Extreme storms are becoming more frequent and intense with climate change. Assessing lake ecosystem responses to extreme storms (resistance) and their capacity to recover (resilience) is critical for predicting the future of lake ecosystems in a stormier world. Here we provide a systematic, standardized, and quantitative approach for identifying critical processes shaping lake ecosystem resistance following extreme storms. We identified 576 extreme wind storms for 8 lakes in Europe and North America. We calculated the resistance and resilience of each lake’s surface water temperature and oxygen saturation following each storm. Sharp decreases and increases in epilimnetic temperature and oxygen saturation caused by extreme storms resulted in unpredictable changes in lake resilience values across lakes, with a tendency not to return to pre-storm conditions. Resistance was primarily shaped by mean annual chlorophyll a concentration and its overall relationship with other physiochemical lake and storm characteristics. We modeled variation in resistance as a function of both lake and storm conditions, and the results suggested that eutrophic lakes were consistently less resistant to extreme storms compared to oligotrophic lakes. The lakes tended to be most resistant to extreme storms when antecedent surface waters were warm and oxygen saturated, but overall resistance was highest in lakes with low mean annual concentrations of chlorophyll a and total phosphorus. Our findings suggest physiochemical responses of lakes to meteorological forcing are shaped by ecological and/or physical feedback and processes that determine trophic state, such as the influence of differences in nutrient availability and algal growth.