Water footprint (WF) accounting as proposed by the Water Footprint Network (WFN) can potentially provide important information for water resource management, especially in water scarce countries relying on irrigation to help meet their food requirements. However, calculating accurate WFs of short-season vegetable crops such as carrots, cabbage, beetroot, broccoli and lettuce presented some challenges. Planting dates and inter-annual weather conditions impact WF results. Joining weather datasets of just rainfall, minimum and maximum temperature with ones that include solar radiation and wind-speed affected crop model estimates and WF results. The functional unit selected can also have a major impact on results. For example, WFs according to the WFN approach do not account for crop residues used for other purposes, like composting and animal feed. Using yields in dry matter rather than fresh mass also impacts WF metrics, making comparisons difficult. To overcome this, using the nutritional value of crops as a functional unit can connect water use more directly to potential benefits derived from different crops and allow more straightforward comparisons. Grey WFs based on nitrogen only disregards water pollution caused by phosphates, pesticides and salinization. Poor understanding of the fate of nitrogen complicates estimation of nitrogen loads into the aquifer.