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The future health and productivity of South Africa's approximately 250 estuaries is dependent on two main factors: management and freshwater inputs. Both management and water allocation decisions involve trade-offs between conservation and various types of utilisation. In order to facilitate decision-making in both of these spheres, it is necessary to understand the relative conservation importance of different estuaries. 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). Thirtythree 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. In total, 32 estuaries were identified as 'required protected areas', including 10 which are already protected. An estuary's importance status (including 'required protected area' status) will influence the choice of management class and hence freshwater allocation under the country's new Water Act, and can be used to assist the development of a new management strategy for estuaries, which is currently underway.

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Journal of Aquatic Science is co-published by NISC (Pty) Ltd and Informa UK Limited (trading as Taylor & Francis Group) water and to the quality of the water concerned' (OSPAR 2003). Eutrophication is characterised by a surge in primary production in response to nutrient loading that results in a loss of submerged aquatic vegetation, oxygen depletion, harmful algal blooms, imbalanced food webs, lower biodiversity, altered biogeochemical cycling and fish-kills (Conley et al. 2009; Ferreira et al. 2011; Lemley and Adams 2019a; Van Niekerk et al. 2019a). Depending on the scale of nutrient enrichment and the type of estuary, these impacts can cause the state of an estuary to change from one dominated by macrophytes to another dominated by phytoplankton and/or macroalgae (Dahlgren and Kautsky 2004; Smith and Schindler 2009; Nunes and Adams 2014; Lemley et al. 2018c). South Africa has a range of estuary types that occur across four biogeographic regions; cool temperate, warm temperate, subtropical and tropical (Whitfield 1992; Van Niekerk et al. 2020). Nutrient enrichment is a serious concern not only in temporarily closed estuaries (e.g. Groot Brak), but also in large permanently open systems