Multiple habitats were investigated in a known fish nursery area to further understand habitat partitioning among juveniles in the lower reaches of the warm temperate, permanently open Swartkops Estuary, South Africa. Fishes were collected using a 30-m seine net with a mesh size of 10 mm in sand, mud, creek and vegetated habitat types. Each habitat type was sampled in two locations twice per season from February 2013 to January 2014. Shallow-water creeks and vegetated habitats with coverage of Zostera capensis and Spartina maritima were found to be important use areas for numerous solely estuarine and marine estuarine-dependent species. This was evidenced by the high species diversity, abundance and size range per species occurring in these habitats. Seasonal trends were similar to those in previous studies worldwide, where higher abundances of juveniles of marine estuarine-dependent species coincided with summer recruitment into estuarine nurseries. However, recruitment appears to begin as early as late winter in some species, a phenomenon probably linked to a warming climate. Both resident species and those utilizing the area as a nursery area show a large degree of plasticity in habitat use in the lower reaches of the estuary, which became apparent when multiple habitats were compared. The drivers of these patterns involve a complex interaction of species, habitat type, behaviour, feeding, predator avoidance and physico-chemical factors occurring in the estuary.