The Ward Hunt Ice Shelf (83°02′N, 74°00′W) is an ∼40 m thick ice feature that occupies a large embayment along Canada's northernmost coast. Sediments cover 10% of its surface and provide a habitat for diverse microbial communities. These assemblages form an organo-sedimentary matrix (microbial mat) composed of cold-tolerant cyanobacteria and several other types of organisms. We investigated the environmental properties (temperature, irradiance, conductivity and nutrient concentration) of the microbial mat habitat and the effect of the microbial mats on the surface topography of the ice shelf. The low albedo of microbial mats relative to the surrounding snow and ice encouraged meltwater production, thereby extending the growth season to 61 days despite only 52 days with mean temperatures above 0 °C. We found large excursions in salinity near the microbial mat during freeze-up and melt, and 54% of all ponds sampled had conductivity profiles indicating stratification. Nutrient concentrations within the microbial mats were up to two orders of magnitude higher than those found in the water column, which underscores the differences between the microbial mat microenvironment and the overall bulk properties of the cryo-ecosystem. The average ice surface ablation in the microbial mat-rich study site was 1·22 m year−1, two times higher than values measured in areas of the ice shelf where mats were less prevalent. We demonstrate with topographic surveys that the microbial mats promote differential ablation and conclude that the cohesive microbial aggregates trap and stabilize sediment, reduce albedo, and thereby influence the surface morphology of the ice shelf. Copyright © 2006 John Wiley & Sons, Ltd.