Amid the growing population, climate change and decreasing water availability, water resources planning faces the challenge of achieving efficient and equitable water use, mainly in food production, its greatest consumer. The sustainability of agricultural water consumption in the Cachapoal River basin (34°S 71°O) is assessed using the blue (WFS_blue) and gray water footprint sustainability (WFS_gray) indicators under conditions of climate variability. The WFS_blue indicator of agricultural water consumption showed unsustainability in the upper basin in the dry year (2007), indicating severe water scarcity in autumn and low scarcity in spring, and in the wet year (2005), in which moderate water scarcity was observed only in spring, as a result of the decrease in blue water availability (WA_blue) and the increase in the blue water footprint (WF_blue), exceeding environmental flow requirements and the environmental carrying capacity. An opposite situation was found in the lower basin, where no water scarcity was observed in the analyzed years. Surface water quality, based on the concentration of fertilizers applied to crops, was observed to be more affected and unsustainable (WFS_gray) in the upper basin in the autumn and winter period of the dry year (2007). Currently, the indicators can be applied to provide useful information on the sustainability of water use in basins in order to establish and meet water resources protection objectives.