Proper assessments of degradation for lotic ecosystems are of a great importance, given that they provide essential ecosystem services and host some of the most endangered habitats. Currently, one of the most frequently used ways to assess lotic ecosystems integrity is the Water Framework Directive. It implies but important investments in material and human resources, while it is also time consuming. The implementation of a set of indicators, based on available public data, with the aim of assessing the lotic ecosystems integrity could be a good alternative, especially when focusing on large territories. The current study aims at creating a methodology to assess the degradation level of lotic ecosystems, by integrating the above-mentioned indicators into a GIS based multicriteria analysis. The proposed methodology was applied on a sector of one of the most important rivers in Romania, Mureș. The results we have achieved roved the efficacy of this method. In analyses of this kind, the accuracy of the output is directly related to the quality of input data (resolution, update and generalization level), thus a key element in our research was to process and compatibilize the available data to increase accuracy.