Considering the dilution of sewage and the interaction between river water and bottom sediments, a mathematical model for the conversion of pollutants in water bodies has been developed. Taking the small rivers in northern Vietnam (Ban Thi River and Dai River in the Red River Basin) as an example, it shows that more than 60% of the chemical composition of the river waters studied is determined by the interaction of the following factors: Co-precipitation of sediments and trace elements on solid particles, and sediments at the bottom of the river. The impact of water runoff is first manifested in the change of solid runoff, and to a lesser extent in the process of regulating the water, which takes longer to establish equilibrium in the solution. On the basis of the proposed model, a simplified version of the model and a standardized pollutant discharge method have been developed for whether there is an option of river water chemical composition observation data. In this case, the influence of interaction with bottom sediments is indirectly considered through the structure of the model and its parameter values. The simplified model was tested with the Jinjiang River in the Poyang Lake Basin as an example.