Abstract Introduced Lake Trout Salvelinus namaycush threaten native Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri in Yellowstone Lake, Yellowstone National Park, where gill nets have been used to suppress subadult and adult Lake Trout since 1995. However, survival of embryonic and larval life history stages can have profound effects on the population dynamics of Lake Trout. Inducing additional mortality at those stages, especially if used in concert with intensive gillnetting of older fish, could enhance overall suppression efforts. Therefore, we conducted controlled field experiments at Yellowstone Lake to systematically evaluate the effects of sediment deposition and ground Lake Trout carcass deposition on Lake Trout embryos in pre-positioned incubators. Sediment deposition caused dissolved oxygen concentrations to decline below lethal levels for a prolonged overwinter period (92 d). Embryo mortality among overwintering incubators varied from 97.0 ± 5.3% (mean ± SE) at the substrate surface to 100.0 ± 0.0% at 20 cm below the substrate surface. Decomposition of ground carcass material on spawning sites caused dissolved oxygen concentrations to decline to lethal levels (<3.4 mg/L) for about 9 d after biomass application rates of 14 and 28 kg/m2 in treatment plots. Exposure to ground carcass material resulted in 100.0 ± 0.0% embryo mortality at the substrate surface and within interstices 20 cm below the surface in 14- and 28-kg/m2 biomass treatments. Embryo mortality was probably caused by hypoxic conditions within substrates in both experiments. The deposition of sediment and ground Lake Trout carcass material on Lake Trout spawning sites in Yellowstone Lake could provide an additional source of mortality in ongoing Lake Trout suppression efforts. These methods may also be beneficial in other systems when incorporated in an integrated pest management approach targeting multiple life history stages of invasive freshwater fish.