The paper describes the establishment and testing of an algorithm for developing sustainable management plans associated with groundwater source protection against potential pollutants and discusses the effectiveness of individual systems. The applied methodology pertains to groundwater resource management, particularly those cases that involve riverbank filtration. Namely, groundwater (numerical) modeling is employed to examine the groundwater regime and balance, as well as to create protection systems and illustrate their effectiveness. Particle tracking analysis is used to study pollutants’ travel and residence time. On the other hand, PEST with regularization is employed to estimate the numerical model parameters. The proposed method is used in a real case study, which examines the application of the developed algorithm to the protection of a drinking water supply source from an industrial zone, which is a potential source of pollution. The research presented in the paper opens new avenues for future studies involving mathematical multicriteria optimization and decision making about optimal groundwater source protection management plans.