The invasion, boom, collapse, and reestablishment of a population of the planktivorous threadfin shad in Clear Lake, California, USA, were documented over a 20-year period, as were the effects of changing shad populations on diet and mercury (Hg) bioaccumulation in nearshore fishes. Threadfin shad competitively displaced other planktivorous fish in the lake, such as inland silversides, young-of-year (YOY) largemouth bass, and YOY bluegill, by reducing zooplankton abundance. As a result, all three species shifted from a diet that was dominated by zooplankton to one that was almost entirely zoobenthos. Stable carbon isotopes corroborated this pattern with each species becoming enriched in delta13C, which is elevated in benthic vs. pelagic organisms. Concomitant with these changes, Hg concentrations increased by approximately 50% in all three species. In contrast, obligate benthivores such as prickly sculpin showed no relationship between diet or delta13C and the presence of threadfin shad, suggesting that effects of the shad were not strongly linked to the benthic fish community. There were also no changes in Hg concentrations of prickly sculpin. The temporary extirpation of threadfin shad from the lake resulted in zooplankton densities, foraging patterns, isotope ratios, and Hg concentrations in pelagic fishes returning to pre-shad values. These results indicate that even transient perturbations of the structure of freshwater food webs can result in significant alterations in the bioaccumulation of Hg and that food webs in lakes can be highly resilient.