Abstract The structure and diversity of the microplankton, between 10 and 200 μm in size, were quantified during a Lagrangian SF 6 tracer experiment in the North Sea (59°N and 03°E) during June 1999. The experiment was conducted within a developing Emiliania huxleyi -rich phytoplankton bloom. Distinct thermoclines characterised the water column. The surface mixed layer extended to between 15 and 30 m, and the subsurface layer reached a depth of between 45 and 55 m. Despite the relatively high abundance of E. huxleyi ( −1 ), a diverse plankton community was observed throughout the study, with 59 autotrophic and 57 heterotrophic microplankton species being identified. Distinct spatial patterns were observed in the plankton, as smaller cells were common in the surface layer and larger species characterised the subsurface waters. The microplankton communities in the two layers, were found to be significantly different from each other. Prorocentrum minimum and P-Nitzschia ‘delicatissima ’ were the dominant microphytoplankton species in surface waters, while the larger diatom species P-Nitzschia ‘seriata’, Chaetoceros radicans , and Rhizosolenia stolterfothii were common in the subsurface layer. The microzooplankton were dominated by oligotrich ciliates and dinoflagellates, with smaller forms such as Strombidium spp., Diplopsalis sp., and Protoperidinium cf. cerasus characterising surface waters, and larger species, Strombidium ovale, Gyrodinium fusiforme , and Gyrodinium sp. dominating the subsurface layer. Significant temporal changes were observed in the composition of the surface-layer microplankton community, as well as in the structure of the subsurface microzooplankton. Measures of diversity indicated that there were significant differences in the microphytoplankton between surface and subsurface waters and that the temporal changes in the surface layer were also significant. These changes coincided with an increase in microzooplankton grazing pressure and a shift in the species composition of the mesozooplankton. Coupled with observations that regenerated nutrients provided an important nitrogen supply for phytoplankton growth during this study, our data suggest that ‘top-down’ control played an important role in enhancing diversity and determining the structure of the plankton in the stratified northern North Sea, during the summer. The significant changes observed in the microplankton during this study, occurred over a relatively short period of ca. 9 days and emphasise the importance of understanding short-term fluctuations in order to make accurate longer-term predictions.