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Groundwater discharge could be a major, but as yet poorly constrained, source of carbon dioxide to lakes, wetlands, rivers, estuaries, and coastal waters. We demonstrate how coupled radon (222Rn, a natural groundwater tracer) and pCO2 measurements in water can be easily performed using commercially available gas analysers. Portable, automated radon and pCO2 gas analysers were connected in series and a closed air loop was established with gas equilibration devices (GED). We experimentally assessed the advantages and disadvantages of six GED. Response times shorter than 30 min for 222Rn and 5 min for pCO2 were achieved. Field trials revealed significant positive correlations between 222Rn and pCO2 in estuarine waterways and in a mangrove tidal creek, implying that submarine groundwater discharge was a source of CO2 to surface water. The described system can provide high resolution, high precision concentrations of both radon and pCO2 with nearly no additional effort compared to measuring only one of these gases. Coupling automated 222Rn and pCO2 measurements can provide new insights into how groundwater seepage contributes to aquatic carbon budgets.