The biomass and distribution of black clam (Villorita cyprinoides) in Vembanad, a tropical estuary located along the southwest coast of India varied significantly. Sampling was done in freshwater-dominated zone in the south (distal) and brackish water zone in the north (proximal), during pre and post monsoon seasons. Clam biomass was estimated from samples, collected from different stations during the study period. Water transparency and temperature were measured at the sample sites. Water samples were collected and analysed for salinity, dissolved oxygen (DO), pH and hardness. There was a significant difference in the clam biomass during the two seasons in the distal zone, and those collected from the distal and proximal zones during pre-monsoon season. The data were further analysed to determine the factors affecting the clam biomass distribution in the two zones and seasons. Factor analyses, comparing the distal zone during two seasons and zonal variations were similar to earlier observations. Step wise regression analyses found that dissolved oxygen (adjusted R2 = 0.3) is the only variable affecting clam survival during pre-monsoon period in the distal and proximal zones. A geographic map of the region obtained from the Indian satellite sensor LISS (Linear Image Self Scanner) was used along with in situ data to map the results using inverse distance weightage model.