A mathematical model was used to simulate interannual patterns of biomass accumulation within benthic microbial mats of two Antarctic lakes. Lakes Hoare and Vanda are in the Dry Valley region of Southern Victoria Land, and are both perennially ice covered. The model combines experimentally derived observations of light/photosynthesis relationships and rates of respiration of mats from a range of depths in these lakes, with data on incident radiation and the optical properties of the ice and water column. The model was used to estimate daily and annual production and, using measured carbon content, the potential vertical accumulation of the mats over a year. An annual pattern of photosynthesis was predicted for both lakes, with net production from October to February and net respiration at other times. Predicted rates and patterns of net photosynthesis were remarkably similar in the two lakes, despite differences in light climate: the ice of Lake Hoare transmits 1–4% incident radiation, whereas that of Lake Vanda transmits up to 20%. Maximum daily rates of 15–20 μg carbon cm−2 were predicted to occur at approximately 10 m depth in both lakes. Maximum annual rates of carbon fixation (at 10–12 m depth) in both lakes were c. 1.2 mg carbon cm−2 equating to approximately 0.1–4 mm vertical accumulation of mat each year. Experimental studies of microbial mats in the lakes revealed horizontal laminations of similar thickness to model estimates, supporting the hypothesis that these were annual layers. Differences between model estimates and observations were found in deeper water in Lake Vanda, where considerably more material accumulated than was predicted.