A flow injection analyser coupled with a gas diffusion membrane and a conductometric microdetector was adapted for the field analysis of natural concentrations of free dissolved CO2 and dissolved inorganic carbon in natural waters and used in a number of field campaigns for marine water monitoring. The dissolved gaseous CO2 presents naturally, or that generated by acidification of the sample, is separated by diffusion using a hydrophobic semipermeable gas porous membrane, and the permeating gas is incorporated into a stream of deionised water and measured by means of an electrical conductometric microdetector. In order to make the system suitable and easy to use for in-field measurements aboard oceanographic ships, the single components of the analyser were compacted into a robust and easy to use system. The calibration of the system is carried out by using standard solutions of potassium bicarbonate at two concentration ranges. Calibration and sample measurements are carried out inside a temperature-constant chamber at 25 °C and in an inert atmosphere (N2). The detection and quantification limits of the method, evaluated as 3 and 10 times the standard deviation of a series of measurements of the matrix solution were 2.9 and 9.6 μmol/kg of CO2, respectively. Data quality for dissolved inorganic carbon was checked with replicate measurements of a certified reference material (A. Dickson, Scripps Institution of Oceanography, University of California, San Diego), both accuracy and repeatability were -3.3% and 10%, respectively. Optimization, performance qualification of the system and its application in various natural water samples are reported and discussed. In the future, the calibration step will be operated automatically in order to improve the analytical performance and the applicability will be increased in the course of experimental surveys carried out both in marine and freshwater ecosystems. Considering the present stage of development of the method, it can only be applied for studying of the carbon cycle in oxic environments.