Estuarine projects can change local topography and influence water transport and saltwater intrusion. The Changjiang (Yangtze) River estuary is a multichannel estuary, and four major reclamation projects have been implemented in the Changjiang River estuary in recent years: the Xincun Shoal reclamation project (RP-XCS), the Qingcao Shoal reclamation project (RP-QCS), the Eastern Hengsha Shoal reclamation project (RP-EHS), and the Nanhui Shoal reclamation project (RP-NHS). The effects of the four reclamation projects and each project on the saltwater intrusion and water resources in the Changjiang River estuary were simulated in a 3D numerical model. Results show that for a multichannel estuary, local reclamation projects change the local topography and water diversion ratio (WDR) between channels and influence water and salt transport and freshwater utilization in the estuary. During spring tide, under the cumulative effect of the four reclamation projects, the salinity decreases by approximately 0.5 in the upper reaches of the North Branch and increases by 0.5–1.0 in the middle and lower reaches of the North Branch. In the North Channel, the salinity decreases by approximately 0.5. In the North Passage, the salinity increases by 0.5–1.0. In the South Passage, the salinity increases by approximately 0.5 in the upper reaches and decreases by 0.2–0.5 on the north side of the middle and lower reaches. During neap tide, the cumulative effects of the four reclamation projects and the individual projects are similar to those during spring tide, but there are some differences. The effects of an individual reclamation project on WDR and saltwater intrusion during spring and neap tides are simulated and analyzed in detail. The cumulative effect of the four reclamation projects favors freshwater usage in the Changjiang River estuary.