AbstractFrom March 2002 to until April 2003 we investigated the seasonal nutrient and phytoplankton dynamics in the central Bornholm Basin (Baltic Sea) within the framework of the German GLOBEC Project. We choose a nested approach consisting of vertical fluorescence profiles, phytoplankton counts and nutrient analyses. The Fluoroprobe (MultiProbe, BBE Moldaenke) is capable of distinguishing four algal groups (Cryptophyceae, Cyanophyceae, Chlorophyceae, Bacillariophyceae + Dinophyceae). Winter nutrient concentrations were about 5 μM NO3 and 0.5 μM PO4 in the central Basin. The spring phytoplankton bloom was dominated by the diatom Skeletonema sp. and reached a maximum of about 270 μg C/l before the onset of the seasonal stratification. Protozooplankton was dominated by the Mesodinium rubrum (a phototrophic ciliate = Myrionecta rubra) and reached a maximum biomass of about 200–300 μg C/l about 2 weeks after the demise of the diatom spring bloom. During summer, the water column was stratified and a subsurface maximum developed near the thermocline consisting of Bacillariophyceae, Cryptophycea and other phototrophic flagellates. Phytoplankton and protozooplankton biomass was generally low. Nutrient concentrations point towards a nitrogen limitation during this period. The stratification period ended during September and surface nutrient concentrations increased again. Protozooplankton reached a second maximum during September. With the Fluoroprobe small scale structures in the plankton community could be detected like a subsurface Cryptophyceae maximum near the thermocline that however, could not be confirmed by cell counts. The chlorophyll a estimate of the Fluoroprobe was in good agreement with the phytoplankton biomass estimated from counts. We conclude that only by combining modern sensing technology with microscopy, the small-scale dynamics and taxonomic spectrum of the plankton can be fully captured.