In this study, we investigated the carbonate system in sediments and water columns from five stations in the Sea of Japan (East Sea) (JES) during the R/V Hakuho Maru KH-10-2 research cruise in the summer of 2010. The total alkalinity (TA) and pH were measured. Adopting a saturation degree of 91% and 80% for the lysocline depth and calcite compensation depth (CCD), respectively, we found that those depths corresponded to 1360 and 1980 m. A comparison of the calcite saturation depths, lysocline depths, and CCD depths obtained for 1999 and 2010 suggests that acidification of the interior of the JES occurred. Sediment cores were retrieved using a multi-corer. In the sediment cores, a sharp decrease in the pH by 0.3–0.4 pH units was observed in the subsurface horizons (0–10 cm) compared with the pH of the seawater from the bottom horizons. The TA in the porewaters was significantly higher than that in the overlying seawater. The anaerobic degradation of organic matter is probably the main cause for the increasing TA in the sediments. The porewaters were significantly undersaturated with calcite and aragonite, except in that from the shallowest station, where the sediments below 7.5 cm were saturated, and even supersaturated, with calcite and aragonite. A linear correlation between the dissolved inorganic carbon and the TA for sediments with a slope of 0.9993 was found, despite there being potentially different ways for the diagenesis of the organic matter to occur. The diagenesis of organic matter in the top sediments of the JES forms gradients of TA and CO2* concentrations on the interface of “bottom water–sediments”. Averaged fluxes of TA and dissolved inorganic carbon (DIC) from the sediments to the bottom waters estimated by means of Fickian diffusion were calculated as 44 and 89 mmol/(m2 year) for TA and DIC, respectively.
