The nutrient concentrations at depths of 0–200 m in the southern area of the Japan Sea were investigated at 97 stations during six cruises between June and October in 2013 and 2014. The nutrient concentrations at the surface were depleted to less than 0.1 µM, except for silicates, which remained at 0.8–5 µM, and increased below the nutricline, at depths of 20–125 m. The vertical profiles of nitrate, silicate, and/or phosphate concentrations between 131°30′E–139°40′E and 35°50′N–40°40′N showed a peak in the subsurface layer at 40, 71, and 6 stations, respectively, and nutrient inversions occurred at macroscale widths. The subsurface nutrient maximum occurred at depths of 20–150 m in waters at temperatures of 15–16°C and potential densities of 25.3–25.5 σθ, on average. The depths of the subsurface nutrient maximum were generally associated with a salinity maximum originating in the bottom water of the shallow Tsushima Strait. The nutrient inversions were disturbed by phytoplankton consumption, as indicated by the presence of the subsurface chlorophyll maximum at the same depth or below the salinity maximum at stations without nutrient inversions. Therefore, it was inferred that remineralization of nutrients near the bottom, from the East China Sea to the Tsushima Strait, and horizontal advection by the Tsushima Warm Current below the euphotic layer induced macroscale subsurface nutrient inversions in the southern Japan Sea.