The fish community structure of two contrasting estuaries, one with a well developed mangrove forest (Mngazana) and the other without mangroves (Mngazi) was compared. Both the Mngazi and Mngazana estuary fish communities were dominated by marine species, reflecting the importance of these systems as nursery areas for marine fishes. The Mngazi Estuary contained 18% more estuarine fishes in terms of catch per unit effort (CPUE) than the Mngazana Estuary. The reduced tidal influence due to the narrow mouth opening is a possible reason for the heightened CPUE of estuarine species in the Mngazi estuary. The recorded higher diversity of fish species in the Mngazana Estuary when compared with the Mngazi Estuary was attributed to the greater influence of the marine environment due to the wide permanently open mouth, as well as the presence of a variety of habitats in this system. In both estuaries tropical and temperate species were captured, confirming the transitional nature of their biogeographic location which is situated close to the boundary between the subtropical and warm temperate regions of the Southern African coastline. Contrary to previous studies, which recorded seasonal changes in the proportions of tropical and temperate species, the proportions of tropical species remained unchanged at approximately 70% during the January and June sampling occasions. Global warming as a possible reason for the increased dominance of tropical species is discussed. Although several studies in southern Africa have investigated estuarine food web structure, none have compared mangrove and non-mangrove estuaries. In this study, the primary sources of carbon utilised by the fish fauna in the Mngazi and Mngazana estuaries was investigated. The carbon isotopic values of fishes in both estuaries displayed a continuum rather than a tight clustering around particular energy sources. Most detritus feeders of the family Mugilidae (mullets) from both estuaries were relatively more enriched than other fish taxa. The isotopic values of the mullet species suggest a diet derived from relatively enriched carbon sources such as benthic microalgae, the eelgrass Zostera capensis and associated epiphytes. Based on the isotopic values, piscivorous fishes from both estuaries could not be linked to specific prey fish taxa, but clearly the mullet species were not their main food source. The invertebrate feeders that were found in both estuaries showed greater isotopic variations in the Mngazana Estuary than in the Mngazi Estuary, probably reflecting the higher diversity of habitats (carbon sources) and invertebrate prey species in the Mngazana system. Generally the isotopic signatures of fishes from the Mngazi Estuary were more enriched than those from the Mngazana Estuary, thus indicating the possible effect of δ¹³C depleted mangrove derived carbon in the latter system.