As a bending and branching river, Fujiangsha waterway is the only watercourse where three channels can navigate in Nanjing-Taicang reach of the Yangtze River. Due to the special river configuration and complex water-sediment movement, it is quite difficult to select a primary navigable branch in building the 12.5 m deep-water channel. The waterway has a broad riverbed on which sediment from the upper reach is mostly deposited. In addition, affected by the tide, erosion and sedimentation of the riverbed tend to change periodically. Based on a long-term understanding of regular patterns for water-sediment movement in this waterway, it is concluded from an analysis on integrated river regime conditions of the southern, northern and middle channels that: 1) since the southern channel is too bend and narrow, sedimentation at the convex bank makes it difficult to be controlled and maintained, especially a “S”-shaped reverse sharp bend is adverse to the safe passage of large ships; 2) both northern and middle channels have foundation conditions of building a one-lane navigation channel. A branch selection proposal is presented, namely “the two channels in north branch is constructed into a 12.5 m deep-water channel where a ship can sail in a traffic lane manner, and the southern branch keeps its existing condition as a good deep-water channel”.