Natural disturbances along with human interference make the tropical estuaries amongst the most disturbed areas globally. In spite of this, information on the seasonal variability of macrofauna from tropical estuaries is few. Temporal variability of macrofaunal community from Mormugao Bay, Zuari estuary, on the west coast of India was examined from 2003 to 2004 at seven stations. Environmental variability was assessed through physicochemical parameters of water and sediment. The changes in macrobenthic community were assessed using abundance, biomass and species diversity indices. The environmental parameters showed a significant seasonal variation influenced by monsoonal changes. The changes in the environmental conditions brought about variation in the macrobenthic community. Macrofaunal abundance, biomass and species diversity were the highest during post-monsoon influenced by recruitment. In monsoon, the macrobenthic community was dominated by polychaetes (92.17%), whereas bivalves dominated during the post-monsoon (57.7%). The macrofauna showed drastic decline during the stable pre-monsoon season, a period when the highest abundance of fauna is observed in the tropical estuary. Therefore, the macrobenthic community in the area did not follow the seasonal trend generally observed in a tropical estuary. Further, the community during pre-monsoon season was dominated by the opportunistic polychaete species indicating a possible influence of harbour activities in structuring the benthic community of the area.