The waters of rivers are not only used for consumption, industry and agriculture but have also found their way into the transport and energy generation sectors. Many disturbances introduced into the aquatic environment are of the natural variety, which are the result of “admixtures” contained in water, e.g., through contact with soil, and of man-made types, which are directly related to humanities destructive influences. In the presented examinations, the most important processes affecting the spread and transport of these pollutants are taken into account, i.e., advection and diffusion. The authors present observations on the influence of the diffusion phenomenon on river flow modelling processes. Such an approach allows for the separation of the dynamics of water flow and the dynamics of transport of the dissolved substance mass. Specifically, phenomena occurring in relation to spatial coordinates, time and variable parameter values in the proposed mathematical model were analysed. Ultimately, this research will contribute to the correct design and implementation of a complementary diffusion module as an extension to an intelligent water quality control and monitoring system. The Intelligent Analytical Computing Control System architecture under development already includes other modules such as the Intelligent Filtration and Prediction Module and, complemented by the Intelligent Diffusion Module, provides a complementary tool for monitoring river hydromorphology. Implementation of the above solution will help to improve water quality, thus preventing and eliminating the appearance of undesirable pollutants in rivers, and increase the standard of living in the current threatened environmental world.