1.The lakes and ponds in the Larsemann Hills and Bolingen Islands (East-Antarctica) are characterised by cyanobacteria-dominated, benthic microbial mat communities. A 56-lake dataset representing the limnological diversity among the more than 150 lakes and ponds in the region was developed to identify the nature and quantify the effects of the abiotic conditions structuring the cyanobacterial and diatom communities. 2.Limnological diversity in the lakes of the Larsemann Hills and Bolingen Islands is primarily determined by salinity and salinity related variables (concentrations of major ions, conductivity and alkalinity), and variation in lake morphometry (depth, catchment and lake area). Low pigment, phosphate and nitrogen concentrations, and DOC and TOC levels in the water column of most lakes underscore the ecological success of benthic microbial mats in this region. 3.Benthic communities consisted of prostrate, sometimes finely laminated mats, flake mats, epilithic and interstitial microbial mats. Mat physiognomy and chlorophyll/carotenoid ratios were strongly related to lake depth, but not to salinity. 4.Morphological-taxonomic analyses revealed the presence of 27 diatom morphospecies and 34 cyanobacterial morphotypes. Mats of shallow lakes (interstitial and flake mats) and those of deeper lakes (prostrate mats) were characterized by different dominant cyanobacterial morphotypes. No relationship was found between the distribution of these morphotypes and salinity. In contrast, variation in diatom species composition was strongly related to both lake depth and salinity. Shallow ponds are mainly characterised by aerial diatoms (e.g. Diadesmis cf. perpusilla and Hantzschia spp.). In deep lakes, communities are dominated by Psammothidium abundans and Stauroforma inermis. Lakes with conductivities higher than 1.5 mS/cm become susceptible to freezing out of salts and hence pronounced salinity fluctuations. In these lakes Psammothidium abundans and Stauroforma inermis are replaced by Amphora veneta. Stomatocysts were only important in shallow freshwater lakes. 5.Ice cover influences microbial mat structure and composition both directly by physical disturbance in shallow lakes and by influencing light availability in deeper lakes, as well as indirectly by generating salinity increases and promoting the development of seasonal anoxia. 6.The relationship between diatom species composition and salinity and depth is statistically significant. Transfer functions based on these data can therefore be used in paleolimnological reconstruction to infer changes in the precipitation-evaporation balance in continental Antarctic lakes. These data were also collected under the auspices of the Micromat Project, Biodiversity of Microbial mats in Antarctica (see the URL below). The fields in this dataset are: Lake Lake number Location Latitude Longitude Altitude (m) Area (ha) Catchment (ha) Depth (m) Distance from Plateau Distance from Sea Geology Substrate Presence Absence pH Alkalinity Nitrate Nitrite Ammonium Silicate Phosphate Oxygen Salinity Turbidity Conductivity Sodium Potassium Calcium Magnesium Chlorine Sulphur Bicarbonate Hydrocarbonate Total Organic Carbon Dissolved Organic Carbon