Abstract Heterotrophic activity and related measures of pelagic microorganisms were studied in the Northeast Water Polynya, (NEWP 77–82°N, 10–15°W) in 1993 during a FS Polarstern cruise. A bottom water sampler (BWS), which enabled collection of distinct 12 1 water samples at variable heights above the seabed, was used to study the distribution of various biological parameters with high vertical resolution in the benthic boundary layer (BBL). Samples were taken in the water column from varying depths in the intermediate water column (IWC) down to 5 m above bottom using a CTD as well as at 40, 20, 12 and 7 cm above the sea bed using the bottom water sampler. Total suspended matter, particulate organic carbon and nitrogen (POC, PON), chlorophyll a equivalents (chl. a equiv.), bacterial abundance and size distribution and microbial activity were determined in each of the samples. Most of the deep samples (IWC and BBL, maximum water depth 479 m) came from warmer Atlantic influenced water that fills a circular trough system on the northeast Greenland shelf. In general the activity of the microbial community, cell-specific activity and concentrations of POC and chl. a equiv. were significantly higher in the BBL compared to the IWC. Microbial activity appeared to be independent of the quantity of available POC, indicating the nutritional importance of dissolved organic matter for microorganisms. The spatial distribution of particle composition and microbial activity in the BBL was strongly determined by the anticyclonic current pattern and the spatial pattern of primary production in the polynya. Close coupling of biological processes in the surface waters and particle composition and microbial activity in the BBL were found below areas of fluctuating ice cover and above 260 m water depth in the northeastern Westwind Trough. Highest microbial activity occurred in the heavily ice covered Belgica Trough, although only remnants of freshly produced organic matter were present. In the open polynya near-bottom particle properties were mainly determined by lateral advection. The benthic boundary layer is shown to represent a distinct environment, with small scale vertical distribution of particle properties and stimulated microbial activity, indicating that rapid modification of organic matter occurs in the BBL before its final incorporation into the sediment.