Water footprint (WF), a comprehensive indicator of water resources appropriation, has evolved as an efficient tool to improve the management and sustainability of water resources. This study quantifies the blue and green WF of major cereals crops in India using high resolution soil and climatic datasets. A comprehensive modelling framework, consisting of Evapotranspiration based Irrigation Requirement (ETIR) tool, was developed for WF assessment. For assessing climate change impact on WF, multi-model ensemble climate change scenarios were generated using the hybrid-delta ensemble method for RCP4.5 and RCP6.0 and future period of 2030s and 2050s. The total WF of the cereal crops are projected to change in the range of − 3.2 to 6.3% under different RCPs in future periods. Although, the national level green and blue WF is projected to change marginally, distinct trends were observed for Kharif (rainy season—June to September) and rabi (winter season—October to February) crops. The blue WF of paddy is likely to decrease by 9.6%, while for wheat it may increase by 4.4% under RCP4.5 during 2050s. The green WF of rabi crops viz. wheat and maize is likely to increase in the range of 20.0 to 24.1% and 9.9 to 16.2%, respectively. This study provides insights into the influences of climate change on future water footprints of crop production and puts forth regional strategies for future water resource management. In view of future variability in the WFs, a water footprint-based optimization for relocation of crop cultivation areas with the aim of minimising the blue water use would be possible management alternative.