Assessing water environment change by grey water footprint has become a hot topic of water environment related researches. To understand the agricultural water environment in Chongqing, the grey water footprint of crop farming in Chongqing in 2007 was calculated, and the space difference was analyzed by relating grey water footprint with agricultural non-point source pollution. Results showed that 1) the grey water footprint of crop farming in Chongqing in 2007 was 2 208.88×10⁶ m³,which means 2 208.88×10⁶ m³ of freshwater was needed to dilute the pollutants from crop farming for a good condition of water environment; 2) the density of gray water footprint on crop farming in many counties of Chongqing differs slightly; 3) the intensity of gray water footprint on crop farming is high in eastern counties and low in western counties of Chongqing; 4) the pressure index of water environment in western counties is higher than that of eastern counties, and the water environment has been polluted by crop farming in 13 newly-developed counties of Chongqing. The research indicates that more attention should be paid to the pollution from crop farming.