Residual water level is an important factor affecting water depth; the water level depends primarily on river discharge, tidal conditions, and wind stress, and it can change significantly with time and space. Studying the temporal and spatial variations in residual water levels—and the respective influencing factors—is of great scientific significance and can be applied to estuarine water level prediction, water resources utilization, seawall design, flood protection, and navigation. In this paper, we used a validated three-dimensional numerical model of the estuary and coast to: simulate the temporal and spatial variations in the residual water levels of the Changjiang Estuary; analyze the impacts of river discharge, tidal conditions, and wind stress on residual water levels; and determine the dynamic mechanisms for its change. The spatial and temporal variations in residual water levels of the Changjiang Estuary is driven primarily by the fact that upstream residual water levels are higher than downstream levels because of runoff force. The highest residual water level appears in September, reaches 0.861, 0.754, 0.629, 0.554, and 0.298 m at Xuliujing, Chongxi, Nanmen, Baozhen, and the easternmost section of the northern dike of the Deepwater Navigation Channel, respectively. The lowest residual water level appears in: January for Xuliujing (0.420 m) and Chongxi (0.391 m), February for Nanmen (0.313 m) and Baozhen (0.291 m), and April for the easternmost section of the northern dike of the Deepwater Navigation Channel (0.111 m). The residual water level in the North Branch is lower than the level in the South Branch, because a small amount of river water flows into the North Branch. The residual water level is higher in the South Channel than the one in the North Channel. Within the South Channel itself, furthermore, the water level is higher on the south side than the north due to the Coriolis force, which makes the water turn to the right. By using numerical experiments to compare the impact of different factors, we found that runoff has the largest impact on residual water levels, tidal conditions have the second largest impact, and wind has minimal impact. The monthly mean river discharge is largest in July, which should lead to the highest residual water level, but southeasterly winds prevail in the same period leading to small residual water levels. The river discharge in September remains high and northerly winds prevail, driving the Ekman water transport landward and resulting in a residual water level rise in the estuary. The interaction between the river discharge and the northeasterly wind makes the residual water level highest in September rather than in July. In conclusion, this study revealed the dynamic mechanism explaining the highest residual water level observed in September.