A new Fine Scale Sampler (FSS) was designed and used in the Loire River plume (Bay of Biscay, France) in order to study phytoplankton distribution in highly stratified water columns. The FSS consists of a linear array of 15 sampling bottles, set horizontally at 20 cm intervals. Data acquired from the CTD and fluorescence probe of the FSS enable it to be precisely positioned at the depth of the highest density gradient or at the chlorophyll a maximum. The FSS made it possible to investigate fine scale vertical distribution of phytoplankton and relationships with water density, nutrient concentrations or light availability, for spring and summer conditions. Under spring conditions, the entire upper layer exhibited a dominant diatom population (Chaetoceros sociale, Thalassiosira rotula) above 15 m with evident uptake in dissolved inorganic nutrients and the maximum concentration of dinoflagellates (mainly small forms of Gymnodinium spp. and Gyrodinium spp.) was located 16 m deep, where light energy began to be a limiting factor for phytoplankton growth. During summer conditions, the maximum phytoplankton biomass (10 μg l−1 of chlorophyll a) was only concentrated in the 2 m thick pycnocline layer, located at a depth of 12 m. The diatom C. sociale was dominant in the phytoplankton peak. Dinoflagellates (Dinophysis acuminata and Gymnodinium spp.) were also concentrated around the density gradient. Low inorganic nitrogen concentration (<0.2 μmol l−1) was responsible for the limitation of phytoplankton production in the surface layer above the pycnocline, and the phytoplankton growth was irradiance-limited underneath the pycnocline.