Lakes are sentinels of climate change because their physical and chemical conditions integrate regional climate, local weather, and watershed-scale land cover and hydrology. In southwest Alaska, these lakes provide critical habitat for iconic populations of sockeye salmon and other species, underpinning regional culture, ecology, and economy. To evaluate how long-term changes in climate and watershed conditions influence lake temperature and water quality, we analyzed 15 years of vertical profile data collected by the National Park Service Inventory and Monitoring Program in lakes of Katmai and Lake Clark National Parks and Preserves. Using in situ measurements, downscaled climate data, and remotely sensed lake and watershed characteristics, we developed separate models for mixed and stratified lakes. For stratified systems, we identified drivers of epilimnetic and hypolimnetic temperatures as well as thermal gradients between layers. We then applied future climate projections to assess potential trajectories of lake thermal structure under continued warming and shifting precipitation regimes Our results indicate that lake thermal conditions respond not only to contemporaneous summer weather, but also to legacy effects of temperature, precipitation, and wind from preceding fall and winter seasons. Lake size and morphometry, glacier influence, and surrounding land cover further mediate these responses. Together, these findings highlight the importance of cross-seasonal and landscape-level controls on subarctic lake thermal dynamics and provide a foundation for salmon habitat modeling, long-term monitoring, and climate-adaptive management in Alaska’s national parks.