Some species of microbial heterotrophic communities (14C glucose uptake and respiration; viable nad total bacterial numbers) and autotrophic communities (primary production rate, chlorophyll a, phytoplankton cell counts and generic diversity) were studied from Bombay harbour-Thana creek-Bassein creek confluence. Extremely low microbial heterotrophic activity observed from the polluted zones of this confluence directly implied signs of environmental deterioration. Besides suggesting eutrophication, higher concentrations of chlorophyll a and primary production in the locations receiving industrial waste were also important as indicators of resistant phytoplankton communities. Low generic diversity indices and low rates of 14C glucose uptake by the natural microbial assemblages from the interior locations suggest a general deterioration of the biological processes. Results of this study highlight the deviation from the classical stimulation of heterotrophic activity previously reported for several eutrophic estuaries