This paper presents a hydroinformatics management tool designed to optimize the program of measures (PoM) to achieve the European Water Framework Directive (WFD) objectives in the internal Catalonian watersheds. The tool incorporates the Qual2kw water quality model to simulate the effects of the PoM used to reduce pollution pressure on the hydrologic network. It includes a Multi-Objective Evolutionary Algorithm (MOEA) to identify efficient trade-offs between PoM cost and water quality. It also uses multi-criteria visualization and statistical analysis tools as a user-friendly interface. This management tool is based on the Pressure–Impact concept, selecting the most effective combinations of sewage treatment technologies from millions of technologically admissible combinations. Moreover, the tool is oriented to guide stakeholders and water managers in their decision-making processes. Some guidelines are also given in this paper on the use of analytical relationships from the field of evolutionary multi-criteria optimization algorithms for different parameters (elitism, crossover and mutation rate, population size) to ensure that the MOEA is competently designed to navigate the criteria space of the management problem. Additionally, this paper analyzes the results of applying the management tool in the Muga watershed, whereby guaranteeing its convergence within a reasonable computational time, in order to simplify the decision-making process.