Here we document the regional effects of Tropical Cyclone Irene on thermal structure and ecosystem metabolism in nine lakes and reservoirs in northeastern North America using a network of high-frequency, in situ, automated sensors. Thermal stability declined within hours in all systems following passage of Irene, and the magnitude of change was related to the volume of water falling on the lake and catchment relative to lake volume. Across systems, temperature change predicted the change in primary production, but changes in mixed-layer thickness did not affect metabolism. Instead, respiration became a driver of ecosystem metabolism that was decoupled from in-lake primary production, likely due to addition of terrestrially derived carbon. Regionally, energetic disturbance of thermal structure was shorter-lived than disturbance from inflows of terrestrial materials. Given predicted regional increases in intense rain events with climate change, the magnitude and longevity of ecological impacts of these storms will be greater in systems with large catchments relative to lake volume, particularly when significant material is available for transport from the catchment. This case illustrates the power of automated sensor networks and associated human networks in assessing both system response and the characteristics that mediate physical and ecological responses to extreme events.