This dataset describes the dissolved cobalt and manganese distributions in the East China Sea. Other parameters such as salinity, water temperature, potential density, dissolved oxygen, and nutrient (nitrate, phosphate, and silicate) concentrations are also included. Seawater samples used for generating this dataset were obtained during the KS-15-6 cruise onboard R/V Shinsei Maru between July and August 2015 (Stn1 to Stn15), and during the KH-15-3 cruise onboard R/V Hakuho Maru in October 2015 (F1, D4, B8, and I1). Dissolved cobalt concentrations were determined using cathodic stripping voltammetry at the University of Tokyo and by using inductively coupled plasma - mass spectrometry (ICP-MS) at Kanazawa University, Japan. Meanwhile, dissolved manganese concentrations were determined using ICP-MS at both the University of Tokyo and Kanazawa University. All samples were irradiated with ultraviolet light before analysis.