This study compares the fish assemblages in a range of intertidal salt marsh creeks in the Kariega Estuary, South Africa, as well as highlighting any differences between the ichthyofaunal structure of the creeks and adjacent Zostera bed habitats. The superimposition of environmental variables on the creek biotic groupings (60% similarity level) indicated consistent relationships between both the creek water depth and mouth area with the major creek fish clusters. Water temperature, salinity and turbidity did not display any pattern which could explain the disparity between the ichthyofaunal groupings. The results also indicated that intertidal creeks form a unique littoral habitat within the Kariega Estuary, with ichthyofaunal compositions very different to those found in nearby eelgrass beds. Furthermore, intertidal creeks in the Kariega system appear to be similar to creeks found elsewhere in the world in that their fish assemblages are dominated by 0+ juveniles, have a conspicuous marine transient and estuarine resident component, and very few piscivorous representatives. These results also give weight to the hypothesis that southern African salt marsh creek habitats serve as temporary refuges to juvenile fishes, a role that has also been proposed in other parts of the world.