This work presents the principles of two-dimensional modeling of pollutant transport in natural watercourses. The model incorporates water flow computation, both aspects of sediment transport (suspended and bed-load), as well as the processes of nonconservative pollutant transport including its interaction with sediment particles by adsorption/desorption. Deriving the governing equations for pollutant transport included the dissolved and adsorbed pollutant. The exchange between the dissolved and adsorbed pollutant was described using a first order kinetic process, while the modeling of the exchange coefficients remained closely related to the sediment surface available for adsorption.