LAUSR

Anthropogenic production of greenhouse gases (GHGs) has intensified the need to constrain estimates of natural atmospheric sources from both terrestrial and marine systems. Estuaries are known sources of carbon dioxide (CO2) and methane (CH4); however, less is known about GHG dynamics in subterranean estuaries (STEs). We evaluate CO2 and CH4 dynamics in three proximal STEs bordering Indian River Lagoon, Florida, where groundwater flows through siliciclastic sediments with minor carbonate mineral contents. Although the three STEs have similar mineralogical and flow characteristics, CO2 and CH4 concentrations vary by orders of magnitude. Nonconservative mixing of both gases is observed, and CH4 is generally produced while CO2 is sequestered. The extent of methanogenesis is linked to the redox potential of inflowing groundwaters, as well as degree of CH4 oxidation, which results mostly from anaerobic oxidation of methane. Methane concentrations vary by orders of magnitude, and stable isotopic signatures suggest differences in the microbial production pathway between sites. CO2 is sequestered due to the production of alkalinity relative to dissolved inorganic carbon, which occurs both through rapid CaCO3 dissolution at the shoreline as low‐pH groundwater from the siliciclastic aquifer interacts with carbonate minerals in lagoon sediments, as well as redox reactions, particularly sulfate reduction and denitrification. These results demonstrate a high variability in CO2 and CH4 concentrations, and thus fluxes, even among geographically constrained and hydrogeologically similar STEs. Although STEs are sources of both CO2 and CH4 to surface waters, the variability of production and consumption complicates global estimates of GHG fluxes from STEs.