Invasive species require management to mitigate their harmful effects on native biodiversity and ecosystem processes. However, such management can also have negative, unintended consequences on non-target taxa, ecosystem processes, and food web dynamics. In Yellowstone Lake, invasive lake trout (Salvelinus namaycush) have caused a decline in the native Yellowstone cutthroat trout (Oncorhynchus clarkii bouvieri) population. To suppress the invader, lake trout carcasses are deposited on the species’ spawning sites, causing embryo mortality by reducing dissolved oxygen as they decay. The non-target effects of carcass treatment are unknown, but benthic invertebrates may be sensitive to reductions in dissolved oxygen. Benthic invertebrate taxa have varying hypoxia tolerances; caddisflies (Trichoptera, family Limnephilidae) are hypoxia sensitive while amphipods Gammarus lacustris and Hyallela azteca are hypoxia tolerant. Both are widespread and abundant in Yellowstone Lake and comprise a large proportion of fish diets, so changes in their abundances could alter food web dynamics. We conducted an in situ experiment to determine if carcass deposition causes mortality in these two taxa of benthic invertebrates. The probability of mortality for caddisflies was 3.15 times higher in carcass treatments as compared to controls, while amphipod mortality did not change in response to carcass treatment. Amphipods, which contribute most significantly to fish diets, are unlikely to be reduced in response to carcass deposition, which is confined to a small fraction of the lake where lake trout spawn, limiting the possibility for lake-wide effects. We conclude that carcass deposition is unlikely to alter the availability of invertebrates as a food source for fish in Yellowstone Lake.