Harnessing the natural resources is one of the basis of natural economy in developing countries. The wise use of such resources is very important to sustain the balance between immediate benefits and maintenance of the ecosystem. In Phewa, Begnas and Rupa lakes of Pokhara Valley, plankton feeding fish farming in net cage,enclosure and open water stocking is one of the effective example of natural resources utilisation which sustains a number of households in surrounding lakes for economic activities. These lakes are also used for drinking water, hydroelectricity, irrigation and recreation etc. However, the understanding of trophic status of the lakes is very important for long term sustainable use of the lakes in harmony with human activities. Here, we present the trophic status of three lakes of Pokhara Valley and discuss the impacts of human and natural activities on the trophic status of the lake. The study shows that heavy rain fall in the valley during monsoon is one of the strongest natural forces which flush out the accumulated nutrients from the lakes and migrate the eutrophication processes. Recommendations for sustainable use of lake water have also been discussed.