Irrigation areas, as the major wheat producers in China, are facing water resources and environment problems which were led by huge water and fertilizer consumption in wheat production. To comprehensively assess these issues, the total water footprint (WFT) of wheat and production water footprint (WF) for per unit mass of wheat were calculated based on monthly meteorological and agricultural data from the Baojixia Irrigation Area (BIA) during the period of 1994—2010. Mann-Kendall trend test and the GIS based inverse distance weighted spatial interpolation were applied to analyze the temporal and spatial variations of wheat water footprint indices. Furthermore, the logarithmic mean Divisia index decomposition (LMDI) method was employed to quantify the contributions of driving factors for changes in WFT. The result showed that the average values of wheat WFT and WF were 673 million m3 and 1.04m3/kg, while the green, blue and grey components accounted for 34.51%, 30.16% and 35.33%, respectively. The WFT and WF of wheat were declined significantly with slops of -17 million m3/a and -0.02m3/(kg·a), respectively. The averages of WF and its green and blue components (1994—2010) rose gradually from southeast to northwest in BIA, however, the grey production water footprint was increased from center of the BIA to both sides. By LMDI method, the WFT in BIA was highly depended on human activities (-113.57%) rather than climate change (13.57%). The driving factors in order of importance were irrigation quota (-56.58%), total plant area (-55.78%), rate of wheat plant area (-43.76%), nitrogen fertilizer per hectare (39.96%), climate change (13.48%) and irrigation water utilization coefficient (2.59%). Excessive fertilization was common in BIA, which caused serious water pollution and huge amount of grey consumption. Meanwhile, the low irrigation water utilization coefficient in BIA led to more water wasted in conveyance. Based on the research, the practical suggestions for improving WFT and WF were fertilizer reduction and construction for high irrigation water utilization coefficient.