Climate change increases the magnitude and frequency of extreme weather events. This includes severe summer storms altering lake physical structure, biodiversity and ecosystem processes. However, insights into lake responses to extreme storms and the underlying mechanisms primarily rest on unreplicated and observational case studies, without separating effects of physical forcing from secondary drivers such as external nutrient and dissolved organic matter inputs. In a large-scale replicated experiment conducted in a unique enclosure facility mimicking realistic environmental conditions, we tested how storm-induced mixing entails changes in lake ecosystems. Consequences include altered phytoplankton composition, nutrient, oxygen and carbon dynamics, with potential negative feedbacks on climate through organic matter sequestration. These experimental results are reflected in a minimal dynamical model and are also supported by observations made during a natural severe storm. An important practical implication is that efforts to abate lake eutrophication needs to accommodate the projected increases in extreme weather situations.