Understanding how complex aquatic ecosystems function is vital for the conservation and management of species and natural resources. This project tackles the issue by developing mechanistic tools using which ecosystem functioning can be predicted under alternative scenarios regarding eg human use, climate change, fishing, and environmental alterations. The project objectives are two fold: the development of methodology and theory and their application to three aquatic study systems. Within the methodology development part, we developed a modelling tool that can be used to predict contemporary species evolution in an aquatic ecosystem context. This can develop understanding of evolutionary consequences of external drivers and species interactions. Namely, population collapses, lack of recovery from disturbances, and biodiversity loss are burning issues today. Their mitigation and appropriate management to restore natural populations will require understanding of the ecosystem functioning, as species exist within communities and ecosystems, not alone in isolation from other species. The objectives of the present project aimed to close this knowledge gap by improving understanding and predictive methodology of ecosystem structure and functioning in the context of aquatic ecosystems.