Details are given herein of the development and application of a three-dimensional layer integrated numerical model to predict geo-morphological changes in estuarine waters. An Alternating Direction Implicit finite difference algorithm has been used for solving the governing differential equations, which include the conservation of mass and momentum for the hydrodynamics, the transport equation for suspended sediment fluxes and the sediment mass conservation equation for bed level changes. The model includes a modified term for the initiation of motion, which takes account of the unsteady nature of the flow. Model predictions have been compared with results of other model studies reported in the literature and also laboratory measurements, with the refined criteria for the initiation of motion for tidal currents giving improved results. Finally, the model has been applied to predict bed level changes due to suspended sediment fluxes in the Humber Estuary, UK. Details are given herein of development and application of a three-dimensional layer integrated numerical model to predict geo-morphological changes in estuarine waters. An Alternating Direction Implicit finite difference algorithm has been used for solving the governing differential equations, which include the conservation of mass and momentum for the hydrodynamics, the transport equation for suspended sediment fluxes and the sediment mass conservation equation for bed level changes. The model includes a modified term for the initiation of motion, which takes account of the unsteady nature of the flow. Model predictions have been compared with results of other model studies reported in the literature and also laboratory measurements, with the refined criteria for the initiation of motion for tidal currents giving improved results. Finally, the model has been applied to predict bed level changes due to suspended sediment fluxes in the Humber Estuary, UK.