Estuaries are complex, dynamic and productive ecosystems as they form the interface between marine and freshwater environments. The health of estuaries and delivery of ecosystem services is dependent on adequate freshwater inflow that is threatened by a growing population, land use and climate changes. Challenges in setting and implementing environmental flow requirements are discussed and compared globally. In South Africa the National Water Act calls for an ecological reserve to be set before water can be allocated to different users. Ecological water requirements have been determined for 40% of South Africa’s estuaries and some of the lessons learnt are that environmental flow requirements are unique for individual estuaries and cannot be extrapolated from one estuary to another. Although water can be released from dams to supply the environmental flow this does not mimic the entire natural flow regime and floods are still needed to flush the estuary. Implementation of environmental flows requires a holistic catchment-to-coast management approach involving collaboration between government departments. Completed studies have improved our understanding of the functioning of different types of estuaries and shown that size and scale largely determine environmental flow requirements but that each estuary also has unique features that determine sensitivity to inflow alteration.