This paper presents a depth-averaged sediment transport model with emphasis on morphodynamic processes near coastal inlets and navigation channels. The model solves the depth-averaged two-dimensional non-equilibrium transport equation of total-load sediment, considering bed-material hiding and exposure, avalanching and sediment transport over hard bottoms. The model is coupled with a depth-averaged circulation model and a spectral wave transformation model. Predicted bed changes are compared with measurements for two laboratory experiments of channel infilling and in a field study at Shinnecock Inlet, Long Island, NY. The results indicate that the model is capable of predicting the general trends of morphology change and provides a useful tool for engineering applications such as coastal sediment management, navigation channel maintenance, and beach erosion protection.