With large topographic gradients, rifted basins serve as efficient traps for particulate matter from adjacent lands and the ocean surface. However, the fate of organic carbon in the sediment, mostly unaltered by the hydrothermal activities known to occur in young rifts, remains poorly understood. In this study, we present an examination of diagenetic activities and carbon remineralization based on the first complete suite of pore-water data of sediment marginally affected by hydrothermal activities in the Southern Okinawa Trough (SOT). The sediment showed an oxygen penetration depth of 1 cm, consumption of NO3− in the top 1 cm, smeared profiles of Mn2+ and Fe2+ with the latter reaching up to 450 μmol L−1, and relatively unchanged SO42− concentrations with depth. Net production rates of dissolved species resolved from pore-water profiles provide an estimate of 1.68 ± 0.21 mmol C m−2 d−1 as the total carbon remineralization rate in the upper 30 cm sediment column, with aerobic carbon oxidation being the major pathway. The rate, one order of magnitude lower than that of the adjacent East China Sea, is attributed to the lower bottom-water temperature and carbon flux in the trough. The high carbon burial efficiency of SOT (68% of carbon reaching the seafloor and processed thereunder) reflects the combined effects of small mountain rivers and rifting-induced particle trapping.