This dataset includes stable isotope (δ¹³C and δ¹⁵N) measurements of four ground-dwelling carabid beetle species, along with baseline samples from plants, soil and invertebrate bycatch collected in freshwater and saltwater marshes along the Elbe estuary in northern Germany. The data support analyses of resource integration and transfer within estuarine ecotones on biogeochemical processes and consumer-mediated carbon fluxes. The overarching goal is to understand how carabid beetle assemblages contribute to ecosystem connectivity, functioning, and carbon cycling within these ecotonal systems. This research is part of the graduate school program “Biota-Mediated Effects on Carbon Cycling in Estuaries”.