Quantification of the relationship between agricultural water use and social development is important for the balance between conserving water resources and sustainable economic development. The agricultural water footprint (AWF) from crop production across 11 provinces in the Yangtze River Basin (YRB) of China, from 1999 to 2018, was calculated in the current paper. The driving factors which affected the provincial AWF were revealed using the logarithmic mean Divisia index (LMDI) model, based on a temporal and spatial variation assessment. The results showed that, with a growth rate of 1.95% per year, the annual AWF of the in the basin was 441.6 Gm3 (green water accounted for 73.63% of this) in the observed two decades. The Jiangsu, Anhui, Hubei and Sichuan provinces jointly accounted for 54% of the total AWF of the region. Cereal, cotton and fruit crops contributed most of the AWF, and determined the trends of the AWF over time. With the development of the economy and market demand, the dominant crop contributing to the AWF has shifted, from cereal and cotton around 2000, to cereals and fruits at present. The economic level was the main contributing factor driving the AWF. However, water use intensity was the most important factor which inhibited the growth of the AWF. Irrigation technology and the degree of urbanization also played a certain inhibitory role. There were significant differences in the driving effects among the different provinces. A comprehensive evaluation of the AWF and analysis of its driving factors provides a solid foundation for optimizing planting structure, strengthening water resource management, and enhancing regional exchanges and cooperation.