Thin layers are vertically compressed, horizontally extensive, highly concentrated features comprised of plankton and/or particles. They are critical components of the marine ecosystem, likely playing a key role in the life histories and evolutionary trajectories of species found in, or, interacting with them. These structures have been reported in diverse marine environments around the globe. However, the mechanisms of thin layer formation/dissipation in the southwestern Atlantic Ocean were unknown until this contribution. To assess the temporal evolution of thin phytoplankton layers on the inner shelf off Ubatuba, Brazil, we conducted two oceanographic fixed station cruises, including optics, acoustics, and imaging techniques. Over a period of 2 days, three thin layers were observed: within the pycnocline close to the maximum stratification, and below the pycnocline where phytoplankton were affected by enhanced nutrient supply provided by the South Atlantic Central Water (SACW). Changes in regional wind patterns influenced the presence of SACW, which directly affected shear and stratification: the primary physical mechanisms we attribute to thin layer formation in this region. The associated biological mechanisms contributing to thin layer formation were biomass accumulation (in situ growth) and likely the mobility of dinoflagellates. The dominant organisms in the thin layer depths and surroundings, by our in situ imaging system, were cyanobacteria, diatoms, dinoflagellates, and crustaceans. Thin Layers likely have crucial importance for meso‐oligotrophic environments, representing important feeding resources for higher trophic levels.