The stable oxygen isotope (δ18O) values of biogenic calcium carbonates (CaCO3) present in hard tissues of marine organisms vary with the δ18O of the surrounding seawater (δ18Osw) and water temperature. Consequently, the ambient water temperature when marine organisms existed can be estimated using δ18O of CaCO3 with δ18Osw. Thus, the aims of this study were to reveal the spatiotemporal variations in δ18Osw and their correlations with salinity in the East Asian marginal seas. We collected seawater samples (n = 2222) at 1394 stations around Japan, primarily from the surface layer of the East China Sea (ECS) and Sea of Japan (SOJ), from 2015 to 2021. We analyzed δ18Osw and the stable hydrogen isotope of seawater (δDsw) along with the measured water temperature and salinity. The δ18Osw and δDsw values ranged from –3.48‰ to +0.45‰, and –21.5‰ to +2.3‰, respectively. In our full data, both δ18Osw and δDsw had positive linear relationships with salinity as follows: δ18Osw = 0.235 × salinity – 7.94 (r2 = 0.85) and δDsw = 1.56 × salinity – 52.9 (r2 = 0.85). Furthermore, the relationship between δ18Osw and δDsw for full data as follows: δDsw = 6.44 × δ18Osw – 0.18 (r2 = 0.96). These relationships varied across seasons, areas (the ECS or SOJ), and water depths. In particular, δ18Osw and δDsw of less-saline water were different in the ECS and SOJ. These fine-scale, wide-range, and high-precision δ18Osw and δDsw datasets can contribute to paleoceanography, environmental analysis, oceanography, and fisheries science.