This study devises a method for prioritising South African estuaries on the basis of conservation importance, and presents the results of a ranking based on the collation of existing data for all South African estuaries. Estuaries are scored in terms of their size, type and biogeographical zone, habitats and biota (plants, invertebrates, fish and birds). Thirty-three estuaries are currently under formal protection, but they are not representative of all estuarine biodiversity. We performed a complementarity analysis, incorporating data on abundance where available, to determine the minimum set of estuaries that includes all known species of plants, invertebrates, fishes and birds. Keywords: Water-management allocations, South African estuaries, Conservation priority assessments.