The effects of timing, frequency and duration of mouth opening and marine overwash events on fish assemblages in two, adjacent temporarily open/closed estuaries were investigated. Sampling was conducted biannually over two years during summer and winter, using selective sampling gear to target estuarine-associated marine species. During this period the East Kleinemonde Estuary opened more frequently than the West Kleinemonde Estuary and it also experienced a greater number of bar overwash events when larval recruitment can occur. The timing of mouth opening and the frequency of marine overwash events did not influence species richness of marine-spawning species but had a pronounced effect on abundances (catch-per-unit-effort) of species. The species composition of both estuaries was similar, but the catch-per-unit-effort in the East Kleinemonde Estuary was more than three times greater than that of the West Kleinemonde Estuary. The East Kleinemonde also supported a greater proportion of immature individuals of Rhabdosargus holubi and Monodactylus falciformis, and the length frequency distributions of both these species differed significantly between the two estuaries. The larger fish sizes in the West Kleinemonde Estuary were attributed to the prolonged mouth closure that resulted in the trapping of larger juveniles and mature fish within the estuary.