Abstract The carbonate system of marine-derived brines and its stable isotope composition are described. The study was conducted in the evaporation pans of a solar salt production plant (simulated sabkha environment) in which ca. 50% of the evaporation area is dominated by microbial mat communities (MMC). MMC are the modern equivalents of fossil stromatolites as old as Early Archean; hence, investigation of the impact of their photosynthetic activity on the carbonate system in the aquatic environment is relevant to the research of the ancient carbon cycle. Total dissolved CO 2 (C T) decreases by ca. 50% of its original value as brine concentration increases from 1.5 to 4 times “mean” seawater. Roughly 70% of the original total alkalinity is precipitated as calcium carbonate at this salinity range. The relations between total alkalinity A T and C T (both normalized to salinity) suggest that the brines are depleted in C T by up to 50% with respect to equilibrium with atmospheric CO 2. This large C T deficit is driven by the intense photosynthetic activity of the MMC. Considerable depletion in 13C was observed despite the photosynthetic activity which normally causes a 13C enrichment in C T. δ 13 C T values down to −9%. were observed in brine concentration range of 2 to 6 times “mean” seawater. We suggest that the C T deficit is causing an invasion of isotopically light CO 2 from the atmosphere into the brine driven by chemical enhancement similar to that observed by Baertschi (1952) and Craig (1953, 1954) in alkaline solutions. Mass balance calculation for one of the evaporation pans is compatible with the suggested mechanism of chemically enhanced atmospheric invasion of 12C enriched CO 2. This kinetic isotope fractionation may serve as an alternative explanation to that of fresh water runoff for some negative δ 13 C values of laminated carbonates from evaporitic sections found in the geological record. In addition, at least part of the large scatter observed in the δ 13 C vs. age curve for carbonates and organic matter from Precambrian stromatolitic environments may be explained by this mechanism rather than by late metamorphism and maturation processes.