The contribution of submarine groundwater discharge (SGD) to oceanic metal budgets is only beginning to be explored. Here, we demonstrate that biogeochemical processes in a northern Florida subterranean estuary (STE) significantly alter U and Ba concentrations entering the coastal ocean via SGD. Tidal pumping controlled the distribution of dissolved metals in shallow beach groundwater. Hourly observations of intertidal groundwaters revealed high U and low Ba concentrations at high tide as a result of seawater infiltration into the coastal aquifer. During ebb tide, U decreased and Ba increased due to freshwater dilution and, more importantly, biogeochemical reactions that removed U and added Ba to solution. U removal was apparently a result of precipitation following the reduction of U(VI) to U(IV). A significant correlation between Ba and dissolved organic carbon (DOC) in shallow beach groundwaters implied a common source, likely the mineralization of marine particulate organic matter driven into the beach face by tidal pumping. In deeper groundwaters, where the labile organic matter had been depleted, Ba correlated with Mn. We estimate that net SGD fluxes were − 163 and + 1660 μmol m− 1 d− 1 for U and Ba, respectively (or − 1 and + 8 μmol m− 2 d− 1 if a 200-m wide seepage area is considered). Our results support the emerging concept that subterranean estuaries are natural biogeochemical reactors where metal concentrations are altered relative to conservative mixing between terrestrial and marine endmembers. These deviations from conservative mixing significantly influence SGD-derived trace metal fluxes.