Air temperatures are rising across the globe, with polar regions experiencing greater increases compared to the global average, which may be mirrored in water temperatures of freshwater ecosystems. We hypothesized that freshwater wetlands could be sensitive barometers of climate change because atmospheric conditions may exert a stronger control on these wetlands than in previously studied streams. Here, we used nine years of paired air and water temperatures from 20 ponds across two subarctic wetland complexes in Alaska to fit Bayesian models of air-water relationships and then projected future changes in water temperature. Ponds showed strong air-water coupling, highlighting their vulnerability to thermal stress. Maximum mean annual temperatures of 18-22 °C were forecast under IPCC Representative Concentration Pathway 8.5, with an 80-90% probability of exceeding the thermal threshold for coho salmon growth within this century. Our analysis predicts future thermal stress in northern wetland ecosystems, with cascading effects on stream biota, emphasizing the importance of both temperature and location when predicting the impacts of climate change.