As for the shortage that only fishery production function was considered for water area by traditional ecological footprint, the researchers put forward the water ecological footprint. However, at the present, the basic theory and model of water ecological footprint were quite deficient. In order to solve the above problem, the paper proposed the concept and model of water ecological footprint based on ecosystem services and carried out relevant calculation and analysis with the example of Guangxi in 2003-2010. The results showed: (1) In the water-fishery accounts, freshwater fishery ecological footprint was in an upward trend; freshwater fishery biological carrying capacity was comparatively high and stable; freshwater fishery ecological surplus was more while its ecological pressure was less. (2) In the water resources accounts, freshwater ecological footprint rose more quickly at first and then fell slowly. The carrying capacity of water resources was higher but the fluctuation range in 2007-2010 was larger. Water resources ecological surplus was more while their ecological pressure was less. (3) In the water environment accounts, water pollution ecological footprint rose slowly, and then fell greatly and finally picked up gradually. The trend of water environment carrying capacity was consistent with the water resources carrying capacity. The results showed water environment ecological deficit and ecological insecurity in most years. (4) Freshwater fishery ecological pressure