My career so far has provided the opportunity to explore how global change affects the functioning of aquatic ecosystems from intermittent streams to deep lakes. Processes such as the transport and cycling of organic matter reflect the connectivity of inland waters to their watersheds and the activities of their biological communities. However, our knowledge of benchmark rates of ecosystem functioning and how they are expected to respond to environmental change or management is often limited. In my talk I will provide examples of how land-use and climate change have impacted organic matter dynamics in streams and lakes and describe a case study for restoring in-stream processes in agricultural landscapes. I will then consider some of the current challenges and opportunities for incorporating ecosystem functioning in environmental flow policy and management.