The groundwater level has been continuously decreasing due to climate change and long-time overexploitation in the Xiong ’an New Area, North China, which caused the enhanced mixing of groundwater in different aquifers and significant changes in regional groundwater chemistry characteristics. In this study, groundwater and sediment pore-water in drilling cores obtained from a 600 m borehole were investigated to evaluate hydrogeochemical processes in shallow and deep aquifers and paleo-environmental evolution in the past ca. 3.10 Ma. Results showed that there was no obvious change overall in chemical composition along the direction of groundwater runoff, but different hydrochemical processes occurred in shallow and deep groundwater in the vertical direction. Shallow groundwater ( 1000 mg/L) and high concentrations of Mn and Fe, while deep groundwater had better water quality with lower salinity. The high TDS values mostly occurred in aquifers with depth 500 m below land surface. Water isotopes showed that aquifer pore-water mostly originated from meteoric water under the influence of evaporation, and aquitard pore-water belonged to Paleo meteoric water. In addition, the evolution of the paleoclimate since 3.10 Ma BP was reconstructed, and four climate periods were determined by the δ18O profiles of pore-water and sporopollen records from sediments at different depths. It can be inferred that the Quaternary Pleistocene (0.78‒2.58 Ma BP) was dominated by the cold and dry climate of the glacial period, with three interglacial intervals of warm and humid climate. What’s more, this study demonstrates the possibilities of the applications of pore-water on the hydrogeochemical study and further supports the finding that pore-water could retain the feature of paleo-sedimentary water.