Abstract: An estuary is a unique area exhibiting environmental and biological gradients. The estuarine species prefer an optimum niche along this gradient. The environmental parameters have relative influence on species diversity, biomass and population density of macrobenthos. We analysed the density and distribution of the edible clam, Paphia malabarica in the two tropical estuaries (Ashtamudi estuary, a deep lake and Kayamkulam estuary, a shallow lake in the south-west coast of India) in relation to the varying environmental factors for two years. The observations clearly indicated the existence of significant relationship between the biological and environmental variables. The density and distribution of the clam illustrated spatio-temporal variations in relation to the changing hydrologic and sediment parameters. Peak clam density values were obtained in the premonsoon followed by postmonsoon and least in the monsoon. The lower reaches were denser than the upper reaches of the estuary. The results of the study revealed that the density and distribution of the clam Paphia malabarica in the two estuaries were predominantly influenced by the environmental parameters such as salinity, organic carbon, sediment pH and sand fraction of sediment. The density and distribution of the clam was found decreasing in a decreasing gradient of these factors.