Pakistan possesses the fourth largest irrigation network in the world, serving 20.2 million hectares of cultivated land. With an increasing irrigated area, Pakistan is short of freshwater resources and faces severe water scarcity and food security challenges. This is the first comprehensive study on the water footprint (WF) of crop production in Peshawar Basin. WF is defined as the volume of freshwater required to produce goods and services. In this study, we assessed the blue and green water footprints (WFs) and annual blue and green water consumption of major crops (maize, rice, tobacco, wheat, barley, sugarcane, and sugar beet) in Peshawar Basin, Pakistan. The Global Water Footprint Assessment Standard (GWFAS) and AquaCrop model were used to model the daily WF of each crop from 1986 to 2015. In addition, the blue water scarcity, in the context of available surface water, and economic water productivity (EWP) of these crops were assessed. The 30 year average blue and green WFs of major crops revealed that maize had the highest blue and green WFs (7077 and 2744 m3/ton, respectively) and sugarcane had the lowest blue and green WFs (174 and 45 m3/ton, respectively). The average annual consumption of blue water by major crops in the basin was 1.9 billion m3, where 67% was used for sugarcane and maize, covering 48% of the cropland. The average annual consumption of green water was 1.0 billion m3, where 68% was used for wheat and sugarcane, covering 67% of the cropland. The WFs of all crops exceeded the global average. The results showed that annually the basin is supplied with 30 billion m3 of freshwater. Annually, 3 billion m3 of freshwater leaves the basin unutilized. The average annual blue water consumption by major crops is 31% of the total available surface water (6 billion m3) in the basin. Tobacco and sugar beet had the highest blue and green EWP while wheat and maize had the lowest. The findings of this study can help the water management authorities in formulating a comprehensive policy for efficient utilization of available water resources in Peshawar Basin.