Dissolved organic matter is an important constituent of the marine carbon cycle. Hydrothermal sediments in the Guaymas Basin (Gulf of California) release DOM into the ocean, impacting deep-sea ecosystems and the marine carbon cycle. This dataset includes molecular data of dissolved organic matter (DOM) from porewater and Soxhlet-extracted sediment samples collected during IODP Expedition 385 to the Guaymas Basin in 2019 from Sites 385-U1545, 385-U1547, 385-U1550, and 385-U1551. Additionally, two seawater samples from Atlantis expedition AT37-06 (dives 4864 and 4865) were analyzed. Hot-water Soxhlet extractions were performed on sediment samples to simulate DOM mobilization via hydrothermal circulation from the particulate phase. The DOM molecular composition was analyzed on solid-phase extracted (SPE) DOM using Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS). DOM molecular indices were calculated from the relative intensities derived from FT-ICR-MS. Furthermore, concentrations of dissolved organic carbon (DOC), total dissolved nitrogen (TDN), as well as dissolved organic nitrogen, sulfur, and phosphorus of SPE-DOM (DONSPE, DOSSPE, DOPSPE) and SPE-DOM stable carbon isotope data were determined. The DOC mobilization potentials were calculated to compare the porewater DOC concentrations with the water-extractable hot-water Soxhlet extraction DOC concentrations. Therefore, we expressed DOC concentrations in DOCPW and DOCWE in relation to the original TOC contents. Detailed methods are provided in Knoke et al. (in review, GCA).