Among the Sustainable Development Goals (SDGs) established in the 2030 Agenda, goals 6.3, regarding clean water and improve of water quality, and 6.5, regarding integrated water resources management, highlight the need for the implementation of successful environmental water quality monitoring programs of transboundary river waterbodies. In the present study, the designation of high priority areas for water quality monitoring of Drin transboundary watershed is performed using a suitability model, a GIS-based multicriteria decision analysis (GIS-MCDA) approach that takes into consideration the most important conditioning factors that impose pressures on rivers. Based on the results, the methodological approach used manages to sufficiently delimit the areas with increased need for water quality monitoring in the Drin watershed, and the validation procedure produces a correlation coefficient of 0.454 (statistically significant at a 0.01 level). Limitations arise in the case of a lack of detailed information or inaccurate input data and due to the inconsistency among the input data and the different methodological approaches regarding the information collection of each country involved. These restrictions foreground the need for cooperation between the countries involved regarding the exchange of scientific knowledge and common legislation, so as to achieve integrated, effective, and sustainable management of water resources of the area.