Abstract The extent of the differences between atmospheric and lake heatwaves remains unclear. Here we analysed daily surface water and air temperature data from 265 lakes worldwide (2000–2022) to compare heatwave trends, spatial distributions, and key differences. We find that lake heatwaves are more severe than atmospheric heatwaves, with longer accumulated heatwave days (29.7 days vs. 18.0 days), a shorter reoccurrence period (86.9 days vs. 121.4 days), and greater accumulated heat. Additionally, the frequency and total heatwave days have increased faster for lake heatwaves than for atmospheric heatwaves. When both types co-occur, heatwave severity intensifies. From a long-term perspective, reduced wind speed is the key driver of the differences between lake heatwaves and atmospheric heatwaves. Spatially, lake location is the primary determinant, followed by lake area and depth. Under a fixed-baseline high-emission scenario, by 2100, the difference is expected to diminish as air temperatures rise faster than water temperatures.