Coastal environments are faced with constant habitat modification and biodiversity loss due to human occupation. Estuaries are considered to be highly productive and shelter heterogeneous habitats such as mangrove forests, tidal creeks, tidal mud flats and sandy beaches, which are important for the maintenance of natural resources. The present study aims to evaluate how different shallow juvenile habitats (sandy beaches, mangrove shoreline habitats and dense macrophyte habitats) influence fish during their early life stages in a tropical estuary of Brazil. Monthly samples using a beach seine net from July 2012 to June 2013 were collected in eight shallow areas of the São Mateus River estuary. The fish assemblage comprised mainly juvenile and small-sized fish, which included ecologically and commercially important species. Small recruits of Atherinella brasiliensis and Ctenogobius boleosoma were most abundant in the autumn, while Rhinosardinia bahiensis and Centropomus undecimalis were highly abundant during the winter. The water salinity recorded in the mid and lower estuarine portions was the most important variable for the distribution of A. brasiliensis and Sphoeroides spengleri, whereas Anchovia clupeoides, C. undecimalis, C. parallelus and Gobionellus oceanicus were positively correlated with the water depth of the upper estuarine portion. The fish species T. paulistanus, Genidens genidens and Achirus lineatus were related to the water turbidity in the upper portion. Thus, the heterogeneous shallow water habitats (and their associated environmental parameters) of the São Mateus River estuary are potential nursery grounds for the early life stages of a variety of fish species, which highlights the importance of these areas for local biodiversity management.