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We present the results of multiparametric observations designed to follow the phytoplankton dynamics and interrelated physical, chemical and biological processes in the Gulf of Finland (Baltic Sea). Data were acquired by an autonomous moored water column profiler, an acoustic Doppler current profiler, a flow-through system installed aboard a ferry and by profiling and discrete water sampling aboard research vessels in July and August 2009. The main aim of the study was to investigate the processes responsible for the formation and maintenance of sub-surface maxima of phytoplankton biomass. We suggest that the environmental conditions caused by the prevailing atmospheric and oceanographic forcing (wind; vertical stratification; basin-wide, mesoscale and sub-mesoscale processes) are preferred by certain species/taxonomic groups and explain the migration patterns of phytoplankton. Nocturnal downward migration of phytoplankton with a swimming speed up to 1.6 m h occurred when the community was dominated by the dinoflagellate Heterocapsa triquetra. The observed splitting of the population into two vertically separated biomass maxima suggests that the H. triquetra cells, which reached the sub-surface layers with high nutrient concentrations, experienced bi-diurnal or asynchronous (when swimming upwards) vertical migration. The most intense sub-surface biomass maxima, on some occasions with the biomass much higher than that in the surface layer, were detected in connection to the sub-mesoscale intrusions below the depth of the strongest vertical density gradient. [ABSTRACT FROM AUTHOR]