The coastal zone is not only a terrestrial-marine buffer system but also the main site of the organic matter decomposition process, which complicates the identification of the sources of bioactive elements (C, N and S) and the factors that control C-N-S cycling. Here, a multi-isotope approach is developed to distinguish C, N and S sources and the associated geochemical processes in a coastal aquifer system of the Pearl River Delta (PRD), China. The PRD is characterized as a typical multilayer groundwater system with a reducing environment in the confined aquifers and an oxidizing environment in the unconfined aquifer. For the groundwater samples from the unconfined aquifer, the δ15N values showed that the ammonium and nitrate originated from manure and sewage, the δ13C-DIC indicated that dissolved inorganic carbon (DIC) was mainly derived from soil CO2 and weathering of carbonate rocks, and the δ34S and δ18O signals of sulfate suggested that SO42− originated from the dissolution of continental evaporate. The oxidizing environment and the positive relationship between δ15N-NO3− and δ18O-NO3− suggested that nitrification and denitrification were the key factors influencing the transformation of nitrogen in the unconfined aquifer. No obvious correlation between C, N and S content and isotopic composition suggested C-N-S was loosely coupled in this aquifer.For the groundwater samples in the confined aquifers, the δD-H2O and δ18O-H2O signals suggested that partially confined groundwater samples were affected by seawater intrusion. In the non-seawater intrusion region (NSI zone), the C, N and S content combined with C, N and S isotopic composition indicated that ammonium was derived from the mineralization of organic matter, sulfate mainly originated from rock weathering, and DIC mainly originated from carbonate mineral dissolution and the CO2 produced by organic matter mineralization. Extremely high CH4 concentrations suggested the existence of methanogenesis, while the molar ratio of CH4/(CH4 + (1 + α) × CO2) indicated that both acetate fermentation and CO2 reduction were ubiquitous. CO2 reduction had a stronger isotopic fractionation effect on the δ13C-DIC values, thus, the relatively high δ13C-DIC values were observed. The electron acceptor was the key factor for organic matter mineralization, and CO2 acted as the main electron acceptor in the NSI Zone. Accordingly, acetate fermentation and CO2 reduction became the key factors driving ammonium release in the NSI zone. In the seawater intrusion region (SI zone), ammonium was derived from the mineralization of organic matter, sulfate was derived from the mixing of fresh water and seawater, and DIC was derived from carbonate mineral dissolution, seawater and the CO2 produced by organic matter mineralization. The δ34S-SO42− showed a positive correlation with δ18O-SO42− and a negative correlation with SO42−, suggesting the existence of bacterial sulfate reduction (BSR). High CH4 concentrations also suggested the existence of methanogenesis. The CH4/(CH4 + (1 + α) × CO2) ratios indicated that CO2 reduction existed in more than half of the confined groundwater samples in the SI zone. C-N-S was highly coupled in this region because both BSR and methanogenesis can increase the DIC content, while BSR enriches lighter carbon isotopes and methanogenesis enriches heavier carbon isotopes; thus, a wide range of δ13C-DIC values was found in SI zone. Sulfate or both sulfate and CO2 were the electron acceptors. Accordingly, acetate fermentation, sulfur reduction and CO2 reduction worked together to promote ammonium release for the groundwater samples in the SI Zone. However, the exhaustion of sulfate will make CO2 reduction the key factor for organic matter mineralization in the future.