A systematic analysis on the effects of the changed interactive relationships between rivers and lakes on fairway depth can help to support the sustainable development of the “Gold waterway” of the Yangtze River. In this study, we investigate the variation characteristics of water and sediment, and the relationships between the evolution of shoals and channels and the fairway depth, in the Lake Dongting-Jingjiang Reach confluence of the Yangtze River. The results indicate that since the operation of the Three Gorges Project, the split ratio of watersplit and the sediment distribution of the three outlets of Lake Dongting continued to decrease. Along with the decreasing flow of Lake Dongting, the relative increase in the runoff of the Jingjiang Reach increases the riverbed erosion scouring intensity, which keep the split ratio of water split and the sediment distribution of the three outlets at a lower value. The riverbed erosion scouring of the Jingjiang Reach has created a promising foundation for an increase in the waterway dimensions. However, the length of the reach fail to meet the requirement of 4.5 m× 200 m (water depth × width) is 12.6 km in the river-lake confluence, accounting for 68.35% of the total length of obstructed navigation. The mechanisms of the obstructed navigation are as follow: at the reach affected by the first outlet (Songzikou), a 4.5 m flume has been formed, but its width is less than 200 m. The instability of water split and the shrinkage of bottomland restrict the stability of channel conditions. Moreover, the reductions of low-flow water level and the phenomenon of “steep slope and rapid current” affect the ships' safety. At the reach (Taipingkou) affected by the second outlet, the shrinkage of the bottomland, and the intersecting braided river channels make the low-flow routes unstable, the water depth being less than 4.5 m. At the reach (Ouchikou) affected by the third outlet, the shoreline of the reach has collapsed and retreated significantly. Additionally, point bar beach erosion scouring has led to the downstream movement of sediment, which have caused the downstream waterway width at the reach to be reduced to less than 200 m or formed shoals with a water depth of less than 4.5 m. Owing to the characteristics of scouring and deposition in the bends reaches and the jacking effect of the lake's outflow backwater, the water depth of some shoals are less than 4.5 m in the navigation waterway. However, the jacking effect of the lake's outflow backwater is weakening, which benefits the improvement of channel conditions.