This dataset presents detailed information on the sampling sites, dissolved organic carbon (DOC) concentrations, and molecular characteristics of solid-phase extracted DOC (SPE-DOC) from bottom water (BW) and porewater (PW) samples collected in the German Bight, North Sea, during RV Heincke cruises HE582 and HE595. The data include average elemental compositions (C, H, O, N, S, P) and relative abundances of major compound classes and structural groups derived from FT-ICR-MS analysis. These molecular-level results provide insights into compositional differences between BW and PW DOM and reveal the selective preservation and transformation processes governing organic matter across the sediment–water interface.