Non-native species have invaded most ecosystems and methods are needed to manage them, especially in locations with sensitive species where they cannot be easily extirpated. Gillnetting for invasive lake trout [Salvelinus namaycush (Walbaum, 1792)] in Yellowstone Lake, Yellowstone National Park, USA began in 1995 and their carcasses are deposited into deep areas. This suppression method was recently supplemented by adding carcasses to shallow (< 20 m) spawning sites during the autumn spawning period to decrease dissolved oxygen through decomposition, suffocating lake trout embryos. We measured ammonium concentrations (shallow and deep sites), algal biomass, and ammonium uptake by phytoplankton and periphyton (shallow sites only) to investigate the degree to which carcasses caused bottom-up effects. Ammonium concentrations increased in autumn and were higher at deep sites than shallow sites. Algal biomass and ammonium uptake did not increase after adding carcasses, suggesting minimal effects. Periphyton biomass was 9 times higher than phytoplankton, but phytoplankton demanded 4.5 times more ammonium. Returning lake trout carcasses to deep areas of the lake may cause a second algal bloom. Assessing how novel management techniques alter the environment helps managers develop the most successful mitigation strategies that are effective without causing adverse effects to other portions of the ecosystem.