The Pomeranian Bight (southern Baltic Sea) is a mixing zone between waters of the Baltic Proper and the river Oder, which drains a densely populated and highly industrialised catchment of central Europe. The bight is a nondepositional area, and all material produced in its water column, from erosion of strata at the seafloor and cliffs, and delivered by rivers, is transported near the seafloor to the depositional areas of the Arkona, Bornholm and Gdansk basins. In this contribution, we assess the origin, transformation and mass fluxes of material through the bight based on an integrated field study conducted in the period 1996–1998. The transport mechanism is by wave- and current-induced resuspension and settling cycles, which effectively enrich organic-rich material and associated substances (organic pollutants, heavy metals) in deeper water; the estimated transport time is less than 6 months. The phases in which the material is transported are suspended matter in the water column, a particle- and aggregate-rich benthic boundary layer of <1 m above the seafloor and a layer of fluffy material fed from the two other sources that covers the sandy near-shore sediments as a discrete phase; it collects up to 130 g m −2 of particulate material after quiescent periods lasting several days. It is easily resuspended at shear velocities around 5 cm s −1 and is recycled into the suspended matter and benthic boundary layer pools of material. In deeper waters (>20 m water depth), the fluffy layer is not readily distinguished from the underlying soft, organic-rich sediment and the change in physical and chemical properties is gradual. The organic matter passing through the coastal zone in the southern Baltic is unaffected by biological or chemical modifications in composition. We find no evidence for a preferential removal of nitrogen or phosphorus, even if the speciation of phosphorus changes from biological compounds to minerals. The compositional changes which we see, i.e., in the nitrogen isotopic composition and in trace metal concentrations, are mainly caused by dilution of the river signal. In the case of polyaromatic hydrocarbons (PAH), different solubilities and compound stabilities affect the concentrations as well and result in the enhanced accumulation of stable compounds in Arkona Basin. Seasonal changes are pronounced in the amount of freshly produced biomass, as is seen in phytoplankton pigments and their degradation products, but significant amounts of fresh biomass are swept out of the bay and supply the Arkona Basin benthic community with additional nutrition. An imbalance in carbon import and export emerges from mass balance calculations: 50,000 t of organic carbon per year may be exported, which cannot be accounted for by known sources in the river or the bight. We may exclude erosion of early Holocene peat exposures at the seafloor as a possible source, but cannot exclude either errors in our export estimate, or large-scale erosion of other organic carbon pools, for example, the stock of seaweed and its substrate in the Greifswalder Bodden.