Monitoring marine phytoplankton is essential to understanding marine ecosystems functioning, especially in productive regions like the English Channel. This study applied high-throughput sequencing (HTS) and automated pulse shape-recording flow cytometry (PSR FCM) to investigate the spatial and seasonal variability of phytoplankton diversity in French waters of the English Channel during the ECOPEL cruises in April (spring) and July (summer) 2018. Our findings revealed significant seasonal shifts in size, structure, total red fluorescence (FLR, a biomass proxy) and community composition. PSR FCM provided high-resolution size class discrimination, revealing an increase in picoeukaryote abundance and lower FLR in summer compared to spring. HTS enabled detailed taxonomic insights: in spring, picoeukaryotes (e.g. Ostreococcus) dominated in the Western English Channel, except in Finistère/Celtic Seas, where microphytoplankton represented the majority of reads. Nanoeukaryotes ( Phaeocystis) dominated in the Eastern English Channel. In summer, diversity increased, with co-dominance of picoeukaryotes ( Micromonas, Bathycoccus, Ostreococcus), microphytoplankton ( Chaetoceros, Leptocylindrus, Guinardia) and nanoeucaryotes ( Teleaulax, Gephyrocapsa) in the Bay of Seine. Beyond a pronounced west-east disparity, the Bay of Seine exhibited remarkable taxonomic and functional diversity, with high local contribution to beta diversity (LCBD) values in both seasons. Diversity patterns were strongly influenced by temperature and nutrient concentrations (phosphate, nitrogen), with secondary influences from salinity and turbidity. PSR FCM further revealed sub-mesoscale variability in abundance and size structure, complementing the mesoscale patterns observed through HTS. This study highlights the importance of integrating both methods to capture fine-scale phytoplankton dynamics and high-resolution diversity, thereby enhancing ecosystem management, espcecially in nutrient-sensitive, productive marine regions.