The carbon dioxide flux at the air/water interface in lakes was calculated after the determination of H2CO3* (free CO2) and atmospheric CO2 using flow injection analysis (FIA) coupled to a conductometric detector. The method is based on the diffusion of CO2 through a hydrophobic membrane into a flow of deionized water, generating a gradient of conductivity proportional to the concentration of CO2 in the sample. Using one experimental set-up, the speciation of the inorganic carbon (H2CO3* and dissolved inorganic carbon) was accomplished by simply adjusting the sample pH. The determination of CO2 in the atmosphere was carried out by direct injection of the gaseous samples. The FIA apparatus was taken into the field and CO2 fluxes were evaluated in several Brazilian lakes. In these lakes, representing different eutrophic stages, the CO2 flux varied from -242 (invasive) up to 3227 (evasive) mumol CO2 m-2 h-1.