Details are given herein of the development and application of a three-dimensional layer-integrated model to predict suspended sediment fluxes in estuarine and coastal waters. The model involves using the finite difference technique to solve the equations of mass and momentum conservation and the transport equation for suspended sediment. The operator splitting technique and a highly accurate finite difference scheme have been used to solve the suspended sediment transport equation. The model has been tested against analytical solutions and laboratory measurements for different flow types and boundary conditions, and has also been applied to predict suspended sediment fluxes in the Humber Estuary, UK.