Freshwater ecosystems are facing severe threats by human activities. As a consequence of this, they can get disturbed. In developing countries, like India, freshwater lakes are endangered primarily by agricultural activities, which often accelerate erosion and the runoff. The massive application of pesticides and chemical fertilizers to agricultural lands is one reason for eutrophication in the Kolleru Lake. Industrial pollution causes deteriorating water quality and makes them unfit for drinking water to the inhabitants of the villages around the Kolleru Lake. Besides, the indiscriminate rise of fishponds across the lake is another source of pollution to the lake. The different natural and anthropogenic influences increase the highly complex ecosystem of the lake. Managing these ecosystems is a challenging task. Due to the lack of an integrated approach and comprehensive environmental policy, Kolleru Lake has been becoming an ecological crisis area. Diffuse pollution sources are still remaining. Together with inadequate management planning and actions, they are contributing to the deterioration of the water body of the Kolleru Lake. Therefore, the objectives of this study are to ascertain the priority control areas aiming at socio-economic development for the long turn protection of the lake water quality by applying the Best Management Practices (BMPs). For this purpose, the Soil and Water Assessment Tool (SWAT) was used to identify the critical areas of the lake’s catchment in terms of pollution from agricultural runoff into the tributaries of the Kolleru Lake and the lake itself. Further, suggestions were provided for the implementation of agricultural management practices to minimize pollution levels.