<p>The arid regions of western China are rich in coal resources but suffer from severe groundwater scarcity. Coal mining has significantly altered groundwater systems and flow fields. Taking the Yushuquan Coal Mine in Xinjiang as a study area, this study integrates multivariate statistical, hydrogeochemical, and hydrogen–oxygen stable isotope analyses to investigate variations in groundwater quantity and chemistry across different aquifers before and after mining, aiming to elucidate the evolution of groundwater flow patterns under mining disturbance. Results show that mining has modified the regional groundwater pressure field and generated new flow pathways, enhancing hydraulic connectivity between previously independent aquifers. Consequently, the groundwater flow system evolves from a stratified to a coupled pattern. Hydrochemical evolution is governed by three dominant coupled modes: (1) Ion migration and enrichment, mainly in the deep aquifer, where dewatering promotes the convergence of highly mineralized water and the enrichment of Na⁺, Cl⁻, and SO₄²⁻; (2) Mixing processes, representing enhanced vertical hydraulic exchange between shallow and deep aquifers via mining-induced fractures; and (3) Water–rock interactions, where evaporite dissolution and pyrite oxidation control SO₄²⁻ enrichment and high mineralization. Stable isotope data suggest that shallow groundwater is recharged by precipitation and affected by evaporation fractionation, while deep groundwater is relatively depleted. The isotopic signature of mine water lies between the two, confirming strengthened vertical connectivity. Accordingly, a “dual-layer circulation with three evolution patterns” conceptual model was proposed, revealing the process whereby mining disturbance enhances connectivity and subsequently alters regional groundwater circulation pattern. This study provides a scientific basis for groundwater resource management in arid mining regions.</p>