Water Footprint Assessment is a fast-growing field of research, but as yet little attention has been paid to the uncertainties involved. This study investigates the sensitivity of and uncertainty in crop water footprint (in m3 t−1) estimates related to uncertainties in important input variables. The study focuses on the green (from rainfall) and blue (from irrigation) water footprint of producing maize, soybean, rice, and wheat at the scale of the Yellow River basin in the period 1996–2005. A grid-based daily water balance model at a 5 by 5 arcmin resolution was applied to compute green and blue water footprints of the four crops in the Yellow River basin in the period considered. The one-at-a-time method was carried out to analyse the sensitivity of the crop water footprint to fractional changes of seven individual input variables and parameters: precipitation (PR), reference evapotranspiration (ET0), crop coefficient (Kc), crop calendar (planting date with constant growing degree days), soil water content at field capacity (Smax), yield response factor (Ky) and maximum yield (Ym). Uncertainties in crop water footprint estimates related to uncertainties in four key input variables: PR, ET0, Kc, and crop calendar were quantified through Monte Carlo simulations. The results show that the sensitivities and uncertainties differ across crop types. In general, the water footprint of crops is most sensitive to ET0 and Kc, followed by the crop calendar. Blue water footprints were more sensitive to input variability than green water footprints. The smaller the annual blue water footprint is, the higher its sensitivity to changes in PR, ET0, and Kc. The uncertainties in the total water footprint of a crop due to combined uncertainties in climatic inputs (PR and ET0) were about ±20% (at 95% confidence interval). The effect of uncertainties in ET0was dominant compared to that of PR. The uncertainties in the total water footprint of a crop as a result of combined key input uncertainties were on average ±30% (at 95% confidence level).