Under the influence of mining activities, investigating hydrological processes is an important cornerstone of water resources and eco-environment protection. In this study, the spatio-temporal variations of stable isotopic compositions (delta D and delta 18O) of river water and groundwater in five periods of a hydrological year were analyzed to identify the origin and hydraulic connection of water bodies in the mining district under mining disturbance. The delta D and delta 18O indicate that the water bodies in the study area are mainly recharged by local precipitation and undergo evaporation. There is a close hydraulic connection between river water, mine water, and groundwater, and the deep confined water is affected by the river water and phreatic water due to the developing water-conducting fractures. The delta 18O of phreatic water in each period is depleted in the southwest and enriched in the northeast of the study area. The delta 18O of confined water has an obvious spatial variation in the wet season due to the combined effects of opencast working and underground mining, whereas uniform spatial variation is observed in the dry season. Compared with the dry season, mining disturbances have a greater impact on river water and groundwater in the wet season. The difference in spatial variation of delta 18O between phreatic and confined water may be attributed to the easier recovery of phreatic water than confined water after mining disturbance. This finding provides important information about the hydrological characteristics of the Pingshuo mining district.