This paper presents a Decision Support System (DSS) to assist in the issuing of wastewater discharge and water abstraction rights, including the evaluation of alternative pollution control strategies used to facilitate the analysis and implementation of the instrument. The DSS substantiates its analysis with the use of evolutionary algorithms for the optimization of water demand and wastewater discharge allocation. It intends to maximize the uses and minimize the costs of wastewater treatment measures, according to the limits imposed by the water quality standards. Among the strategies considered for the issuing of permits were the compliance with environmental legislation for wastewater discharge, the equality between water users, the water quality standards set by the water bodies’ classification, and the restrictions imposed by the responsible controlling water agency. The DSS’s results were satisfactory to the strategies analyzed, as they complied with the restrictions and penalties imposed to the objective function. The main objective of the proposed strategies is to evaluate the performance of the DSS in getting the results, as well as to analyze the flexibility of the algorithms when new restrictions and penalties are introduced in the decision making process.