It is important to understand the changes in the chemical composition and connectivity of each aquifer in the arid-semi-arid riverine mines under the driving force of coal mining and to establish a rapid identification of water sources in the riverine mines, which is important for the protection of groundwater resources and safe production in the study area. By analyzing the numerical characteristics of conventional elements, cluster analysis and the deuterium–oxygen and tritium isotopes of different aquifers, the groundwater chemical characteristics and hydraulic connections of each aquifer were determined. Three identification charts (Piper and Durov identification charts of conventional hydrochemical components and deuterium–tritium isotope identification charts) were established to enable the rapid identification of each aquifer water source. The results showed that the main recharge source of groundwater in the study area was atmospheric precipitation. There was a significant indigenous connection between the Quaternary aquifer and the Zhiluo Formation aquifer but a limited indigenous connection between the Zhiluo Formation aquifer and the Yan'an Formation aquifer, creating local groundwater systems that altered the local groundwater circulation patterns, driven by coal mining. Three identification charts were established to determine the water inrush sources and propose targeted solutions for water inrush from different aquifers in the Shendong mining area based on the differences in hydrochemical ion characteristics as well as deuterium–oxygen and tritium isotopes.