Environmental conditions, both external to and within three shallow ponds of the McMurdo Ice Shelf, were measured over an annual cycle between January 1997 and January 1998. We combined this with a study of the response of the benthic microbial mat communities to the transition from summer conditions to winter freezing. Over the study period air temperature was above 0°C for a few days during summer. At this time pond temperatures were higher than air temperatures, with evidence of thermo-haline stratification. The shallow areas of ponds froze between late February and early March, with bottom waters in the deepest pond remaining unfrozen until early June. Minimum winter air temperatures were below −40°C. There was little evidence of freezing point depression due to freeze-concentration of solutes, except at the very bottom of ponds. In the most conductive pond investigated, the temperature of basal freezing was −4°C and conductivity did not exceed approximately 60 mS cm−1 immediately prior to freezing. Microbial mats remained photosynthetically active up to conductivities between 40 and 80 mS cm−1, and were able to acclimate to lowered irradiance associated with ice formation. Although photosynthesis and respiration were reduced by 11% and 40% respectively at temperatures of −2°C compared to 1°C, there was no difference in light harvesting efficiency. Results from this study suggest that light limitation of photosynthesis, or freezing, determine the growth season for the microbial communities, depending on depth.