As transitional environments between land and sea, estuaries are among the most diverse and productive environments and represent an important component of the global C cycle. Estuaries are characterized by high temporal dynamics due to variable external forcing (e.g. freshwater discharge, ocean currents, tidal energy) and by pronounced spatial gradients in, e.g., salinity, hydrodynamics, and oxygen availability (estuarine gradients). Along estuarine gradients, ecosystems of intertidal areas (vegetated tidal marshes, intertidal flats with microphytobenthos communities) and subtidal channels (benthic and pelagic ecosystems) are tightly linked and produce, transport and process large amounts of terrestrial and aquatic organic matter. Although recent research has exemplified the potential high relevance of plant- and phytoplankton-microbe interactions and herbivory as controls of C fluxes in tidal marshes and estuarine channels, key processes governing estuarine C cycling are still poorly understood. The RTG 2530 aims to systematically analyze biota-mediated effects on estuarine C cycling considering estuarine gradients and dynamics, linkages among estuarine ecosystems, and effects of global change.