The world’s population growth in various ways impacts the waters environment, and these impacts have been observed since the twentieth century. However, paleolimnological data indicates that anthropogenic activities have been affecting the aquatic ecosystem for a long time ago. The primary determinant of the lake ecosystem damage is the change and utilization of the catchment area landscapes, which contributes to siltation as well as nutrient supply. The increased activities of agriculture and domestic work are the main causes of eutrophication due to nutrient input. Additionally, the cage aquaculture in the lake waters has led to oxygen depletion in the lower water column as an impact of organic loading input. Furthermore, habitat modification, including disturbance to the shore zone, has led to changes in riparian areas. Ultimately, these processes impact the biota population structure and degrade the lake ecosystem. Therefore, understanding the anthropogenic factors and their impact on the lake ecosystem will enable humans to control their activities and manage their impact on the ecosystem.