Abstract: Economically developed coastal areas have a high water demand, and their groundwater resources can be threatened by salinization. Many methods and tracers have been used to discriminate the source of salinization because a single method does not yield reliable results. In this paper, the shallow confined coastal plain aquifer, north of the downstream Yangtze River in China, is used as a case study to investigate the origin of the salinity and the relevant geochemical processes for this aquifer. Multiple environmental tracers of major ions, minor ions (Br−, I−), and isotopes (18O, 2H, 13C, 87Sr, 3H, 14C) were used so as to provide reliable conclusions. The TDS distribution of the aquifer has an increasing trend, from below 500 mg/L in the inland areas to more than 20,000 mg/L around the southeast coastline. The water chemical type evolves from HCO3-Ca to Cl-Na as the TDS increases. The results suggest that the groundwater salinity is influenced by seawater intrusion. The seawater proportions in the groundwater samples range from 0.07% to 94.41% and show the same spatial distribution pattern as TDS. The 3H and 14C values show that the highest salinity was mainly caused by a seawater transgression around 6000a B.P. The aquifer is also affected by other hydrogeochemical processes: base exchange has enriched Ca2+ and depleted K+ and Na+, sulfate reduction has reduced the concentration of SO42− and enriched HCO3−, and iodine-rich organic matter decomposition has enriched the concentration of I−. The iodine enrichment also suggests paleo-seawater intrusion. In addition, the precipitation of carbonate minerals has decreased the concentration of Ca2+, Mg2+, and HCO3−, albeit to a limited extent.