Since the 1970s, at approximately 10-year intervals, 4 national-scale freshwater conservation plans have been developed for South Africa. These 4 plans reflect different but broadly advancing approaches to conservation planning. We provide an overview of 3 historical plans and a more detailed discussion of the most recent plan which is based on a systematic approach. The main principles of systematic conservation planning, namely, to achieve representation, persistence, and efficiency, are introduced. We then describe how these principles were used to develop National Freshwater Ecosystem Priority Areas (FEPAs) for the whole of South Africa. A strong implementation orientation influenced the development of FEPAs. End users were engaged throughout the planning process and map products were designed with user needs as well as relevant policy and legal contexts in mind. We believe that the process that was followed in developing FEPAs marks a new level of implementation-driven planning. The remaining constraints to effective implementation now lie mainly on the side of the receiving environment – i.e. the operating environments of those agencies with mandates to manage and conserve freshwater ecosystems. To this end, we highlight 4 potential catalysts for effective implementation in the receiving environment, namely, absorptive capacity, multi-party cooperation, science extension, and adaptive management. We conclude by calling for a new and broad research initiative linked to implementing FEPAs.