Abstract: Change of channel storage is a direct quantitative indication of river bed evolution. Boundary conditions and sediment transport are the major factors to change the channel volume. Topographic data of the North Branch of Yangtze River Estuary from 1986 to 2013 is collected for digital underwater elevation model during different periods by GIS technology. With the models channel storage variation and river bed evolution are analyzed in the paper. The results show that the channel volume under elevation 0 meter decreases 711 million cubic meters in the North Branch of Yangtze River Estuary since 1986. Among those, 400 million cubic meters, accounted for 56.3 per cent is caused by enclosure of side foreland and the rest 311 million cubic meters, accounted for 43.7 per cent is the result of sediment deposition. Specifically, in the upper reach, sediment deposition is the main factors for channel storage reduction and comprehensive development and utilization of the waterway ought to be in accord with characteristics of sediment transport. In the middle of the branch, reclamation on marginal bank and growth of sandbar towards bank are the main causes of channel storage reduction. With the boundary condition adjustment, it is strengthened of constraint of river flow and erosion in riverbed, and the bathymetry is advantageous to develop and utilize of the waterway after river cross-section adjustment. In the lower reach, both sediment deposition and reclamation on marginal bank are the major reasons for river storage shrinks, while the effect of the former is slightly larger than that of the latter. Because the groove under elevation -5 meters stable exists, river regime has basic conditions for development and utilization of the waterway in the lower reach. And there is margin for reclamation in the future on the south bank.