Net ecosystem production was examined in the Mandovi and Zuari estuaries (southwestern India) and the adjoining coastal waters for a period of 1 yr (January to December 1998). The study period encompassed premonsoon, monsoon, and postmonsoon seasons. At the estuarine stations, net ecosystem production showed monthly variation and a transition from net autotrophy of 49 mmol C m−2 d−1 during the nonmonsoon seasons (premonsoon and postmonsoon) to net heterotrophy of —46 mmol C m−2 d−1 in the monsoon season. Seasonal monsoon‐driven changes such as increased allochthonous inputs resulted in enhanced heterotrophic respiration and reduced primary production in the estuaries. In the coastal station, the monthly variation in net ecosystem production was not significant, and net heterotrophy was prevalent whenever measurements were made, thereby potentially serving as the net source of carbon dioxide to the atmosphere. Results suggest that the excess organic matter from these tropical estuaries supports heterotrophy in the adjacent coastal ecosystem.