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The three-dimensional (3-D) flow structures and suspended-load sediment transport processes in the dam area of the Three Gorges Project (TGP) with large water depth were simulated by a 3-D mathematical model. The characteristics of flow structures and suspended-load concentration distribution were analyzed based on the simulated results. Strong 3-D features of flow structures can be found in the dam area, the secondary currents are significant. The suspended-load sediment concentration reduced much faster in wider valley areas, where deposits accumulated. Due to impact of secondary currents, the maximum concentration of suspended-load occurs at the convex side while the minimum at the concave side. It demonstrates that the 3-D numerical modeling is a useful prediction technique and research tool to enhance our understanding of flow structures and mass transport processes in natural rivers with complex boundary.