The need to mitigate the ecological effects of climate change is accelerating the development of renewable energy technologies. Floating photovoltaic systems (FPV) is an important advance of the energy industry and is spreading fast across the globe. A key challenge remains to ensure that climate mitigation strategies are not triggering novel, unexpected and counterproductive impacts on biodiversity and ecosystems that can counterbalance their ecological benefits. FPV can affect lakes’ ecosystem services through abrupt changes in biodiversity and ecosystem functioning through changes in abiotic conditions in lakes (e.g., light arrival, water mixing, oxygenation) that can ultimately alter the composition of plant and animal communities, with cascading effects on ecosystem functioning. To date, however, empirical assessments of these impacts are still lacking. ECLIPSE aims to provide an integrative assessment of the ecological impacts of FPV on lakes ecosystems by (1) measuring the in-situ impacts of FPV on biodiversity and ecosystem functioning; (2) experimentally quantifying the context-dependency of these effects; (3) predicting the impacts of FPV on lakes under climate change scenarios; and (4) providing evidence-based guidelines for FPV deployment. An innovative combination of methods will be used to quantify food web architecture (stable isotope analyses) and ecosystem functioning (lake metabolism and carbon balance) incorporating in situ lake monitoring, mesocosm experiments, and ecological modeling. ECLIPSE is highly innovative as it will answer an applied question with ecological and socio-economic implications providing fundamental knowledge on ecosystem responses to abrupt environmental changes.