The transport of health-related organic micropollutans has been a major water quality and environmental issue in the past few decades. Because of their high toxicity, long environmental half-life and high bioaccumulation factors, many of the hydrophobic organic pollutants (HOPs) are listed as priority pollutants in many countries. Although not all of the chemical and physical factors should be considered in the fate of transportation of all chemicals, a simple one-dimensional mathematical model used to simulate all of the factors was conceptually developed (Bobba et al., 1996). In that study, most important parameters needed in the model were empirically fitted. For numerical simulation of the behaviors of pollutants in the environment, it is important to provide a feasible chemical and physical transport mechanism to describe the geo-chemical and geophysical interactions involved in the system. In this study a general two-dimensional hydrodynamic numerical simulation model is developed .This model can readily extend to a three-dimensional one. The model includes all possible physical and chemical factors that might affect the transport of the pollutants. For validation and demonstration purpose, only sorption-desorption between specified dissolved organic material and phase are studied in the present study. The hydrodynamic model is verified by comparing with the reported numerical results. The numerical model then incorporates the sorption-desorption terms and the sediment effects. From the results of the simulation, the sorption-desorption mechanism and sediment scavenge effect are founded to significantly affects the pollutants fate and transport of an outfall discharge.