Advective flows of seawater and fresh groundwater through coastal aquifers form a unique ecohydrological interface, the subterranean estuary (STE). Here, freshly produced marine organic matter and oxygen mix with groundwater, which is low in oxygen and contains aged organic carbon (OC) from terrestrial sources. Along the groundwater flow paths, dissolved organic matter (DOM) is degraded and inorganic electron acceptors are successively used up. Because of the different DOM sources and ages, exact degradation pathways are often difficult to disentangle, especially in high-energy environments with dynamic changes in beach morphology, source composition, and hydraulic gradients. From a case study site on a barrier island in the German North Sea, we present detailed biogeochemical data from freshwater lens groundwater, seawater, and beach porewater samples collected over different seasons. The samples were analyzed for physico-chemistry (e.g., salinity, temperature, dissolved silicate), (reduced) electron acceptors (e.g., oxygen, nitrate, and iron), and dissolved organic carbon (DOC). DOM was isolated and molecularly characterized via soft-ionization ultra-high-resolution mass spectrometry, and molecular formulae were identified in each sample. We found that the islands’ freshwater lens harbors a surprisingly high DOM molecular diversity and heterogeneity, possibly due to patchy distributions of buried peat lenses. Furthermore, a comparison of DOM composition of the endmembers indicated that the Spiekeroog high-energy beach STE conveys chemically modified, terrestrial DOM from the inland freshwater lens to the coastal ocean. In the beach intertidal zone, porewater DOC concentrations, lability of DOM and oxygen concentrations, decreased while dissolved (reduced) iron and dissolved silicate concentrations increased. This observation is consistent with the assumption of a continuous degradation of labile DOM along a cross-shore gradient, even in this dynamic environment. Accordingly, molecular properties of DOM indicated enhanced degradation, and “humic-like” fluorescent DOM fraction increased along the flow paths, likely through accumulation of compounds less susceptible to microbial consumption. Our data indicate that the high-energy beach STE is likely a net sink of OC from the terrestrial and marine realm, and that barrier islands such as Spiekeroog may act as efficient “digestors” of organic matter.