The focus of ecosystem restoration has recently shifted from pure rehabilitation objectives to both improving ecological functioning and the delivery of ecosystem services. However, these different targets need to be integrated to create a unified, synergistic and balanced restoration approach. This should be done by combining state-of-the-art knowledge from natural and social sciences to create manageable units of restoration that consider both the temporal and multiple spatial scales of ecosystems, legislative units and policy agendas. Only by considering these aspects combined can we accomplish more cost-efficient restoration resulting in resilient ecosystems that provide a wealth of ecosystem services and the possibility for sustainable economic development in the future. We propose a novel conceptual framework that will yield more effective ecosystem restoration: the Operational Restoration Unit (ORU). This is based on scale-dependent restoration actions that can adhere easily to the relevant environmental legislation, encompass the spatial and temporal resilience of aquatic ecosystems and consider the sum of human pressures acting on water bodies. This opens up possibilities for an effective integration of the restoration agenda into the delivery of major policy objectives of economic growth, regional development and human security.