Bhopal, the capital of Madhya Pradesh is gifted with number of water resources of multiple uses. However most of the water bodies have shrunken because of siltation, illegal land filling, conversion, and encroachment. The combination of all these factors ultimately resulted in deterioration of water quality and loss of species. The present study therefore was undertaken to evaluate the impact of urbanization on water quality and bio-diversity of the 10 lakes and wetlands situated within the municipal area of the city. A comparison of data generated over the years depicts considerable reduction in total number of species in the water bodies like Upper Lake, Hathaikheda and Sarangpani Lake.