The larval fish assemblage was studied in the permanently open Sundays Estuary on the southeast coast of South Africa. Seasonal samples were collected between winter 2007 and autumn 2009 at eight sites along the estuary by means of boat-based plankton tows using two modified Working Party 2 (WP2) nets. Salinity ranged from 1.5–36.5 and temperature from 11.6–26.8°C during the study period. A total of 8174 larval and early juvenile fishes were caught, representing 12 families and 23 taxa. The Clupeidae, Gobiidae and Blenniidae were the numerically dominant fish families. Common species included Gilchristella aestuarias (Clupeidae), Omobranchus woodi (Blenniidae), Caffrogobius gilchristi, Glossogobius callidus (Gobiidae), Liza dumerilii and Myxus capensis (Mugilidae), largely reflecting the adult assemblage of the estuary. Catches varied significantly between seasons, but not between sites and salinity zones within the estuary. Highest catches were recorded in summer (mean of 464 and 928 larvae per 100 m3 in 2008 and 2009, respectively). Species diversity also varied seasonally, with highest diversity occurring during summer. Highest larval fish density occurred in the euhaline zone while the oligohaline zone supported the highest diversity. Estuarine-resident species (category I) dominated the system (91%). The preflexion stage of development dominated the catches suggesting a high degree of local production in the Sundays Estuary. Larval sizes of the estuarine-resident G. aestuarias and catadromous species M. capensis tended to increase towards the middle and upper reaches of the estuary. Important variables regulating larval fish dynamics in the Sundays Estuary included salinity, temperature and turbidity.