Water ecological protection is an important task for demonstration zone of green and integrated ecological Development of the Yangtze River Delta. Shallow groundwater is an organic part of the water ecological system. To clarify the chemical characteristics and genetic mechanisms of shallow groundwater in this region, this study systematically analyzed the hydrogeochemical processes by using a variety of methods such as statistical analysis, Gibbs diagrams, Piper threeline diagrams, correlation analysis, and principal component (factor) analysis. The results showed that the shallow groundwater is slightly alkaline water, with HCO-3 as the main anion, and Na+ and Ca2+ as the main cation. Most of the microconfined groundwater belongs to brackish water and saltwater, which with higher NH4+content than phreatic water. Correlation analysis indicated that most of the major ions in the groundwater are mainly regulated by natural processes. High concentrations of Na+, Mg2+, and NH4+ are conducive to the accumulation of I- in groundwater. Four factors extracted from factor analysis explain 85. 375% of the total variance and are related to salinity, organic matter, pH, and sulfate, respectively. Overall, salinity, pH, and sulfate are related to natural processes, and Factor 2 represents anthropogenic processes, which cannot be completely separated from natural processes.