We investigated the temporal dynamics and trophic role of different nanoflagellates in surface waters of the Gulf of Gdańsk (Baltic Sea) between April and October 2007. Two 18S rRNA gene clone libraries were constructed from samples collected in spring and summer, and weekly changes in the abundances of five phylogenetic groups were studied by fluorescence in situ hybridization with newly designed probes. Stramenopiles affiliated with MAST-6 and Pedinellales were most numerous in spring but rare in summer. Both groups formed short-lived blooms during a sudden drop of salinity due to riverine influx (from 7.1 to 6.2 practical salinity units). The analysis of food vacuole content suggested that MAST-6 nanoflagellates were herbivorous, whereas bacterivory was found both in plastidic and aplastidic pedinellid populations. Members of an uncultured lineage of aplastidic, bacterivorous cercozoans distantly related to Ebria tripartita were more abundant in summer when water temperatures exceeded 17°C. Multicellular trophonts and/or free-living single cell stages of two lineages of Group 1 parasitic Syndiniales (alveolates) were present in spring and early summer. One of these alveolate populations repeatedly peaked before and after the freshwater influx, but was conspicuously absent throughout the period of decreased salinity. Our results indicate that nanoflagellate populations in coastal surface waters may form short-lived blooms that can only be detected by high-frequency sampling, and that may be related both to seasonal development and to sporadic (e.g. mixing) events. In view of their trophic diversity we moreover suggest that nanoflagellates in eutrophic coastal waters should not be regarded as a single functional unit.