In recent years, fuzzy-logic-based methods have demonstrated to be appropriated to address uncertainty and subjectivity in environmental problems. In the present study, a methodology based on fuzzy inference systems (FIS) to assess water quality is proposed. A water quality index calculated with fuzzy reasoning has been developed. The relative importance of water quality indicators involved in the fuzzy inference process has been dealt with a multi-attribute decision-aiding method. The potential application of the fuzzy index has been tested with a case study. A data set collected from the Ebro River (Spain) by two different environmental protection agencies has been used. The current findings, managed within a geographic information system, clearly agree with official reports and expert opinions about the pollution problems in the studied area. Therefore, this methodology emerges as a suitable and alternative tool to be used in developing effective water management plans.