Drifting larval fish assemblages were investigated at three sections in the middle reach of the Yangtze River downstream of the Three Gorges Dam to reveal recovery gradients and to identify the major environmental factors influencing their temporal and spatial patterns. Larval fish in the river section closest to the dam showed lower abundance, later occurrence, narrower temporal niche breadth, and more pairs of dominant species with high niche overlap than those further from the dam. Water temperature, transparency, and discharge significantly influenced the larval fish assemblages. They showed longitudinal gradients of increased water temperature, decreased transparency, and increased discharge in a downstream direction. Our results suggested that hypolimnetic and clean water discharge from the dam heavily impacted larval fish assemblage in the river section near the dam. With an increased distance to the dam and the input of some major tributaries, this impact was gradually buffered, thus forming the longitudinal recovery gradients. We suggest that priority for conservation should shift from river sections closer to the dam to those further from the dam.