In Yellowstone Lake, Wyoming, the largest inland population of nonhybridized Yellowstone Cutthroat Trout Oncorhynchus clarkii bouvieri, hereafter Cutthroat Trout, declined throughout the 2000s because of predation from invasive Lake Trout Salvelinus namaycush, drought, and whirling disease Myxobolus cerebralis. To maintain ecosystem function and conserve Cutthroat Trout, a Lake Trout gill netting suppression program was established in 1995, decreasing Lake Trout abundance and biomass. Yet, the response of Cutthroat Trout to varying Lake Trout suppression levels, collectively with the influence of disease and climate, is unknown. We developed an ecosystem model (calibrated to historical data) to forecast (2020–2050) whether Cutthroat Trout would achieve recovery benchmarks given disease, varying suppression effort, and climate change. Lake Trout suppression influenced Cutthroat Trout recovery; current suppression effort levels resulted in Cutthroat Trout recovering from historical lows in the early 2000s. However, Cutthroat Trout did not achieve conservation benchmarks when incorporating the influence of disease and climate. Therefore, the National Park Service intends to incorporate age-specific abundance, spawner biomass, or both in conservation benchmarks to provide better indication of how management actions and environmental conditions influence Cutthroat Trout. Our results illustrate how complex interactions within an ecosystem must be simultaneously considered to establish and achieve realistic benchmarks for species of conservation concern.