Phytoplankton size structure has a profound effect on the ecology of aquatic environments and, cumulatively, may impact biogeochemical cycling at the global scale. Here we present results of a coastal study where spatial variations in phytoplankton size-structure are analyzed. We use a new methodology that combines simultaneous measures obtained with a laser in situ scattering and transmissometry instrument (LISST) and fluorescence profiles to assess the size-structure of phytoplankton in situ. Our results show spatial variations in the dominant size of phytoplankton associated with coastal circulation patterns at relatively large scales (1–10 km). We compare the measured variations with the simulated preferential concentration patterns obtained with a numerical model to assess the role of advection by ocean currents. This physical preferential concentration mechanism has important ecological impacts from the phytoplankton level to the whole ecosystem.