The flooding and pollution of water resources on the de-occupied territories require developing and improving the methods of filtration calculations for the polluted water that passes through damaged protective screens, as well as the analysis of pollutant migration through the aquifer. The article deals with the issue of theoretical substantiation of filtration losses due to damage to the protective screen at the stage of supported filtration. Using as an example the main channel of the Inhulets irrigation system, which has undergone significant pollution, it was established that in the calculations, the conditional filtration coefficient of the concrete cladding based on the long-term operation and the impact of active hostilities can be ignored, and the filtration losses of water can be calculated using the same methods as for the canal without cladding. Primary restoration of the system can be carried out with local building materials, which is more economically beneficial. The arrangement of the cladding requires a theoretical justification of its thickness and construction. This choice is to be made by determining the magnitude of the water pressure drop when filtering through the cladding, depending on its design. The article proposes arranging a channel drainage along the main channel to prevent flooding and salinization of the soil, as well as reuse the drainage water after appropriate water treatment. It is shown that when calculating the filtration losses of water from the main channel to the tubular drainage, it is advisable to take into account the filtration resistance of the channel cladding. The dependence of pressure loss on the cladding is presented, according to which such a calculation can be performed and the effectiveness of the antifiltration protection with various design features can be determined.