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ABSTRACT To ascertain the origin and salinisation of porewater in Quanzhou Bay, China, the chemical and isotopic compositions of groundwater samples collected from aquifers and porewater samples extracted from three 10‐m depth Holocene boreholes were analysed. Aquifer groundwater is dominated by freshwater with a 3 H content ranging from 1.7 to 2.8 TU, suggesting modern precipitation recharge. Aquitard porewater shows an increasing salinity from 146.2 to 7645.4 mg/L towards the sea. The relationship between δ 18 O and δ 2 H, and the positive correlation between δ 18 O and Cl − , along with the average mass Cl/Br ratio of 348.3, indicate that the saline porewater is of marine origin. However, in the inland CZ02 and CZ03 boreholes, the porewater is fresh, and the original seawater in the marine layer has been flushed out. The high NO 3 − concentrations and lower Cl/Br ratio of 58.6 observed in the shallow aquifer‐aquitard system indicate manure and sewage input, as well as the decomposition of marine organic matter. In addition to seawater, porewater chemical compositions have been further modified by mineral dissolution and cation exchange and adsorption, as suggested by typical ion ratios and 87 Sr/ 86 Sr ratios ranging from 0.70727 to 0.70959. A typical cross‐sectional paleo‐hydrogeologic model presented the groundwater salinity evolution throughout the Holocene. The saline porewater, originating from the Holocene transgression, is still trapped within the thin marine aquitard in the bedrock‐dominated coastal zone and affects the groundwater salinity and chemicals in the adjacent aquifer. While most of the shallow groundwater has been freshened by infiltrated rainfall. These findings suggest that the intrusion of paleo‐saline water at the coastal interface may be a primary contributor to groundwater salinisation. Furthermore, during submarine groundwater discharge, elevated nitrate concentrations in the aquitard‐aquifer system may potentially contribute to future ocean eutrophication and acidification.