Biological assessment is a useful alternative for assessing the status of aquatic ecosystems. The planktonic organisms often respond quickly to environmental changes and hence, the magnitude and dynamics of these organisms can provide important indication on the quality of the system. An evaluation of the phytoplankton along with physicochemical parameters was carried out in order to determine the pollution status of Powai and Vihar lakes in Mumbai, India. Algal samples were collected at fortnightly intervals from three sites each in both the lakes. A total of 34 genera of phytoplankters belonging to Chlorophyceae (16), Bacillariophyceae (7), Dinophyceae (1), Euglenophyceae (2) and Cyanophyceae (8) were observed in Powai Lake, whereas in Vihar, a total of 51 genera belonging to Chlorophyceae (25), Bacillariophyceae (12), Dinophyceae (2), Euglenophyceae (1) and Cyanophyceae (11) were observed. Nygaard’s and Palmer’s algal pollution indices have been used for assessing the pollution/trophic status of these water bodies. The analysis of the algal community indicates the mesotrophic condition of Vihar Lake and eutrophic condition of Powai Lake.