This study aims to describe the spatial and temporal distribution patterns of Gobiidae larvae at a tropical estuarine system in south-east Brazil (Macaé). The samples were collected in six stations, through oblique hauls using a bongo net (330 µm mesh size), coupled to a flowmeter, during the night in the ebb and flood tides in March, July and October 2006 and in February 2007. In the Macaé River estuary was collected a total of 1,234 Gobiidae larvae, representing nine taxa. The highest densities occurred in the river mouth during the flood tide in the rainy season. The most abundant groups were: Gobiosoma parri, Gobionellus oceanicus and Ctenogobius boleosoma. Gobiosoma parri was also dominant at the Macaé estuary, which also presented higher densities in the coastal stations during the rainy season (March), both the flood as the ebb tide. Gobionellus oceanicus and Ctenogobius boleosoma were characteristic of the dry season in the mouth and river stations during the flood tide. The abiotic factors chlorophyll-a and temperature were considered biologically significant for Gobiidae larvae distribution. The spatial and seasonal variations together with the tide influence the distribution of the fish larvae Gobiidae family in the Macaé River estuary and its coastal zone.