Community structure of zooplankton at 4 locations, 2 in the coastal waters off Bombay and 2 in interior Thane-Bassein Creek System, Maharashtra, India were studied for a period of one year. Copepods as the major herbivore community contributed 76-83% to total zooplankton population. Decapods were relatively more in the outer (av. 11%) as compared to interior zone (av. 7%). Population density of carnivores were 2-4 times more in the polluted interior segment. Among the different metals studied Cu and Zn contributed 60-89% of the total elements accumulated. In general, concentration of Zn was higher than Cu in different groups. Also levels of Zn in polluted locations were 2 times higher than the outer zone. The maximum concentrations of metals was observed in gelatinous organisms which included a variety of carnivores. Metal concentration in copepods was lower than carnivores. The lowest concentrations of metals in decapods could be due to the effective elimination of a part of the concentrated metal through periodic moulting.