackish, near-anoxic conditions, especially during summer and fall when water temperatures occasionally exceeded 30 degrees Celsius. Total selenium concentrations in water were directly correlated with salinity and inversely correlated with total suspended-solids concentrations. Although 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 mosquitofish, mollies, and red shiner (Cyprinella lutrensis). Dissolved selenium in water samples from the seven intensively monitored drains ranged from 0.700 to 32.8 micrograms per liter (?g/L), with selenate as the major constituent. Selenium concentrations in other matrices varied widely among drains and ponds, with one drain (Trifolium 18) exhibiting especially high concentrations in food chain matrices [particulate organic detritus, 5.98–58.0 micrograms of selenium per gram (?g Se/g); midge larvae, 12.7–50.6 ?g Se/g] and in fish (mosquitofish, 13.2–20.2 ?g Se/g; sailfin mollies, 12.8–30.4 ?g Se/g; all concentrations are based on dry weights). Although selenium was accumulated by all trophic levels, biomagnification (defined as a progressive increase in selenium concentration from one trophic level to the next higher level) in midge larvae and fish occurred only at lower exposure concentrations. Judging mostly from circumstantial evidence, the health and wellbeing of poeciliids and pupfish are not believed to be threatened by ambient exposure to selenium in the drains and ponds.