Ecological footprint model created by Wackernagel is a good method for evaluating the sustainable development and application of water resource, but the method only evaluated the surface water area′s production for harvesting fish and other sea food, and neglected other important production function for water resources including surface water and ground water resources. On the basis of the theoretical framework of ecological footprint model, the computational model was built for managing ecological footprint and ecological carrying capacity of water resources. The three crucial parameters including mean global yield, global equivalent factor, and local yield factor for freshwater resources were determined for evaluating the ecological footprint of water resources.The model was applied to computing the ecological footprint of water resources in Jiangsu Province, China from 1998 to 2003. The results that were in agreement with the real situation sustainable utilization of water resources in Jiangsu Province demonstrated the correctness and scientific of the model. The model compensated the inadequacy of Wackernagels model.