With rapid urbanization, there will be more conflict between human systems and the riverine ecological system, and therefore, ecological operations, practices and research must involve the ecological water replenishment of entire river basins with new modeling tools. In this study, we establish an ecological flow-oriented water resource allocation and simulation framework (E-WAS). Virtual reservoirs and ecological units are added to the water resources network. With new water balance equations for virtual reservoirs and ecological units, the E-WAS can simulate the ecological replenishment process in a river basin and can provide a recommended water replenishment scheme that considers optimization principles. The E-WAS was applied in the Longgang River Basin, Shenzhen, China. 17 ecological units and 45 water supply nodes are considered in the model. A water replenishment scheme that used water from 31 reservoirs and reclaimed water from 7 water sewage plants was selected. This scheme significantly increased the satisfactory degree of ecological water demand and efficiently supported the formulation of a control scheme for the water environment of a basin. The E-WAS framework is similar to model plug-ins but helps to avoid the large workload that is required for model redevelopment and can expand the functions of models quickly.