Subterranean estuaries (STEs) are important biogeochemical land–sea interfaces, where fresh groundwater mixes with seawater in coastal aquifers. However, the sources of dissolved organic matter (DOM) and the connection of its molecular-level processing to pore water chemistry and redox conditions in these ecosystems are still not well understood. We studied the cycling of DOM in the STE of an intertidal sandy beach of the North Sea on spatial and seasonal scales. Ultrahigh-resolution mass spectrometry was used to identify thousands of DOM molecular formulae. These data were interpreted in the context of inorganic pore water chemistry, stable carbon isotope composition of solid-phase extracted (SPE) DOM and chemical tracers for bioavailable (dissolved carbohydrates, DCHOs) as well as biorefractory DOM (dissolved black carbon, DBC). Numerical modelling was used to estimate pore water residence times indicating relatively young pore water in the upper saline plume (USP, < 4 years) and decades-old groundwater in the freshwater discharge tube. The detected levels of dissolved Fe and ammonium in the USP at sediment depths exceeding 50 cm demonstrated suboxic conditions. Statistical analyses revealed complex biotic and abiotic DOM processing apart from conservative mixing of marine and terrestrial endmembers. We propose that the input of bioavailable marine and terrestrial DOM, such as DCHOs, by percolating seawater and meteoric groundwater and its degradation by microbes caused oxygen depletion favoring Fe oxide/hydroxide reduction. In the freshwater discharge tube, the presence of highly aromatic compounds, DBC, and 13C-depleted SPE-DOM indicated the intrusion of meteoric groundwater containing terrestrial DOM. The discharge of this groundwater appears to be a significant source of nutrients (e.g., ammonium) and biorefractory, e.g. combustion-derived, DOM to the adjacent water column