AbstractFloodplain lakes are significant lateral habitats that play an important role in structuring larval fish assemblages in large river–floodplain ecosystems. The abundance of floodplain lakes, including both naturally connected and main stem‐isolated lakes, declines in a downstream direction in the lower reach of the Yangtze River, forming a longitudinal reduction gradient. We investigated whether this longitudinal reduction gradient of floodplain lakes is an essential driver of the larval fish assemblage patterns in the river. Drifting larval fish were investigated weekly during the prevailing spawning season both in 2014 and 2015 among three locations at Wangjiang (WJ), Zhenjiang (ZJ) and Nantong (NT). Thirty‐four species belonging to 28 genera and eight families were identified. The number and abundances of collected species, the reproduction duration for dominant species and the niche breadth of dominant species all exhibit a longitudinal decrease (WJ > ZJ > NT) in the downstream direction. Additionally, the bloom of larval fish tended to occur earlier at WJ than at ZJ and NT. We suggest that these results reflect the crucial effect of floodplain lake distribution in shaping the longitudinal distribution pattern of larval assemblages. Both natural connected lakes and isolated lakes (with irregular connectivity patterns) play a crucial role in recruitment success of freshwater fish in the system. Hence, conservation and management approaches for fish resources should be concentrated on restoring and maintaining river–lake connectivity in the upstream sections of the lower reach of the Yangtze River.