Subterranean estuaries (STEs) are land-ocean interfaces where meteoric fresh groundwater mixes with intruding seawater in a coastal aquifer, before discharging into the adjacent water column. In contrast to surface estuaries, STEs have the potential to amplify concentrations of constituents such as copper (Cu) and iron (Fe) due to long residence times and reductive dissolution of mineral phases along the groundwater flowpaths. However, oxidative precipitation of Fe and Mn at the sediment-water interface may scavenge many constituents again before they reach the coastal water column. Hence, the geochemical impact of the suboxic to anoxic submarine groundwater discharge (SGD) on the oxygenated coastal ocean relies on the capability of constituents such as Cu and Fe to stay in solution across redox boundaries. Here, we propose that dissolved organic matter (DOM) in the STE plays a pivotal role in the speciation of Cu and Fe through (i) fueling reductive dissolution and (ii) providing ligands to form stable metal-DOM complexes, increasing their transfer from the STE into the coastal ocean. We investigated the concentrations and speciation of Cu and Fe, and DOM chemical characteristics, in two beach STEs of a barrier island. By combining well-established techniques with novel quantification and speciation approaches from both the inorganic and organic geochemical realm (size-fractionation filtration, ferrozine detection, voltammetry, sequential DOM extraction, and ultra-high resolution mass spectrometry) we characterized metal-DOM associations down to the molecular level. Overall, pore water from both STEs was enriched with Cu and Fe compared to seawater, which indicated transfer potential for both trace metals across the sediment-water interface. However, Fe gradients from pore water to surface were steeper than those for Cu, indicating a larger net transfer of the latter compared to the former. Our voltammetry data showed that Cu was exclusively organically bound in both STEs and the water column, mostly in soluble form (<20 nm). The majority of >60 newly identified Cu-containing complexes had primarily aliphatic character and N and S in their molecular formulae resembling labile marine DOM, while two Cu-DOM complexes had polyphenol (“humic-like”) molecular formulae indicative of terrestrial vascular plant-derived material. In contrast to Cu, the Fe pool consisted of either reduced, soluble (<20 nm), likely free Fe(II) in the anoxic STE, or of larger colloids (<200 nm and >20 nm) in the fresh groundwater and seawater endmembers, likely as Fe(III)(hydr)oxides stabilized by DOM. Furthermore, while Fe and humic-like DOM seemed to share common sources, all directly identified mobile Fe-DOM complexes appeared to have marine origins. Therefore, organic forms of Fe in the STE may primarily consist of immobile humic-Fe coagulates, partially mobile Fe-nanocolloids, and mobile, N-containing, marine aliphatic Fe-complexes. Our study indicates that aliphatic, N-containing ligands may play an important role in the organic complexation and stabilization of Fe and particularly Cu in the STE, and enable them to cross redox boundaries at the sediment-water interface.