Geochemical cycles occurring at the interface between terrestrial and marine groundwaters, in the so-called subterranean estuary (STE), are not well understood for most elements. This is particularly true of the transition metals, many of which have particular ecological relevance as micronutrients or toxicants. To gain a first approximation of trace metal geochemistry in the mixing zone, we examined the distribution of nine dissolved metals (Fe, Mn, Mo, V, Co, Ni, Cu, Pb, and Al) through a shallow STE in Great South Bay, New York, USA. We also performed a simple kinetic and chemical separation of labile and organic-complexed metal species in the STE. Dissolved Mn showed marked subsurface enrichment (up to 755 µM at 15 cm depth) that was suggestive of diagenetic remobilization. Dissolved Fe, however, was higher by more than three orders-of-magnitude in fresh groundwater (90 µM) as compared to marine groundwater (0.02 µM), and pH-mediated removal was evident as slightly acidic fresh groundwater (pH 6.8) mixed with marine groundwater (pH ∼ 8.0). Dissolved Mo, Co, and Ni were primarily cycled with Mn, and highly elevated concentrations relative to bay surface waters (up to 300, 75, and 44 nM, respectively) were observed in the STE. High levels of dissolved Pb (up to 4250 pM) observed in the fresh groundwater were nearly quantitatively removed within the salinity mixing zone, in conjunction with marked reduction of dissolved Al. Dissolved Cu exhibited non-conservative removal throughout the STE, and was correlated with the redox potential of the porewaters. Substantial percentages (〉 15%) of organic-metal species were only observed for Cu and Ni, suggesting that these complexes were not generally very important for metal cycling in the STE. Kinetically labile species were observed for all metals examined except Cu and Pb, and represented an approximately constant proportion (between 10% and 70%) of the total dissolved pool for each metal, indicating equilibrium between labile and non-labile species throughout the mixing zone. The non-conservative behavior observed for all metals examined in this study suggests that reactions occurring in the STE are vastly important to the source/sink function of permeable sediments, and studies seeking to quantify SGD-derived trace metal fluxes must take into account biogeochemical processes occurring in the subterranean estuary.