Abstract In September 1999, two short-term moorings with cylindrical sediment traps were deployed to collect sinking particles in bottom waters off the Ob and Yenisei river mouths. Samples were studied for their bulk composition, pigments, phytoplankton, microzooplankton, faecal material, amino acids, hexosamines, fatty acids and sterols, and compared to suspended matter and surface sediments in order to obtain information about the nature and cycling of particulate matter in the water column. Plankton counts and organic biogeochemical analyses of sinking particles of the Ob trapshow that an ongoing plankton bloom has been sampled. During the twelve days of sampling we could observe a change of species distribution. Diatoms and copepods have been the dominating phyto- and, respectively, zooplankters during the first phase of the trap deployment. Subsequently, other phytoplankters such as flagellates have become more important, and protozoa and larvaceans have become the dominating zooplankters. Biomarkers and amino acids indicate that the system has shifted from a phytoplankton to a more zooplankton dominated system in the second half of trap deployment. This may be an indication of (i) a propagating plankton bloom with its shift from primary to secondary producers or (ii) the intrusion of different species related to lateral transport in a hydrodynamically active environment. The Ob trap collected fresh surface-derived particulate matter, whereas particles from the Yenisei trap were more degraded and resembled deep water suspension. This material may partly have been derived from resuspended sediments.