This dataset is raw data for the article titled 'Zn isotope composition in the water column of the Northwestern Pacific Ocean: the importance of external sources' currently submitted to Global Biogeochemical Cycles. This data contains the basic hydrological parameters, including temperature, salinity, potential density, potential temperature, dissolved oxygen, phosphate, silicate, and chlorophyll-a concentrations, Zn concentrations, and Zn isotope composition with its analytical internal errors at nine different stations located in the Northwestern Pacific Ocean. The specific locations for the nine stations also can be found in this dataset.