Lake Hovsgol, Mongolia’s largest freshwater lake and the 19th largest lake in the world by volume, is among the world’s most pristine and unique lakes. Despite its remoteness, protected status, and low human population density, Lake Hovsgol is threatened by the synergistic pressures of climate change, water pollution, overfishing, and development. Analysis of local weather station data reveals a 1.8°C increase in air temperature over the last half century, a rate of warming more than three times the global average, which contributes to the drying of many previously reliable streams and the loss of fish spawning habitat. Surveys for pelagic microplastics and shoreline macroplastics indicate that Lake Hovsgol is more polluted than other more developed and densely populated watersheds owing to its lack of waste management system and long residence time. Interviews with herders and park rangers and shoreline surveys for derelict fishing gear suggest that gillnet fishing, though illegal, is an important source of food and income for the resident herder population and that fishing effort is increasing in intensity. Although stable isotope analyses suggest that food web structure has not changed over the past decade, analyses of long-term monitoring data suggest that fish populations, particularly Hovsgol grayling (Thymallus nigrescens), burbot (Lota lota), and roach (Rutilus rutilus), are in decline. It is difficult to know whether these declines are due to overfishing or climate change without robust measurements of fisheries removals, but data-poor stock assessment analyses indicate that plausible levels of fishing have the capacity to overexploit the endangered, endemic Hovsgol grayling population. These issues are likely to be exacerbated as access and tourism increase and the way in which these issues are resolved or ignored in the iconic Lake Hovsgol National Park could shape future protected area management in Mongolia.