This study uses estuarine waterbirds to examine alternative methods for prioritizing sites for conservation. South African estuaries are evaluated using single-criterion and multiple-criteria scoring indices and an iterative technique. The viability of alternative scoring indices for more qualitative data is examined. Species richness, conservation status, total numbers, and percentage of the regional population were considered to be the most important criteria for ranking wetlands in terms of their value to waterbirds. Indices of abundance and site endemism provide an adequate substitute for the last two criteria when biota are difficult to quantify. Sites should be evaluated separately according to single-criterion indices, thereby making the decision process explicit. Biogeographical zones should be considered separately when scoring techniques alone are used to select priority sites for conservation. It is imperative that iterative ('complementarity') analyses, which select the minimum set of sites in which all species can be conserved, take abundance into account, so that viable populations are conserved as far as possible. This selection procedure is flexible, and should be used in conjunction with a scoring-and-ranking procedure. Seven of the 10 estuaries selected by complementarity analysis to conserve waterbirds in South Africa were top ranking sites. Two sites (one high ranking) were selected a posteriori to replace three low ranking sites selected by the program. Keywords: complementarity, estuary, prioritization, South Africa, waterbirds.