We report radiocarbon and stable carbon isotope measurements from vent gas (CO2(g)), dissolved inorganic carbon (DIC), and particulate organic carbon (POC), from two vents of the Kueishantao (KST) shallow-water hydrothermal system, offshore northeast Taiwan. The purpose of this research is to investigate how magmatic-sourced carbon enters various carbon pools in the hydrothermal system. We utilize a precipitation method to eliminate sulfur compounds from CO2 samples to facilitate Accelerator Mass Spectrometry (AMS) analysis, and evaluate radiocarbon background levels during processing to characterize hydrothermal-sourced CO2 that contains negligible radiocarbon. The result shows that both CO2(g) and DIC in the fluids below two vent orifices fall within a narrow range of fraction of modern carbon (F14C) from 0.013 to 0.136 and δ13C from −8.3‰ to −5.1‰. The F14C values correspond to approximately 90% magmatic-sourced carbon in CO2(g) and DIC. A combination of equilibrium and kinetic isotopic fractionation can adequately explain relatively high CO2(g) δ13C to DIC, beneath vent orifices. Above the vent orifices, DIC becomes enriched in both 14C and 13C as a result of physical mixing with ambient seawater. POC F14C values confirm a significant magmatic carbon contribution into the POC pool within the KST system, with rapid hydrothermal circulation. Our results identify the physiochemical processes responsible for magmatic carbon migration from CO2(g) into the DIC pool, and demonstrate how a dual carbon isotope approach can serve as an effective tool in understanding carbon flow in high temperature-low pH hydrothermal systems.