Copious amounts of organic carbon are stored for long periods of time in deep continental groundwaters. Little is known about its composition and cycling, mainly due to the difficulties in obtaining sample material. Cool fracture waters of different origins can be obtained under clean conditions at Äspö Hard Rock Laboratory (Äspö HRL, Sweden), operated by the Swedish Nuclear Fuel and Waste Management Company (SKB). We sampled groundwater from different depth (171 to 507 meter below sea level) in the bedrock fractures in November 2018 and March-April 2019. We assessed water chemistry and dissolved organic matter composition via stable carbon isotopic and molecular-formula level analysis in recent Baltic Sea-influenced to old saline fracture waters in the granitic Fennoscandian shield.Molecular-level dissolved organic matter composition via Fourier-transform ion cyclotron resonance mass spectrometry using electrospray ionization in negative mode (FT-ICR-MS, 15 T Bruker Solarix) was done on solid-phase extracted (PPL) DOM extracts. Relative peak intensities from FT-ICR-MS with molecular formula attributions, elemental ratios and compound group classification of the final dataset are given. ICBM-Ocean was used for processing of FT-ICR mass spectra and formula attribution (Merder et al., 2020; doi:10.1021/acs.analchem.9b05659).