This paper aims to investigate appropriate mathematical models devoted to the optimization of some cleaning processes related to pharmaceutical contaminant removal. In our recent works, we found the rehabilitation of the existing cleaning plants as a viable solution for the removal of this type of micropollutants from waters by introducing efficient techniques such as adsorption on granulated active carbon filters and micro-, nano-, or ultrafiltration. To have these processes under better control and to assure the transfer from small- to large-scale treatment stations, specific mathematical models are necessary. Starting from Navier–Stokes equations and imposing proper boundary conditions, some mathematical physics problems are obtained for which adequate solving methods via variational methods and surjectivity results are proposed. The importance of these solution characterizations consists in their continuation in adequate numerical methods and the possibility to visualize the result by using a CFD program.