In order to contribute to the understanding of estuarine zooplankton dynamics in cool-temperate systems, zooplankton samples were collected by plankton tows, using two modified WP2 nets, in nine estuaries on the south and west coasts of South Africa, seasonally between June 2003 and March 2004. A total of 44 taxa were recorded, comprising 7 phyla, more than 20 orders and 35 families. The copepod Pseudodiaptomus hessei dominated the zooplankton (59% of the total catch by number) and occurred in similar densities to those observed in other South African estuaries. The copepod Acartia africana was the second most abundant species and, together with the amphipod Grandidierella lignorum, was restricted to the south coast estuaries. Zooplankters were more abundant in summer, although high numbers of P. hessei (>66 000 ind m–3) were recorded in the Klein Estuary in winter when the estuary was closed. Pseudodiaptomus hessei, with a maximum density of 97 962 ind m–3, dominated in the mesohaline zone, and A. africana, with a maximum density of 49 994 ind m–3, dominated in the polyhaline zone. These patterns were the result of the combined influence of freshwater inflow, mouth condition and the biogeography of the region on zooplankton density and diversity.