Utilization of saline or sea water for large-scale cultivation of microalgae can potentially provide a leap towards the reduction of both cost and sustainability challenges for biofuel production. The present investigation evaluated the temporal changes in carbohydrates and fatty acids of a halotolerant microalga Scenedesmus sp. IITRIND2 grown in natural seawater salinity to delineate the differential physiological response towards salt stress and subsequent potential for biofuel production. The microalga showed remarkable ability to tolerate different salinity environments under given temperature and light conditions. Such tolerance was attributed to the increase in neutral sugars, such as glucose, mannose, galactose, fucose and ribose, associated with both structural and storage (and potentially osmoprotectant) polymeric carbohydrates. The carbohydrate rearrangements may aid in the remodeling of cellular components to circumvent the detrimental effects of high salinity. The observed high carbohydrate and lipid accumulation in this microalga signifies its potential for integrated bioethanol and biodiesel production. This work provides a basic understanding towards high salinity adaption of Scenedesmus sp. IITRIND2, which could further be explored for identifying targets for halotolerance in other microalgal strains.