Climate change interacts with local processes to threaten biodiversity by disrupting the complex network of ecological interactions. While changes in network interactions drastically affect ecosystems, how ecological networks respond to climate change, in particular warming and nutrient supply fluctuation, is largely unknown. Here, using an equation-free modeling approach on monthly plankton community data in ten Swiss lakes, we show that the number and strength of plankton community interactions fluctuate and respond nonlinearly to water temperature and phosphorus. While lakes show system-specific responses, warming generally reduces network interactions, particularly under high phosphate levels. This network reorganization shifts trophic control of food webs, leading to consumers being controlled by resources. Small grazers and cyanobacteria emerge as sensitive indicators of changes in plankton networks. By exposing the outcomes of a complex interplay between environmental drivers, our results provide tools for studying and advancing our understanding of how climate change impacts entire ecological communities.