The ecological footprint and ecological carrying capacity of water resources in major provinces and cities of the Yangtze River basin were calculated based on improved parameters from conventional model in which the regional per capita water resource amount was replaced by the regional water consumption control index. The driving factors of water resources ecological footprint were also analyzed using the logarithmic mean divisia index (LMDI). Results revealed slight increase in the inter-annual water resources ecological footprint, which reflected the change in water use structure in the basin; regional distribution patterns of water resources ecological footprint also reflected regional GDP to some extent. The results also showed a surplus in the ecological carrying capacity of water resources in Yangtze River Basin; ecological deficit was consistent with the distribution of ecological carrying capacity. Analysis on the driving factors demonstrated that the substantial growth in GDP was the major cause of increase in ecological footprint; population growth and water use structure affected the driving effect of the ecological footprint; and technology inhibited the increase of ecological footprint.