Due to large topography slopes in natural rivers, pollutant concentration embodies a property of three-dimensional distribution when wastewater is discharged from effluents along the bank. With the sigma coordinate along the vertical dimension fitted to both the moving free surface and the bed topography, a three-dimensional numerical model was developed in the present work to address pollutant transport processes in the above-mentioned cases. To avoid the reduction in accuracy caused by spurious diffusion in the case of steep bottom slopes, a formula for horizontal diffusion in the sigma coordinate system was derived. A case study for the side discharge into a straight open-channel flow shows that numerical results are verified well by experimental data. Furthermore, the present model is also verified by the simulation of discharging wastewater from Fuling Phosphorus Factory effluent into the Three Gorges Reservoir and the agreement between the numerical simulation results and field observation data is satisfactory. The change of the mixing zone scope in the water surface versus the layers along the vertical dimension was also discussed in detail. The study shows that a more realistic calculation for pollutant discharge has been provided by the present model than by the depth-average model which predicts an unrealistically smaller mixing zone.