Predators can alter the density and size of lower trophic levels, but fewer studies have demonstrated how nutrient cycling can also be affected.  We measured changes in lower trophic levels in Yellowstone Lake where the illegal introduction of two invasive species and drought caused the decline of Yellowstone cutthroat trout (Oncorhynchus clarki bouvieri).  We show how these changes have altered nutrient cycling by modeling nitrogen sources and sinks in the past when cutthroat trout were abundant and measuring fluxes currently when native trout are less abundant.  Using size-frequency distributions of cutthroat trout, measured excretion rates and an estimate of population size, we calculated cutthroat trout excretion fluxes during two time periods.  We used density, size and an empirical model to calculate zooplankton excretion.  We measured phytoplankton uptakes rates using nitrogen isotopes in enclosures.  We calculated that cutthroat trout excreted 14 times more nitrogen in 1977 compared to 2004 and zooplankton excreted twice as much nitrogen in 1977.  Algal biomass was 4 times higher in the past compared to present concentrations and nitrogen uptake by phytoplankton was lower in 2004.  Therefore, trophic cascades alter densities at lower trophic levels and subsequently influence nutrient cycling.