One of the most important aspects to understand marine organic carbon fluxes is to resolve the molecular mechanisms which convert fresh, labile biomolecules into semi-labile and refractory dissolved and particulate organic compounds in the ocean. In this interdisciplinary project, we carried out a detailed molecular characterisation of dissolved organic matter (DOM) during a north–south transect in the Atlantic surface ocean to relate the data to different biological, climatic, oceanographic, and meteorological regimes. Our goal was to achieve a high-resolution data set for the biogeochemical characterisation of the sources and reactivity of DOM. We applied various biogeochemical analyses for 220 samples from the upper water column (0–200m) and eight deep profiles. Spectroscopic techniques were applied continuously for phytoplankton characterization in a constant sample water flow supplied by a fish system and the moon pool. Radiocarbon dating enabled assessment of DOC residence time. Bacterial abundance and production provided a metabolic context for the DOM characterization work.