Measurement of pCO2 in highly dynamic coastal zones such as the southern Baltic Sea presents many challenges. In this study, we designed a system to measure pCO2 and then validated it in a series of laboratory and seagoing tests. The fast response time of the system was shown to provide a better resolution of CO2 system gradients. In the open waters of the Baltic Sea, the accuracy of the pCO2 measurements (±1.3 µatm) met the requirements of the ICOS (±2.0 µatm). In the coastal zone, there was less consistency between pCO2, DIC and pH measurements, suggesting the need to redefine the quality assurance and control requirements for the measurement of pCO2 in dynamic regions.