Even though continental margins cover only about 7–9% of the world ocean area, they are important sites for organic carbon accumulation and hence play a major role in biogeochemical carbon cycling. Surface sediments from the western and eastern continental shelves of India were studied for their total organic matter content and the labile constituents such as total carbohydrates and proteins to get a better understanding of the hydrological and biogeochemical differences of the two regions on the nature of organic matter reaching the surface sediments. The sampling along the west coast was done during September–October 2003, when upwelling signatures were found to be still persisting along the shelf as evidenced by the low-oxygenated, nutrient-rich surface waters. The eastern shelf was sampled during November–December 2002. The shelf was found to be oxygen saturated and oligotrophic during the season. The surface sediments of the west coast contained a greater quantity of total organic matter when compared to the east coast, but the percentages of labile constituents of total organic matter in the sediments were found to be higher in the east coast by a factor of three as compared to the west coast. The differences in the productivity patterns and the hydrographical conditions were found to exert a major influence on the quantity and composition of organic matter in the surface sediments of the western and eastern continental shelves of India.