Seasonal studies of the vertical flux of organic matter, nutrients, and phytoplankton were carried out in the coastal area of the western Gulf of Finland, the Baltic Sea. The objective was to study the factors that influence the settling loss from the pelagic system, and to assess the magnitude of the seasonal export production in relation to the potential nutrient supply from the external and internal sources, and to the total primary production of the pelagic ecosystem. Moreover, large-scale mesocosm experiments were carried out in order to study the effect of resource supply (bottom-up) and predation control (top-down) on nutrient dynamics and sinking loss from the pelagic system in summer. Methodological aspects of sediment trap measurements, such as sample representativeness, preservation, contamination by planktonic micro-swimmers, and resuspension were also studied, and their effects on sedimentation measurements were assessed. Phytoplankton species composition and life strategies, such as resting stage formation and vertical migration, influence sedimentation rates and the fate of the algal bloom biomass. Diatoms have high settling rates, thus being the major vehicle in the downward transport of organic matter. Vegetative cells of vernal dinoflagellates have low sinking loss rates resulting in prolonged retention and lower sedimentary loss from the dinoflagellate-dominated spring bloom. Sinking losses from the cyanobacterial blooms, which are recurrent phenomena during late summer, are generally low. Thus they are mainly disintegrated and remineralized in the water column, and have minor contribution on the organic matter transport to sediments. Considerable interannual variability in the pelagic retention of nutrients and in the seasonal export flux, in relation to the total primary production, may occur, depending on hydrodynamic fluctuations. The more effective sedimentation and heterotrophic assimilation of nitrogen, in comparison to phosphorus, promote nitrogen limitation in the pelagic new production systems. Thus, a decrease in the external nitrogen loading is required to abate eutrophication and to improve the quality of the coastal waters in the northern Baltic Sea.