Under the background of the ban on deep groundwater extraction in the 20th anniversary, great changes have taken place in the groundwater environment in southern Jiangsu. Based on comprehensive statistical analysis, Piper diagram, Gibbs diagram, chlor- alkali index, ion correlation and other methods, this paper reveal the evolution process of the formation of groundwater at different aquifer in 2009 and 2019. The results show that the chemical type of shallow water is mainly HCO-3—Na+·Ca2+ type, the chemical type of confined pore water is mainly HCO-3—Ca2+·Mg2+ type, and the deep confined water is mainly HCO-3—Na+·Ca2+type. The predominant cations and anions of each aquifer in different periods did not change, and the hydrochemical types evolved to a complex trend. The chemical composition of groundwater is mainly affected by rock weathering, cation exchange adsorption and human activities. Among them, phreatic and I confined water—rock interactions are mainly silicate rocks and carbonate rocks, and deep confined water is silicic acid. Among them, the water—rock interactions process in shallow groundwater and I confined groundwater are dominated by silicate rocks and carbonate rocks, the deep confined water are dominated by silicate rocks and evaporative salt rocks. The research results can provide a scientific basis for the development and management of groundwater resources in southern Jiangsu.