Automated pulse shape-recording flow cytometry was applied to address phytoplankton spatial distribution, at high frequency, in stratified and well mixed water masses in the Western and Central English Channel during the summer-fall transition. Cytometric pulse shapes derived from optical features of single cells allowed the characterization of eight phytoplankton groups. Abundance and total red fluorescence (chlorophyll a autofluorescence) per group were used to define six phytoplankton communities. Their distribution revealed high spatial heterogeneity. Abundance presented a longitudinal gradient for six over the eight groups and succession of brutal shifts along the cruise. Maximum values were often located near the Ushant front in the Western English Channel. A latitudinal gradient characterized the Central English Channel waters under the influence of the Seine estuary. Picophytoplankton (Synechococcus-like cells and picoeukaryotes) represented up to 96% of total abundance and half of the total red fluorescence of the communities near the main front and the Bay of Seine, whereas nanoeukaryotes and microphytoplankton, represented only 4% and less than 1% respectively of total abundance. Both nanoeukaryotes and microphytoplankton dominated the total red fluorescence of the communities of the Central English Channel. The study of traits within each group showed a high variability of traits between communities. The comparison between traits showed that they were independent from each other for some groups (size and red fluorescence per cell for PicoHighFLR and Coccolithophore-like cells; orange and red fluorescence for all the groups), whereas they were dependent for other groups (red fluorescence per cell was dependent of size for picophytoplankton, NanoLowFLR, NanoHighFLR, Cryptophyte-like cells and Microphytoplankton). Variance partitioning revealed that the environmental parameters (temperature, salinity and turbidity) accounted less than spatial descriptors (physical and biological processes) in shaping the communities. Hydrological structures (frontal structures, eddies and tidal streams) were responsible for patches of phytoplankton and defined the structure at the sub-mesoscale (1 – 10 km) in this area.