The present study is carried out to inventorize the variations in plankton and associated benthic fauna in mangrove ecosystem with reference to polluted and unpolluted sites, viz. Bhayandar, Lokhandwala and Dharamtar near Mumbai. A total 34 genera of phytoplankton were identified from all the three stations. Diatoms were most dominant group of phytoplankton in all stations. Zooplankton were identified under 11 groups in which most dominant zooplankton group was tintinnids followed by copepods. Composition of benthic fauna in these present observation showed dominant group polychaetes and barnacles. Dharamtar had maximum number of species occurrence followed by Bhayandar and Lokhandwala. Occurrence of organisms like polychaetes and blue green algal dominance endorses the pollution at Lokhandwala. This study form a base line data for area line Dharamtar and Bhayandar, where developmental processes are on grow. The Mumbai coast has been undergoing major changes due to coastal development and anthropogenic interference especially connection with municipal solid wastes, sewage discharge and aquatic pollution of anthropogenic activity.