Macrofaunal community structure is determined by a number of environmental variables. The riverine run-off during the monsoon brings about drastic changes in the physico-chemical parameters of a tropical estuary. The aim of the present study was to investigate the influence of rainfall in structuring the benthic macrofaunal community of a tropical estuary. The temporal dynamics of the macrobenthic community in the monsoon dominated Mandovi estuary (central west coast of India) was studied fortnightly from June 2007 to June 2009. A fixed location, downstream of the Madovi river, was sampled for benthic and water parameters. Ten replicates were collected during each sampling date using a Van Veen grab (0.04 m2). The macrofaunal abundance showed temporal fluctuation. The multivariate analysis showed the clustering of the samples linked to the environmental parameters (CCA and LINKTREE). The temporal variation observed in the macrofaunal abundance was basically due to changes in abundance of the dominant species. The variation in macrofaunal abundance was brought about by the recruitment and settling of re-suspended adults. It can be concluded that the macrofaunal structuring is influenced by temporal changes in the environment associated with the annual monsoon rainfall. Hence climate induced changes in the monsoonal pattern may affect the macrobenthic assemblages of tropical estuaries.