Atmospheric warming heats lakes, but the causes of variation among basins are poorly understood. Here, multi-decadal profiles of water temperatures, trophic state, and local climate from 345 temperate lakes are combined with data on lake geomorphology and watershed characteristics to identify controls of the relative rates of temperature change in water (WT) and air (AT) during summer. We show that differences in local climate (AT, wind speed, humidity, irradiance), land cover (forest, urban, agriculture), geomorphology (elevation, area/depth ratio), and water transparency explain >30% of the difference in rate of lake heating compared to that of the atmosphere. Importantly, the rate of lake heating slows as air warms (P < 0.001). Clear, cold, and deep lakes, especially at high elevation and in undisturbed catchments, are particularly responsive to changes in atmospheric temperature. We suggest that rates of surface water warming may decline relative to the atmosphere in a warmer future, particularly in sites already experiencing terrestrial development or eutrophication.