The composition, abundance, distribution and seasonality of larval fishes was investigated in the permanently open Kowie Estuary on the temperate southeast coast of South Africa. Larval fishes were sampled within the estuary and marina for a period of two years. Samples were collected seasonally at 14 different sampling stations along the main channel and within the artificially-channelled marina by means of boat-based plankton tows. A total of 11 128 larval fishes were collected, representing 23 families and 38 taxa. Clupeidae and Gobiidae were the dominant fish families, contributing 47.0% and 24.7%, respectively, to the total catch. Common species included Gilchristella aestuaria (Clupeidae), Omobranchus woodii (Blennidae), an unidentified blenniid, Caffrogobius gilchristi, Caffrogobius nudiceps, Glossogobius callidus, Psammogobius knysnaensis (Gobiidae) and Solea turbynei (Soleidae) with the other species contributing <1% to the total catch. Catches varied significantly with season and were highest in summer. Estuary-resident species dominated the overall catch (91%). A notable absence of postflexion larvae and early juveniles characterized the artificial channels. This was attributed to the absence of shallow, marginal water habitat, typical of a good estuarine nursery area. The steep walls of the artificial channels reduce refuge areas, increasing predation by larger piscivores.