Gas emissions from hydrothermal systems can serve as indicators of subsurface activity. In addition to gas sources, hydrothermal gas geochemistry is strongly influenced by secondary processes that occur during/after hydrothermal circulation. Here, we observed statistically significant differences in the geochemical characteristics (except for helium isotopes) of bubbling gases discharged from two adjacent vents in the Northern Luzon Arc. Helium (3He/4He = 4.25–7.09 Ra) in both vents was controlled by mixing between mantle and crustal components, where about 74% of helium was contributed by the mantle. Differences in N2/Ar ratios (∼ 300–330) of the two neighboring springs are attributed to subducted materials and seawater mixing (contributing ∼2.5% N2 and Ar), rather than phase separation in the reaction zone. Specifically, Ar was mainly supplied by atmospheric components that dissolved in the percolated seawater with only 8%–9% contributed by the excess radiogenic 40Ar. Excess N2 relative to Ar was mainly supplied by the decomposition of subducted materials (83%–92%) of the South China Sea plate beneath the Philippine Sea Plate. The Lutao gases showed low CO2 concentrations (0.07–22.2 mmol/mol), despite the high 3He/4He ratios indicating a significant contribution of magmatic components. Magmatic CO2 may have been largely consumed by the high Ca Lutao vent fluids via carbonate precipitation in the reaction zone. Alternatively, stable carbon isotope compositions (δ13C) indicate that Lutao CO2 may be supplied by microbial oxidation of alkanes (e.g., CH4 with concentrations of 14.6–173 mmol/mol in the samples), with fractionation factor ΔCO2–CH4 ranging from −15‰ to −25‰ and conversion rates of <10%. Up to 65% of the CO2 in the 2016 samples experienced secondary calcite precipitation in the discharge zone. Our results indicate that recycled subducted materials could potentially affect the geochemical characteristics of gases discharged from arc-volcanic systems. In addition, the influence of secondary processes needs to be considered before tracing the sources of hydrothermal fluids and/or gases, especially in shallow-water hydrothermal systems.