Although the majority of coastal sediments consist of sandy material, in some areas marine ingression caused the submergence of terrestrial carbon-rich peat soils. This affects the coastal carbon balance, as peat represents a potential carbon source. We performed a column experiment to better understand the coupled flow and biogeochemical processes governing carbon transformations in submerged peat under coastal fresh groundwater (GW) discharge and brackish water intrusion. The columns contained naturally layered sediments with and without peat (organic carbon content in peat 39 AE 14 wt%), alternately supplied with oxygen-rich brackish water from above and oxygen-poor, low-saline GW from below. The low-saline GW discharge through the peat significantly increased the release and ascent of dissolved organic carbon (DOC) from the peat (δ 13 C DOC − 26.9‰ to − 27.7‰), which was accompanied by the production of dissolved inorganic carbon (DIC) and emission of carbon dioxide (CO 2 ), implying DOC mineralization. Oxygen respiration, sulfate (SO 2 − 4 ) reduction, and methane (CH 4 ) formation were differently pronounced in the sediments and were accompanied with higher microbial abundances in peat compared to sand with SO 2 − 4 -reducing bacteria clearly dominating methanogens. With decreasing salinity and SO 2− 4 concentrations, CH 4 emission rates increased from 16.5 to 77.3 μmol m −2 d −1 during a 14-day, low-saline GW discharge phase. In contrast, oxygenated brackish water intrusion resulted in lower DOC and DIC pore water concentrations and significantly lower CH 4 and CO 2 emissions. Our study illustrates the strong dependence of carbon cycling in shallow coastal areas with submerged peat deposits on the flow and mixing dynamics within the subterranean estuary.Sea-level rise is considered to be one of the main impacts of climate change, with significant implications for mineralization processes within coastal wetlands (Nicholls and Cazenave 2010;Neubauer 2013;Plag and Jules-Plag 2013;Hahn et al. 2015;Wang et al. 2016). In particular, coastline retreat may cause submergence of terrestrial, organic carbonrich peat sediments. The extent of submarine peat and the process-based impacts on carbon transformation processes and exchange of trace gases in shallow coastal areas have been poorly addressed. Sediment column experiments are powerful tools to investigate subprocesses and simulate changes of environmental and hydrological conditions. These changes are accelerated by land subsidence of peatland caused by their large-scale drainage for agricultural use. Land subsidence alters the hydrologic exchange processes across the land-sea interface (Nieuwenhuis and Schokking 1997;Hooijer et al. 2012) including changes in surficial runoff, subsurface mixing, and submarine groundwater discharge (SGD).SGD is comprised of all flow of water from the seabed into the coastal ocean, predominantly recirculated seawater (SW), driven by wave action, density gradients, and sea-level dynamics (Robinson et al.