The distribution of bacteriohopanepolyols (BHPs) and intact polar membrane lipids (IPLs) was studied in different soil profiles and in fluvial and marine sediments along the pathway of transport in a small catchment in the high Arctic at Ny-Ålesund, Svalbard (79°N, 12°E). Both groups of cellular membrane lipids have been used as biomarkers for determining major microbial groups and biogeochemical processes in natural environments. Little is known about their distribution and usefulness as environmental markers in the Arctic. In this study, we show that both membrane lipid groups are variably distributed in the drainage area of the Brøggerbreen Glacier, with highest abundance and diversity in the organic mat overlying the mineral soils, as well as in mossy surface soil. The BHP and IPL composition and abundance both indicate a larger community of phototrophic bacteria in the organic mats and fluvial sediments. The greater diversity and abundance of BHPs relative to IPLs in sub-soils, including probable markers for cyanobacteria, suggest a greater resistance to degradation. In contrast, IPL concentration decreased strongly with soil depth, pointing to their rapid degradation. Bacterial IPLs are thus thought to reflect more reliably the biomass of viable phototrophic bacteria. The high concentrations of proposed soil marker BHPs, adenosylhopane and related structures vs. published results and their relative increase with soil depth suggest better preservation and more effective accumulation of the compounds at low temperature. © 2010 Elsevier Ltd.