Abstract The Sea of Japan (SJ) is one of the fastest‐warming regions in the northwestern Pacific Ocean. Despite extensive examinations of long‐term temperature trends, salinity changes remain poorly understood. In this study, we analyzed more than 40 years of observational data to examine long‐term variations in both temperature and salinity. Surface‐limited freshening was found in the southeastern SJ, whereas a robust subsurface freshening emerged in the central SJ off the coast of Japan in spring. This trend is driven by increased river discharge due to enhanced precipitation over Japanese mainland and intensified mesoscale eddy activity, which remotely facilitates offshore freshwater transport. Springtime freshening may shoal the mixed layer, reduce heat content, and promote marine heat waves, potentially affecting marine organisms. Given its broad implications for climate and ecosystems, this phenomenon represents a key aspect of oceanic change in the SJ.