ABSTRACT Many environmental studies have shown that a systems approach, including complete supply chains, is relevant for the assessment of the consequences of production and consumption on natural resources. This can also be applied to water. Although water consumption also includes water supply chains, often irrigation supply chains are excluded in water footprint (WF) studies. Using information from water management studies on water losses, we propose an improved WF method that includes blue crop WFs and WFs of irrigation supply chains indicating total agricultural blue WFs. A systems approach considering not only irrigation technology but whole water supply chains, also distinguishing between surface and groundwater, is needed to improve efficient blue water use in agriculture. This method is applied to the Pakistani part of the Indus basin that includes the largest man-made irrigation network in the world. The total agricultural blue WF is 1.6 times the blue crop WF. Surface water losses vary between 45 and 49%, groundwater losses between 18 and 21% and are smaller than results from water management studies. Differences between provinces and canal commands are large. The identification of hotspots provides a tool to improve water management. Earlier WF studies might have underestimated agricultural water consumption if supply chains are neglected. More water efficient agriculture should take supply chain losses into account probably requiring water management adaptations, which is more a policy than an agriculture task. WFs of supply chains are also relevant for other sectors, like industry or municipal water supply.