Responses in lake temperatures to climate warming have primarily been characterized using seasonal metrics of surface-water temperatures such as summertime or stratified period average temperatures. However, climate warming may not affect water temperatures equally across seasons or depths. We analyzed a long-term dataset (1981–2015) of biweekly water temperature data in six temperate lakes in Wisconsin, U.S.A. to understand (1) variability in monthly rates of surface- and deep-water warming, (2) how those rates compared to summertime average trends, and (3) if monthly heterogeneity in water temperature trends can be predicted by heterogeneity in air temperature trends. Monthly surface-water temperature warming rates varied across the open-water season, ranging from 0.013 in August to 0.073°C yr⁻¹ in September (standard deviation [SD]: 0.025°C yr⁻¹). Deep-water trends during summer varied less among months (SD: 0.006°C yr⁻¹), but varied broadly among lakes (–0.056°C yr⁻¹ to 0.035°C yr⁻¹, SD: 0.034°C yr⁻¹). Trends in monthly surface-water temperatures were well correlated with air temperature trends, suggesting monthly air temperature trends, for which data exist at broad scales, may be a proxy for seasonal patterns in surface-water temperature trends during the open water season in lakes similar to those studied here. Seasonally variable warming has broad implications for how ecological processes respond to climate change, because phenological events such as fish spawning and phytoplankton succession respond to specific, seasonal temperature cues.