In the sediment transport processes, settling and resuspension, there are significant differences between cohesive and non cohesive sediments. In the sediment transport module of the existing model PCFLOW3D only equations for non cohesive sediments are included. Therefore, we assumed that the model does not perform correctly in areas with cohesive sediments. We identified the equations for the cohesive sediment settling, resuspending and transport, and compared them with the equations included in the PCFLOW3D model. Furthermore, the parameters needed for simulations of these transport processes were identified and the significant differences between cohesive and non cohesive sediment were emphasised. We performed simple calculations in order to show the results of both the equations of the PCFLOW3D model and the equations for cohesive sediments, as well as to compare the results to each other. We detected significant discrepancies and concluded that the PCFLOW3D model significantly underestimates the critical bed-shear stress in the areas with cohesive sediments. The thesis is a contribution to better understanding of different transport processes in cohesive and non cohesive sediments. We also proposed adequate equations for upgrading the PCFLOW3D model in order to be used in cohesive sediment areas.