Fine-scale physical structures and ocean dynamics strongly influence and regulate biogeochemical and ecological processes. These processes are particularly challenging to describe and understand because of their ephemeral nature. The OSCAHR (Observing Submesoscale Coupling At High Resolution) campaign has been conducted in fall 2015 in which, a fine-scale structure in the North Western Mediterranean Ligurian subbasin was pre-identified using both satellite and numerical modeling data. Along the ship track, various variables were measured at the surface (temperature, salinity, chlorophyll-a and nutrients concentrations) with ADCP current velocity. We also deployed a new model of CytoSense automated flow cytometer (AFCM) optimized for small and dim cells, for near real-time characterization of surface phytoplankton community structure of surface waters with a spatial resolution of few km and a hourly temporal resolution. For the first time with this type of AFCM we were able to resolve Prochlorococcus and Synechococcus picocyanobacteria. The vertical physical dynamics and biogeochemical properties of the studied area were investigated by continuous high resolution CTD profiles thanks to a moving vessel profiler (MVP) during the vessel underway associated to a 1-m vertical resolution pumping system deployed during fixed stations. The observed fine-scale feature presented a cyclonic structure with a relatively cold core surrounded by warmer waters. Surface waters were totally depleted in nitrate and phosphate. In addition to the doming of the isopycnals by the cyclonic circulation, an intense wind event induced Ekman pumping. The upwelled subsurface cold nutrient-rich water fertilized surface waters, characterized by an increase in Chl-a concentration. Prochlorococcus, pico- and nano-eukaryotes were more abundant in cold core waters while Synechococcus dominated in warm boundary waters. Nanoeukaryote were the main contributors (> 50 %) in terms of pigment content (FLR) and biomass. Biological observations based on the mean cell's red fluorescence recorded by AFCM combined with physical properties of surface waters suggest a distinct origin for two warm boundary waters. Finally, the application of a matrix growth population model based on high-frequency AFCM measurements in warm boundary surface waters provides estimates of in-situ growth rate and apparent net primary production for Prochlorococcus (μ = 0.21 d−1, NPP = 0.11 mgC m−3 d−1) and Synechococcus (μ = 0.72 d−1, NPP = 2.68 mgC m−3 d−1), which corroborate their opposite surface distribution pattern. The innovative adaptive strategy applied during OSCAHR with a combination of several multidisciplinary and complementary approaches involving high-resolution in-situ observations and sampling, remote-sensing and model simulations provided a deeper understanding of the marine biogeochemical dynamics through the first trophic levels.