Developing water-saving agriculture must balance the interests of stakeholders in terms of economic benefits, food and ecological security objectives. The production-based water footprint (PWF), the energy-based water footprint (EWF), and the net benefits-based water footprint (NBWF) (including grey water footprint (GWF)) can be used to evaluate food and ecological security, water use efficiency, and benefits objectives. However, little attention is paid to the multi-dimensional evaluation of water consumption in agriculture. This study quantified the annual PWF, EWF, and NBWF of grain crops, cash crops, and feed crops in the Hetao Irrigation District (HID) over 1995–2017, and analyzed their spatiotemporal evolution characteristics and comparative advantages, then clarified the implications of the three types of water footprints for stakeholders in the HID for crop planning. The results showed the water use efficiency was decreasing and the benefits were increasing. The GWF deserves more attention as it contributed 35%− 40% of the total water footprint. The comparative advantages of the three water footprints revealed that the current crop distribution in the HID only favors benefits. Considering the crop distribution issues in the HID, the adjustment objectives can be determined by combining the connotations of the three types of water footprints, GWF, PWF_blue-green/EWF_blue-green, and NBWF_blue-green, corresponding to stakeholders’ environmental and social-economic interests. This study could provide basic guidance for crop planning and agricultural water management in the HID and similar areas.