Freshwater lenses present valuable water resources on barrier islands. Yet, the biogeochemical processes that control the groundwater quality of these freshwater lenses and how they are affected by the prevailing groundwater dynamics is largely unexplored. In this study we investigated the biogeochemistry of a barrier island freshwater lens with a focus on understanding and quantifying organic matter mineralization, sulfur cycling, and chemical fluxes to the land-ocean interface. We analyzed a comprehensive set of hydrogeochemical field data from Spiekeroog Island (Germany), including stable sulfur isotope signatures of dissolved sulfur species, with a reactive transport modeling approach. Tritium-Helium groundwater ages were used to constrain the hydrogeochemistry as a function of residence time. Our results revealed that freshwater lenses can act as archives for anthropogenic pollution, conserving the high sulfur loads associated with historic atmospheric deposition. We observed two distinct (hydro)biogeochemical patterns, which we attribute to a heterogeneous distribution of reactive organic matter. Those patterns were well replicated by two separate reactive transport models that considered the variations in organic matter reactivity. Simulation and field results demonstrated that net sulfur cycling is dominated by microbial sulfate reduction and subsequent iron sulfide precipitation. In the absence of dissolved oxidants, we attribute the observed high stable sulfur isotope fractionation between dissolved sulfate and sulfide of up to 67‰ to low (<20 pmol mL−1 d−1) microbial sulfate reduction rates. We show that older groundwater becomes progressively enriched in ammonium and phosphate due to the mineralization of organic matter, and we speculate that lens-derived nutrient fluxes may be important for the benthic zone at local groundwater discharge sites, at least seasonally in spring and summer.