In this study, the influence of the spatial and temporal variability of upwelling intensity and the associated biological productivity observed during different phases of summer monsoon along the southwestern continental margin of India (SWCMI) on the d13C and d18O of the inorganic biogenic carbonate shells was investigated. Multispecies benthic bivalve shells (1–5 mm) separated from ten surface sediment samples of SWCMI (off 12N, 10N and 9N) collected during the onset (OSM) and peak (PSM) phase of the summer monsoon of 2009 were analysed for d13C and d18O. Sea surface temperature along the study region indicates prominent upwelling in PSM than in OSM. A comparison of analytical and predicted values for d18O in the bivalve shells confirmed their in situ origin during both the sampling periods. During PSM, the d13C values in the benthic bivalve shells were more depleted in 13C than during OSM which recorded lower values of d13C in dissolved inorganic carbon of bottom waters expected in the study region in PSM due to the upwelled waters, high surface productivity and the associated high degradation of the organic matter in the subsurface and bottom waters. However, this depletion of d13C was not observed in benthic bivalve shells obtained from 10N, since it is influenced by high export fluxes of carbon from the Cochin estuary since early monsoon months