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Deposits in dam areas of large reservoirs, which are commonly composed of fine-grained sediment, are important for reservoir operation. Since the impoundment of the Three Gorges Reservoir (TGR), the sedimentation pattern in the dam area has been unexpected. An integrated dynamic model for fine-grained sediment, which consists of both sediment transport with water flow and gravity-driven fluid mud at the bottom, was proposed. The incipient motion driven by gravity in the form of fluid mud was determined by the critical slope. Shallow flow equations were simplified to simulate the gravity-driven mass transport. The gravity-driven flow model was combined with a 3D Reynolds-averaged water flow and sediment transport model. Solution routines were developed for both models, which were then used to simulate the integral movement of the fine-grained sediment. The simulated sedimentation pattern agreed well with observations in the dam area of the TGR. Most of the deposits were found at the bottom of the main channel, whereas only a few deposits remained on the bank slopes. Due to the gravity-driven flow of fluid mud, the deposits that gathered in the deep channel formed a nearly horizontal surface. By considering the gravity-driven flow, the averaged error of deposition thickness along the thalweg decreased from −13.9 to 2.2 m. This study improved our understanding of the mechanisms of fine-grained sediment transport in large reservoirs and can be used to optimize dam operations.