A method of measuring CO2gas exchange (caused, for example, by microalgal photosynthesis on emersed tidal mudflats) using open flow IR gas analyzers is described. The analyzers are integrated in a conventional portable photosynthesis system (LI-6400, LI-COR, Nebraska, USA), which allows manipulation and automatic recording of environmental parameters at the field site. Special bottomless measuring chambers are placed directly on the surface sediment. Measurements are performed under natural light conditions and ambient CO2concentrations, as well as under different CO2concentrations in air, and various PAR radiation levels produced by a LED light source built into one of the measurement chambers. First results from tidal channel banks in a north Brazilian mangrove system at Bragança (Pará, Brazil) under controlled conditions show a marked response of CO2assimilation to CO2concentration and to irradiance. Photosynthesis at 100 μmol mol−1CO2in air in one sample of a well-developed algal mat was saturated at 309 μmol photons m−2s−1, but increased with increasing ambient CO2concentrations (350 and 1000 μmol mol−1CO2) in the measuring chamber. Net CO2assimilation was 0.8 μmol CO2 m−2s−1at 100 μmol mol−1CO2, 5.9 μmol CO2m−2s−1at 350 μmol mol−1CO2and 9.8 μmol CO2m−2s−1at 1000 μmol mol−1CO2. Compensation irradiance decreased and apparent photon yield increased with ambient CO2concentration. Measurements under natural conditions resulted in a quick response of CO2exchange rates when light conditions changed. We recommend the measuring system for rapid estimations of benthic primary production and as a valuable field research tool in connection with certain ecophysiological aspects under changing environmental conditions.