A key limitation of traditional water resources allocation was that, it only paid attention to the economic benefit of water resources and overlooked its value in the ecological environment, against sustainable management of the rivers. The ecological base flow could be regarded as a water-using department, and the marginal benefit of water remained in the channel was assessed by establishing a new calculation approach. Meanwhile, the marginal benefits of the tertiary industrial water were estimated on the basis of Cobb-Douglas production function. The calculated results were help to achieve the simply allocation of water resources for maximum benefits. Based on the example of the Baoji Section of Weihe River in the dry season, the results indicated that：the water consumption in the secondary industry and tertiary industry decreased from 2001 to 2015, but the marginal benefits were high, and can maintain the status quo；the average marginal benefits of ecological base flow and the primary industry were lower than 5 yuan/m3. Making them be equal can obtain the allocation of water resources 10 m3/s between the ecological base flow and the primary industry, and the corresponding economic benefits and ecological benefits can be satisfied, and the marginal benefits were 1 yuan/m3.