The super-efficiency slack-based measure (SBM) model considering unexpected output was used to measure the water resources utilization efficiency of 20 counties and districts in the water receiving area of the Bailong River Diversion Project in Gansu Province from 2011 to 2020. The Tobit model was used to analyze the main influencing factors of water resources utilization efficiency. The results show that the economic efficiency of water resources in the receiving area shows a downward trend, while the utilization environment and green efficiency of water resources exhibit a steady upward trend. Water use factors, economic level, industrial structure, and water resources endowment promote the economic efficiency of water resources utilization, while urbanization level inhibits the economic efficiency of water resources utilization. Urbanization level has a positive effect on the environmental efficiency of water resources utilization, while industrial structure and water resources endowment have negative effects on the environmental efficiency of water resources utilization. Industrial structure and water resources endowment inhibit the green efficiency of water resources utilization. On the whole, the green efficiency of water resources utilization is greater than the environmental efficiency, and the economic efficiency ranks last; the level of water resources utilization efficiency in the water receiving area is not high from 2011 to 2020. Therefore, the water receiving area needs to optimize the industrial structure, and neighboring counties and districts can strengthen regional cooperation to narrow the differences.