In this study, we analyzed the spatial and temporal variations in the residual water level of the Changjiang Estuary and evaluated the respective causes. To achieve this objective, we used data from the hourly water level at the Chongxi, Nanmen, and Baozhen hydrological stations in the Changjiang Estuary; daily river discharge levels at the Datong hydrological station; and wind speed and direction at the Chongming eastern shoal weather station in 2016 and 2017. The results showed that the residual water level was the highest at Chongxi station and the lowest at Baozhen station among the three hydrological stations in each month. The drops in residual water level among the hydrological stations became smaller during low river discharge and tended to become larger during high river discharge. Higher levels of river discharge were associated with a larger drop in the residual water level. In 2016, the residual water levels at the Chongxi, Nanmen, and Baozhen hydrological stations were lowest in February with values of 2.09, 1.96, and 1.93 m, respectively; similarly, the residual water levels were the highest in July with values of 2.91, 2.62, and 2.50 m, respectively. The residual water level was mainly affected by river discharge, while the wind was also an important influencing factor in the variations observed. Southerly wind made the residual water level decrease, and northerly wind made it increase. In 2017, the minimum monthly mean residual water level occurred in December with values of 2.04, 1.91, and 1.87 m at the Chongxi, Nanmen, and Baozhen hydrological stations, respectively; this coincided with the lowest annual river discharge observed during the same period. The maximum monthly mean residual water level occurred in October with values of 2.79, 2.58, and 2.49 m at the Chongxi, Nanmen, and Baozhen hydrological stations, respectively. Although the river discharge was lower in October than the one in July by 24214 m3/s, the residual water level was higher in October than that in July. The explanation for this phenomenon is the persistent strong northerly wind observed in middle to late October, which produced strong landward Ekman water transport, and resulted in the water level rise. The spatial and temporal variation in the residual water level of the Changjiang Estuary is remarkable, and should be considered in engineering design and theoretical research.