Automated in situ flow cytometry, high-pressure liquid chromatography (HPLC), optical microscopy and fluorometry were combined to monitor phytoplankton over two summer periods (2005 and 2006). In 2006, temperature was higher and nutrients lower than in 2005, generating differences in the phytoplankton assemblages (i.e., abundance and structure). Pigment-size classes based on daily HPLC analysis provided evidence for higher proportions of picoplankton and nanoplankton with higher biomass in 2005 and a dominance of microplankton with lower biomass in 2006, the latter with lower specific diversity, as evidenced by weekly microscopy analyses. Total chlorophyll a estimations from fluorometry measurements recorded every 30 min were higher in 2005 than in 2006, as for the HPLC chlorophyll a concentrations. An automated in situ flow cytometer (Thyssen et al., J Plankton Res 30(9):1027-1040, 2008a) sampled seawater every 30 min. Data analysis yielded the resolution of seven clusters based on light scatter and fluorescence. In 2006, an increase in abundance of the largest cells was observed, confirming pigment and microscopy data. The results suggest that the ecosystem was on a constant renewing process in summer 2005 due to a strong wind event and on a highly productive and recycling way in summer 2006 due to stratification of the upper water layer. Automated submersible flow cytometry confirms to be a powerful tool providing high-resolution data by monitoring phytoplankton at the single cell level. This technology gives access to the shape of the light scatter and fluorescence signals generated by each cell passing through a laser beam and that are linked to size, structure and pigment content of the target cell. When combined with conventional techniques, it further improves our understanding of phytoplankton assemblages.