This study aimed to identify the spatial and temporal patterns of composition and distribution of early life‐history stages of fish along an estuarine gradient. Samples were collected quarterly between April 2010 and January 2011 using conical‐cylindrical plankton nets in the Vaza Barris estuarine river system (NE Brazil). A total of 38,781 fish eggs and 3,526 larvae, representing 20 families and 42 taxa, were caught. The most abundant larval taxa were Microgobius meeki, Ctenogobius gr. smaragdus/boleosoma, Gobionellus oceanicus, Ctenogobius gr. stigmaticus/saepepallens/shufeldti, Bairdiella ronchus, Achirus sp., Trinectes sp., Stellifer rastrifer and S. stellifer, accounting together for 34.5% of the total catch. Ichthyoplankton distributions were characterized by high seasonal and spatial variability mainly attributed to the environmental characteristics of the estuary. Overall, lower estuarine region served as important accumulation areas for ichthyoplankton, concentrating the greatest diversity and abundance. Salinity gradient, water temperature, and inorganic nutrients were the main variables that affected the larval fish assemblages, presumably influencing spawning, development and survival of individuals or through their effect on food supply. Moreover, this study reinforced the concept that hydrological variations may have a strong influence on estuarine species retention and marine species immigration. Finally, this study highlights the importance of estuaries for the growth and maintenance of stocks of fish species, and the development of strategies to protect these habitats is of utmost relevance.