This baseline dataset comprises downcore measurements of pore-water Mn and NO3 for sediment core SO239_17_GC-1 retrieved in the framework of the European collaborative JPI Oceans MiningImpact project onboard R/V SONNE cruise SO239 in 2015. The scientific work during cruise SO239 was part of the first phase of the MiningImpact project (Ecological Aspects of Deep-Sea Mining) and is designed to assess the environmental impacts of deep-sea mining of polymetallic nodules in the Clarion-Clipperton Zone (CCZ) in the Pacific Ocean. The analysis of pore-water Mn was performed on acidified (0.145 M sub-boiling HNO3) aliquots stored at 4°C using an IRIS Intrepid ICP-OES Sectrometer, Thermo Elements. The analysis of pore-water NO3 was performed on frozen (-20°C) aliquots using a QuAAtro Continuous Segmented Flow Analyzer, Seal Analytical. Both analyses were performed at the Marine Geochemistry Lab, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven. For more information see Volz et al., 2018 (https://doi.org/10.1016/j.dsr.2018.08.006).