Scouring winter floods can alter the structure and dynamics of river food webs. We investigated how structural food web alterations influenced ecosystem processes. Our study focuses on how a strong interactor can alter stream reach periphyton accrual, bed metabolism, and nutrient uptake. Previous research has shown the large, armored caddisfly, Dicosmoecus gilvipes, is sensitive to flood scour, so densities vary from year to year with hydrologic variation. Dicosmoecus larvae are capable of suppressing macroalgal biomass when abundant, but grazing larvae disappear after mid-summer, when they undergo diapause and pupation. We manipulated Dicosmoecus density (0 vs 50 m^-2) in experimental channels for 56 days. After 21 days we measured lower periphyton accrual (67% less), productivity (27% less), and ammonium uptake (75% less) where Dicosmoecus was present. We then removed Dicosmoecus from all experimental channels. Thirty-five days later all three processes were still depressed in experimental channels where Dicosmoecus had been present. Our results suggest that climatic or anthropogenic changes to a Mediterranean hydrograph and the subsequent impact on food web structure, can alter river productivity and nutrient retention, and that these process changes persist longer than the grazers that initially triggered them.