The study of sedimentation in ports and harbors is a serious topic in coastal engineering and oceanography studies which is annually accompanied by high dredging costs. Study of sediment transport and determination of deposition and erosion rates are fundamental studies in construction and development of ports. Numerical modeling of fine-grained and cohesive sediments transport and morphodynamics provides an effective tool for understanding sediment problems in coastal areas with fine-grained material. Study of sedimentary processes depends on the type of sediment. Due to this fact that many coastal zones have fine-grained or cohesive sediment, studying of this kind of sediment is important. Fine-grained marine sediments, due to their behavior, have certain complex characteristics compared to other marine sediments. This type of marine sediment can be transported in two phases: suspended load and bed load, each of which has different consequences and characteristics. In this study, a two-dimensional numerical model was used, which includes all processes related to the transport of marine cohesive sediments such as flocculation and its effect on the settling velocity of marine cohesive sediment particles, consolidation of bed layers and transport of marine sediments between layers, changes in bed shear stress under the influence of the simultaneous presence of waves and currents, bed morphology, deposition and erosion. To evaluate the transport of marine sediments, all processes were considered. To simulate fine-grained sediment transport, the main parts of the computational engine are an advection-dispersion engine and some experimental formulas related to cohesive sediment processes. This model determines the rate of erosion and deposition of cohesive sediment under different wave and current conditions. To verify the model performance, the model results were compared with the Finite Volume Coastal Ocean Model (FVCOM) results and field data reported in the Bushehr Bay simulation phase, a case study. In the performance section of the cohesive sediment module, the model results with and without applying morphological changes were compared with the FVCOM model results. The comparisons show that the model successfully simulated the hydrodynamics and cohesive sediment in the Bushehr Bay area in July 2010. The location chosen for comparing sedimentation between the two models is located exactly at the beginning of the outer channel. This location has high dynamics in terms of sedimentation and erosion. This is because the natural outlet path of Bushehr Bay intersects with the outer channel at this location, which results in more complex sedimentation patterns, including deposition and erosion.