In the background of water ecological protection, how to utilize the superfluous coal mine water efficiently has become an urgent problem, especially in northwest China, where the fragile ecological environment needs to be protected but lacks water. To solve this problem, this study proposes a new procedure for the allocation and utilization of mine water aimed at the ecological protection of lakes in an arid and semi-arid area. Based on the water balance method, the ecological water supplement of regional lakes is first estimated according to their different protection goals. Next, a trend analysis of water demand and supply is carried out, and the mine water inflow and available quantity are calculated. Meanwhile, the water resource allocation plan is evaluated systematically. In this study, the procedure is applied to the mine water and lakes in Wushen Banner, Inner Mongolia Autonomous Region of China. The results show that: (1) the lakes can be divided into three classifications according to their ecological protection goals, (2) the available amount of mine water will reach 57.17–81.97 million m3 in 2030, and there are about 46.7 million m3 of water that can be adjusted to reach the optimal utilization in 2020, and (3) the mine water after advanced treatment could meet the requirement of lakes. Finally, it outputs the water supplement path and the water quantity, as well as the water transmission pipelines to each lake, which makes up a new water resources allocation plan and a utilization mode of regional mine water. This utilization mode can provide solutions and ideas for improving the ecological environment of regional lakes and promote the construction of regional ecological safety barriers. Moreover, it can be very helpful for optimizing the allocation of regional water resources, and for improving the reasonable utilization of coal mine water.