We developed a system for measuring the total dissolved inorganic carbon (DIC) concentrations in interstitial water and hydrothermal fluid, which are hard to obtain in large volumes. The system requires a sample volume of only 500 μL, and it takes only 150 s per one sample. The detection limit of this system was estimated to be 66.6 μmol/kg with repeated analysis of CO(2)-free ultrapure water (n = 9). The precision of this nondispersive infrared (NDIR) system was ±3.1% of the relative standard deviations (2σ) by repeated CRM batch 104 (n = 10). This result is much larger than the required precision for oceanographic studies, but is comparable to a previous result of interstitial water analysis. An on-site trial showed a significant DIC enrichment in interstitial water of hydrothermally altered sediment, and is considered to occur by the mixing of hydrothermal fluid. This procedure will achieve carbon dioxide flux calculations from hydrothermal activities, and will bring a more accurate feature on the global carbon cycle.