Estuaries are crucial fish nursery habitats owing to their high productivity and the presence of various microhabitats for the early development of aquatic organisms. This study investigated the temporal and spatial patterns of the species composition and abundance of larval fish assemblages in the Nakdong River estuary, South Korea, through bi-monthly sampling in the inner and outer estuaries. Fifty-five larval taxa were collected, and the larval fish assemblages were dominated by a few species. Engraulis japonicus (28.8%) was the most abundant, followed by Gobiidae sp.1 (22.6%), Clupea pallasii (13.9%), and Omobranchus sp. (6.1%). The species richness, abundance, and diversity tended to be higher during the warm season in the inner estuary. Multivariate analyses revealed that the structures of larval fish assemblages were significantly influenced by the season and site. Spatial and seasonal changes in larval fish assemblages resulted from the different occurrence patterns of common fish larvae in relation to water temperature and salinity. Among the predominant fish larvae, E. japonicus was captured more frequently in more saline outer estuaries during the warm season, whereas Gobiidae sp.1 and C. pallasii were more abundant in less saline inner estuaries during the warm and cold seasons, respectively. The results of this study improve our understanding of larval biodiversity in estuarine habitats in relation to environmental modification and contribute to the evaluation of nursery functions in the Nakdong River estuary.