We investigate whether radon (222Rn) can be used as a tracer of porewater exchange in the Wadden Sea, and whether porewater exchange may drive carbon dioxide, dissolved organic carbon (DOC), total dissolved nitrogen (TDN) and alkalinity dynamics in surface waters. High temporal resolution, automated radon and pCO2 observations were made for about 24 h in five stations along a coastal transect covering upstream brackish water creeks, an enclosed shallow harbour receiving freshwater inputs from the catchment (Neuharlingersiel), and the German Wadden Sea (Spiekeroog Basin). The results revealed clear tidal trends indicative of porewater exchange in the two Wadden Sea stations. All the investigated waterways were a net source of CO2 to the atmosphere with average pCO2 ranging from about 3600 μatm in upstream creeks to about 600 μatm in the Wadden Sea. The input of upstream creek water could be detected only in the small enclosed harbour, but not in the open Wadden Sea. A radon mass balance required porewater exchange rates of about 12 cm day− 1 (equivalent to 1.1% of the tidal prism volume) in the Wadden Sea. Average alkalinity, TDN, DOC, and pCO2 values in porewater were 4.5, 18.8, 1.3, and 9.7 fold higher than in Wadden Sea surface waters. Those enrichments translated into estimated porewater-derived fluxes of 1216–1811, 34–139, 34–71, and 6–57 mmol m− 2 day− 1, respectively, depending on assumptions about porewater endmember concentrations. The porewater derived free CO2fluxes were comparable to the CO2 outgassing rates estimated for the Wadden Sea (7 to 20 mmol m− 2 day− 1). These estimates as well as significant correlations between radon and pCO2 suggest that porewater exchange was a major driver of CO2 outgassing from the Wadden Sea to the atmosphere. Radon can be a useful porewater (or groundwater) tracer in the Wadden Sea in spite of strong winds and well-mixed surface water conditions.