Boron (B), molybdenum (Mo), and selenium (Se) were measured in water, sediment, particulate organic detritus, and in various biota—filamentous algae, net plankton, macroinvertebrates, and fishes—to determine if concentrations were elevated from exposure to agricultural subsurface (tile) drainage during the spring and fall 1987, in the San Joaquin River, California. Concentrations of B and Se, but not Mo, were higher in most samples from reaches receiving tile drainage than in samples from reaches receiving no tile drainage. Maximum concentrations of Se in water (0.025 μg/mL), sediment (3.0 μg/g), invertebrates (14 μg/g), and fishes (17 μg/g) measured during this study exceeded concentrations that are detrimental to sensitive warmwater fishes. Toxic threshold concentrations of B and Mo in fishes and their foods have not been identified. Boron and Mo were not biomagnified in the aquatic food chain, because concentrations of these two elements were usually higher in filamentous algae and detritus than in invertebrates and fishes. Concentrations of Se were lower in filamentous algae than in invertebrates and fishes; however, concentrations of Se in or on detritus were similar to or higher than in invertebrates and fishes. These observations suggest that high concentrations of Se accumulated in invertebrates and fishes through food-chain transfer from Se-enriched detritus rather than from filamentous algae.