A detailed understanding of how cyanobacterial mats in the ponds of the McMurdo Ice Shelf are structured and how they derive their carbon, nitrogen and energy supply was investigated with a broad range of analytical techniques. The light capturing and UV screening properties of the mats were revealed using in situ spectro-radiometery, and by subsequent extraction, analysis and characterisation of ... the pigments by high performance liquid chromatography. 14C and 15N assays in combination with micro-electrode techniques and infra-red gas analysis were used to define the physiological/photosynthetic properties of the mats. Samples were prepared for light and transmission electron microscopy, and certain mat species were brought into culture. Important nitrogen transfers such as N-fixation and denitrification were assayed in the field, and were analysed by gas chromatography. The dissolved nutrients, NH4, NO3, urea and DRP were measured along with conductivity, pH and temperature on samples from 20 ponds. Profiles of oxygen and nutrient concentrations through the mat and in the interstitial water within the mats was investigated. Nitrogen cycling assays were conducted on a range of the mats including ammonification, NH4-, urea and NO3 uptake, denitrification, nitrification and N2 fixation. The distribution of pigments in the cyanobacterial mats and the spectral absorbance of light through the mats was analysed.