Lake evolution and its changes over time are an evident and easily measurable signal of human activities and climate change impacts in mountain regions. This study presents bathymetric modeling of permanent lakes (Begnas and Rara Lakes) located in two different geographic settings of Nepal. Moreover, temporal changes in land cover and soil erosion of the lake watersheds, as well as climatic trends around these lakes, are assessed. This study supports establishing reference sites for exploring scientific evidence on the impacts of anthropogenic and climate change on lake hydrological systems. Second-order polynomial models best represent the relationship between lake depth and volume. Rara Lake had a maximum depth of 169 m with an area of 10.52 km2 and a volume of 1013.305 million cubic meters (Mm3), whereas Begnas Lake had a maximum depth of 12.5 m with an area of 2.98 ± 0.10 km2 and a water volume of 13.539 Mm3 in the year 2019. Both lake regions are experiencing changes in temperature and rainfall. The area and volume of Rara Lake and its watershed have been relatively stable even with minimal land-cover change during the recent decades. Begnas Lake and its watershed have experienced significant changes in the last few decades. This study concludes that human activities in the Begnas Lake watersheds are the primary source of lake area variation rather than climate change.