A model was used to simulate primary production of benthic microbial mats in Lake Hoare, southern Victoria Land, Antarctica, and to compare potential benthic to planktonic production. Photosynthetic and respiratory characteristics of mats from five depths in the lake were extrapolated across depth, surface area and time, to estimate whole-lake, annual net primary production. Variation in under-ice light regimes resulting from changes in ice thickness and transparency, and light extinction in the water column was examined, and an uncertainty analysis of key model parameters performed. Daily mat production estimates were 0.98–37.83 mg C m−2 d−1, depending on depth and PAR, whereas in situ production of phytoplankton averaged 15% of this. Annual patterns of mat production achieved maximum rates of 15–16 g C m−2 y−1 at 10 m depth when ≥ 5% of ambient PAR was transmitted through the ice covering the lake; observed transmittance values were usually ≤ 5%. Increasing underwater PAR had little effect above 5–7% transmittance, as photosynthesis became saturated at this level. Uncertainties in estimates of maximum photosynthetic rate (Pmax), initial slope of photosynthetic-light response (α) and maximum respiration rate (Rmax) explained 72–99% of uncertainty in model behaviour; Pmax was increasingly important at high light levels whereas α was more important at low light levels, however Rmax exerted the greatest influence under most conditions.