Clear Lake (Lake County, CA, USA) is hypereutrophic and used for drinking water, tribal use, and supports a significant fishing economy. The Mendocino Complex (2018), one of the largest wildfires in California's post‐settlement history, burned 40% of the Clear Lake watershed, providing a timely opportunity to study the impacts of historical and current wildfires on this valuable aquatic resource. Using long‐term monthly monitoring data from 1968 to 2019, paired with historical watershed fire data, we found that for the three largest fire years in the watershed's history, 3‐year postfire median July–October epilimnetic total phosphorus (TP) concentrations were below or equal to 3‐year prefire TP concentrations. However, both median TP epilimnetic concentrations and deepwater temperature across the lake have increased since the late 1960s. Long‐term TP increases were more strongly correlated with monthly maximum air temperatures than precipitation, suggesting a potential role of warming‐induced water column stratification, dissolved oxygen (DO) depletion, and high potential for internal phosphorus loading. Hypoxic occurrences were correlated with higher hypolimnetic soluble reactive phosphorus and TP concentrations, but additional high‐frequency monitoring of DO will help determine the duration of anoxia and its contribution to internal phosphorus loading. These long‐term data suggest that for this large, hypereutrophic lake, wildfires did not significantly alter in‐lake TP concentrations based on long‐term, monthly monitoring and that other internal or external sources of TP may mask any wildfire effects. Nonetheless, our study underscores the value of synthesizing decades of water quality, watershed wildfire, and climate data to build a more comprehensive, nuanced picture of multiple long‐term threats to aquatic ecosystems under global change. Moreover, monitoring and studying fire effects across a wide range of lake types beyond this study will help promote more effective lake management during changing climates and increasingly frequent large wildfires.