Water, carbon (C) and nitrogen (N) are important natural resources required for crop production. Footprints of these three natural resources are useful indicators of consumption and pollution. The present project is aimed to determine the water, carbon and nitrogen footprints of major crops of the Indo-Gangetic Plains (IGPs). Field experiments were conducted, and modelling tools were used to quantify water, C and N footprints of rice and wheat crops in IGP. Four locations (Karnal, Delhi, Varanasi and Kalyani) were selected for the study representing different transects of IGP. Carbon footprint (CFP) of rice crop in Karnal and Delhi was found to be higher than Varanasi and Kalyani due to application of more amounts of agri-inputs and more use of farm machineries leading to higher GHG emission. Although GHG emission in wheat is also more in Karnal, higher yield of wheat crop led to lower CFP than Varanasi. Water footprint (WFP) of rice production was higher in Karnal, Delhi and Varanasi than Kalyani region mainly due to higher evapotranspiration. QGIS software was used to prepare geospatial maps of carbon and water footprint for IGP. The study will help in identifying regions and crops having higher footprints and also select alternative management practices which will help in lowering water, C and N footprints of agricultural production. © Springer Nature Singapore Pte Ltd. 2018.