Test panels of aluminium and stainless steel were deployed in the surface waters of Dona Paula Bay, the Arabian Sea and aluminium panels at 10, 30 and 50 m depths at a shelf station in the Bay of Bengal. Microfouling material which developed n these test substrata was analysed for microfouling biomass (as dry weight and/or adenosine triphosphate), carbohydrate content and composition. Neutral carbohydrates were determined as altitol acetates in hydrolysates of the microfouling samples. With increase in the immersion period and the depth of deployment, microfouling biomass and carbohydrate content generally decreased. Eight individual sugars viz. arabinose, fucose, galactose, glucose, mannose, rhamnose, ribose and xylose were identified in the microfouling material by capillary gas chromatography. The relative content of individual sugars varied with the period and depth of immersion. Carbohydrate composition data when interpreted using source parameters, indicated the presence of marine and terrestrial organic matter in the microfouling material obtained from these substrata. The mannose/xylose ratios (<5%), the glucose free weight combined percentage distribution of ribose and fucose (> 12%) as well as arabinose and galactose (>28%) suggest that plankton, non‐woody vascular plant material and grasses appear to be the major sources contributing to the carbohydrates of the microfouling material.