Abstract: 81Kr and 36Cl can both be used to date groundwater beyond the dating range of 14C. 81Kr usually provides reliable groundwater ages because it has uniform initial distribution and negligible subsurface generation, while 36Cl is commonly influenced by subsurface sources or “dead” chloride dissolution. Therefore, the combined use of 81Kr and 36Cl could provide clues on the evolution history of groundwater. In the present study, we performed 36Cl and 81Kr dating of geothermal water in Weihe Basin of China and interpreted the possible cause of disagreement. Two distinct water masses were identified with distinctive isotopic signals: groundwater with significant δ18O shifts (up to −2.0‰), dissolved dead Cl and ages < 1.0 Ma (Cluster A), and older water with little δ18O shifts, negligible dissolved Cl and ages >1.0 Ma (Cluster B). The results confirm the eastward flow path of Cluster B to the Ancient Sanmen Lake with an increasing trend of Cl concentration and age. Modern recharge from the mountains flows to the basin center with intense interaction between water and carbonate under respective reservoir temperatures (100 ∼ 130 °C). These waters flow through the saline stratum emerging from the spillover of the Ancient Sanmen Lake, resulting in higher dead Cl dissolution. A significant linear relationship is observed with the older end-member of ∼1.3Ma under the topographically-driven faster circulation effect. 81Kr ages seem to support the hypothesis that the birth of the modern Yellow River was at about 1.0–1.3 Ma. We inferred the drainage reorganization from the Ancient Sanmen Lake to the modern Yellow River since the Mid-Pleistocene Transition induced the change in groundwater dynamics as well as its chemical evolution. The excavation of the Ancient Sanmen Lake and the accentuated incision of the Weihe River induced groundwater gradient, and therefore the recharge from precipitation from both slopes of the Qinling Mountains in the south and the Beishan Mountains in the north. Our results highlight the effects of dead Cl on 36Cl dating and demonstrate the significant impact of catchment reorganization on groundwater dynamics and its chemistry.