The influence of anthropogenic loading on the distribution of soft bottom benthic organisms of a tropical estuary (Cochin backwaters) was examined. The industrial activities were found to be high in the northern and central part of the estuary, where dissolved inorganic nitrogen (DIN > 210 mu M) and phosphorus (DIP > 6.5 mu M) have caused high abundance of chlorophyll a (up to 73 mg m sup(-3)) and accumulation of organic carbon in sediments (up to 5%). Principal component analysis distinguished three zones in the estuary. The central zone (Z1) was characterized by organic enrichment, low species diversity, and increased number of pollution tolerant species. Long-term deterioration of the estuary is indicated by an increase in the nutrients and chlorophyll a levels by sixfold during the last few decades. Flow restrictions in the lower estuary have lead to a fourfold increase in sediment organic carbon over the period of three decades. The reduced benthic diversity followed by an invasion of opportunistic polychaetes (Capitella capitata), are indicative of a stress in the estuary