Abstract
Climate change has significantly altered the energy dynamics of lakes; however, little is known of how the temporal and spatial variation in energy fluxes impacts the structure and function of lake ecosystems. This study combined long‐term (2011–2018) measurements of lake energy fluxes with environmental, nutrient, and phytoplankton data at five stations to investigate the effects of variably energy fluxes on phytoplankton production and composition in a large, shallow, eutrophic lake (Lake Taihu, China). Overall, atmospheric warming increased heat storage and water temperatures, with energy fluxes exhibiting significant spatial heterogeneity. Specifically, faster rates of energy input and higher energy budgets increases were observed in the clear macrophyte‐rich regions of the lake compared to turbid hypereutrophic habitats. Temporal variation in energy fluxes was a strong predictor of primary production (as chlorophyll a ), the spatial extent of cyanobacterial blooms, and phytoplankton biodiversity at the whole‐lake level, whereas 42.4% of the variation in phytoplankton community composition was explained by a combination of energy fluxes, nutrients, and other environmental factors. Cyanobacterial taxa were significantly correlated with nutrients (total nitrogen and phosphorus), while green algal abundance was associated mainly with variations in the energy budget. These findings highlight the spatial variability of energy fluxes driven by local environmental conditions, underscoring the need for climate adaptation and mitigation strategies to account for heterogeneous energy effects on lake production and structure.