A conceptual model for cool-temperate South African estuaries has been proposed to explain the interactions between zooplankton and larval fishes based on small-scale biological processes. Larval fishes and zooplankton data from nine south and west coast South African estuaries were analyzed in terms of the cumulative density of all species and the density dynamics of the dominant taxa in each group. Larval fish and zooplankton density were positively correlated and varied across seasons, peaking simultaneously in summer, although zooplankton also peaked during the stable conditions of the closed phase of some estuaries. Plankton density was positively correlated with salinity and water temperature and negatively correlated with turbidity. The mesohaline zones of estuaries are highlighted as supporting plankton productivity maxima. These results were attributed to the summer peak in plankton productivity coinciding with the lower rainfall, higher temperatures, and clearer waters that are often typical of the dry summers on the south and west coasts of South Africa. Correlation between selected predator, competitor, and prey species supported the hypothesis that estuaries exhibit extensive reciprocal trophic relationships permitting an ideal feeding environment, which maintains a positive relationship between overall larval fish and zooplankton abundance.