The patterns and determinants of different types of agricultural water footprints in China are poorly understood at the prefecture-city level. In this paper, we evaluate Chinese agricultural water footprints from 2000 to 2017 and analyzed their spatio-temporal characteristics. Our estimation results show that the annual average agricultural water footprint in China was 5.038 × 109 m3, and the proportions of green water, blue water, and gray water were 70%, 9%, and 21%, respectively. In addition, high agricultural water-footprint cities with obvious urban agglomeration effects are mainly located in the Northeast, the Huanghuai River, the Yangtze River Basin, and Northwestern of Xinjiang, while low agricultural water-footprint cities are concentrated in high coastal urbanization-level areas or less developed agricultural areas of the west. We also investigate their determinants using a spatio-temporal fixed-effect model and find that GDP per capita, total investment in fixed assets, the income level of rural residents, the proportion of food grown, spray and drip irrigation technology, low-pressure pipe irrigation technology and seepage control irrigation technology have significant positive impacts on the agricultural water footprint. In contrast, the proportion of secondary and tertiary industries, social retail consumption, urbanization, technology expenditure, and the effective irrigation area proportion have a significant inhibitory effect. The primary determinants of the agricultural water footprint also vary substantially across water footprint categories (green, blue, and gray water footprints) and regions. Our findings imply that the agricultural water footprint should be incorporated into city water resource management and monitoring system.