The huge pit formed after open-pit mining can partially change the local water system. Taking a typical open-pit coal mine in Wuhai City as an example, this study used survey data, hydrological analysis technology and a Rainfall-Run model to analyze the changes in the water system and runoff. The results indicate that the water system in the coal mining site has changed in the confluence path because of the mining pits and dumps formed by coal mining operations. Taking the local conditions into account, a water system restoration scheme using the pit for floodwater storage is proposed, that is, using the pit to retain upstream flood on the basis of an unobstructed downstream river flow. This scheme has several benefits. First, it can reduce the pressure of downstream flood control. Second, the sediment brought by the flood will be stored in the pit, which is conducive to reducing soil erosion. Third, it is conducive to the conservation of regional groundwater. Fourth, the retained water can be used for irrigation, which is conducive to the improvement of the surrounding ecology. The results of this study can provide references for the restoration and management of mining areas and ecological restoration in the arid desert area of Northwest China.