The Ecological Restoration Project Area in Chongming Dongtan National Nature Reserve is located in the East Asian-Australasian Flyway. Different bird species have their own unique requirements for habitat water depth. Water depths for bird habitats can be managed via habitat blocks; the blocks are divided based on the feeding characteristics and spatial distributions of the respective target bird species. Accordingly, the key to effective water depth management is to maintain a suitable water depth in each block. For internal habitat blocks in the southern C zone of the Ecological Restoration Project Area, when a block’s water depth is greater than the maximum critical depth, water is drained to the Suitang River, which sits outside the blocks and inside the coastal levee. Conversely, when the water depth decreases below the minimum critical depth, water is drawn from the Suitang River into the habitat blocks through the sluice gate from the outer Chongming Dongtan. Water level variations in the habitat blocks and the Suitang River and changes in mean water depth of each block are calculated according to water balance principles. These principles take into consideration evaporation, precipitation, plant evapotranspiration, and soil infiltration; moreover, the time and amount of water drained from the habitat blocks or the water drawn from the outer Chongming eastern shoal were also calculated and analyzed. The research results enable a scientific water replenishment plan for ecological water regulation at Chongming Dongtan National Nature Reserve and guidance for building favorable habitats for migratory birds.