Important fish life history and ecological information may be obtained from fish eggs, larvae, and juveniles; therefore, these developmental stages play an important role in environment impact assessments, fishery stock analyses, fish propagation, seeding release, and fish farming. Fish eggs, larvae, and juveniles are mainly found in near-surface waters. Growth and survival during the earliest life stages of fishes are important, because variability in survival during these early developmental stages may lead to great differences in the number of recruits that survive to catchable size. Physical factors, such as ocean circulation, frontal systems, and turbulence, represent major parameters that control the survival and growth of fish eggs, larvae and juveniles. The Yangtze River Estuary is an important spawning ground for many commercially important fishes. Furthermore, salinity and temperature have also been shown to be the most important parameters affecting the distribution and abundance of fish eggs, larvae, and juveniles. In recent decades, the Yangtze River Estuary has been subject to major human-induced environmental changes, particularly following the construction of the Three Gorges Dam in the upper reaches of the river. Negative impacts on fish egg, larval, and juvenile assemblages have been observed in other estuaries after dam construction. However, the potential impact of environmental changes on the fish egg, larval, and juvenile assemblages in the Yangtze River Estuary remain unclear. We investigated the fish egg, larval, and juvenile assemblages in the Yangtze River Estuary (30°30'-31°45' N, 121°15'-123°10' E) in the summers of 2005, 2008, 2009, and 2011. Species composition, distribution pattern, and annual variation in fish eggs, larvae, and juveniles were studied. The results showed that a total of 17 fish species were present in the river. These species belonged to 8 orders and 13 families. Perciformes was the most diverse order, with 11 species; the second group was Cluperformes with 5 species, while all other groups had less than 5 species. The highest number of species was recorded in the summer of 2005 (3 fish eggs, 8 fish larvae), while the lowest number of species was recorded in the summer of 2008 (1 fish egg, 5 fish larvae). Yearly succession of dominant species was observed. For example, sedentary estuarine or coastal species, including Saurida elongate, Gobiidae spp., and Stolephorus chinensis, were the numerically dominant species in 2005. In comparison, the marine migratory species Engraulis japonicus was the dominant species in both 2008 and 2009. Yet, Stolephorus spp. regained dominance in 2011. Fish eggs, larvae, and juveniles were mainly distributed in the waters adjacent to Shengsi Archipelago in 2005. The abundance of fish eggs, larvae, and juveniles was low in 2008, with no noticeable peak being documented in the study area. In 2009, although the abundance of fish eggs was low, the abundance of fish larvae and juveniles increased compared to 2008. Fish larvae and juveniles were mainly distributed in the region near 123°E, off the Yangtze River Estuary. The peak abundance of fish eggs in 2011 was near the mouth of the North branch of the river. In general, salinity may be the most important factor influencing the spatial distribution of fish eggs, larvae, and juveniles in the Yangtze River Estuary.