Rivers represent an essential pathway for waterborne transport, and therefore estuaries are critical coastal areas for a pollution hazard that might lead to eutrophication and general water quality deterioration. When addressing these problems, the decision makers and coastal managers often need additional skills and specialists, so they engage consultants in developing models and providing potential solutions. Different stakeholders’ interests present a challenge in the implementation process of proposed solutions. Nevertheless, if the relevant institutions were presented with a screening tool, enabling them with a certain level of solution ownership, potentially more involvement would occur. There are numerous intertwined physical processes present in the estuary ecosystem, including river discharge, tidal forces, wind-induced stress and water density variations. This research utilizes an analytical model based on ensemble averaging and near-field approximation of the advective-diffusion equation for the case of continuous, steady, conservative solute transport in a stratified, river-dominated estuary. Such an approach significantly reduces the costs and time needed to obtain enough measured data required for common statistical analysis or the need for a more complex numerical model. The developed methodology is implemented into a simple software named CPoRT (Coastal Pollution Risk Tool) within a recently conducted research project funded by European Social Fund.