Coastal groundwater reservoirs are sensitive to the complicated evolution of marine transgressions and regressions in river delta regions. We integrated hydrogeological investigation and hydrogeochemical data with numerical modeling to assess the evolution of the groundwater system in the Pearl River Delta’s aquifer system (in southeastern China). We studied the effects of flow dynamics and redox conditions on the biogeochemical processes of nutrients in the regional groundwater flow systems in response to the transient states related to variable paleoprecipitation and seawater salinity decline from the late Pleistocene to the Holocene. The results from paleo-hydrogeological reconstruction of the aquifer-aquitard system showed that the saline groundwater formed by paleo-seawater intrusion was still present in the old marine aquitard and affected groundwater salinity and chemicals in the adjacent aquifers, while most of the groundwater in the shallow young marine aquitard has been freshened by infiltrated old/fresh rainwater. Consequently, total ammonium and carbon stored in the Pearl River Delta were estimated to be (1.91 ± 1.13) × 107 mol m–1 and (5.74 ± 4.05) × 107 mol m–1, respectively, and the ammonium and bicarbonate fluxes derived from groundwater discharge to the sea were calculated as (90.6 ± 55.9) mol m–1 yr–1 and (301.02 ± 196.23) mol m–1 yr–1, respectively. If the buried ammonium in the delta is released to the sea, it would be equivalent to nearly 205 ± 123 yr of Pearl River fluvial loading. These findings suggest that the chemicals trapped in the deltaic aquifer system during the Holocene could contribute to future ocean eutrophication and acidification.

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