The knowledge of the residence time of formation water is fundamental to understanding the subsurface flow and hydrological setting. To better identify the origin and evolution of coal seam water and its impact on gas storage and production, this study collected coalbed methane co-produced water in the southeast Qinshui Basin and detected chemical and isotopic compositions, especially 36Cl and 129I concentrations. The calculated tracer ages of 129I (5.2–50.6 Ma) and 36Cl (0.13–0.76 Ma) are significantly younger than the age of coal-bearing formation (Pennsylvanian - Cisuralian), indicating freshwater recharge after coal deposition. The model that utilises 129I/I and 36Cl/Cl ratios to constrain the timing of recharge and the proportion of recharge water reveals that over 60% of pre-anthropogenic meteoric water entered coal seams since 10 Ma and mixed with residue initial deposition water, corresponding to the basin inversion in Cenozoic. The spatial distribution of major ion concentrations reveals the primary recharge pathway for meteoric water from coal outcrops at the eastern margin to the basin center. This study demonstrates the occurrence of higher gas production rates from wells that accept water recharge in recent times and suggests the possible potential of the non-stagnant zones for high gas production.