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This study was conducted in Albaninan part of Prespa Park (AL-Prespa) with the aim of assessing the impact of waste management and agricultural activities on lakes water quality. The study is based on: 1) two annual (2013 and 2017) both qualitative and quantitative surveys on waste management and agriculture activities in AL-Prespa, and 2) a field questionnaire survey to explore the attitudes of the residents toward non point source (NPS) pollution control and watershed management. Statistic methods were used to draw conclusions. The findings showed that the impact of waste management and of agricultural production activities in the AL-Prespa lakes can be evaluated as low, but evident. The current discharging practices does not harm significantly the ecosystem, but impacts the quality of lakes water. Findings strongly suggested that the residents’ attitudes toward NPS pollution control in this area were positive. Some remedies are presented. The results taken by this research can provide and enable decision and policy makers to develop policies and measures for improving water quality in AL-Prespa watershed and other similar areas.