Coastal ocean ecosystems are major contributors to the global biogeochemical cycles and biological productivity. Physical factors induced by the turbulent flow play a crucial role in regulating marine ecosystems. However, while large-scale open-ocean dynamics is well described by geostrophy, the role of multiscale transport processes in coastal regions is still poorly understood due to the lack of continuous high-resolution observations. Here, the influence of small-scale dynamics (O(3.5-25) km, i.e. spanning upper submesoscale and mesoscale processes) on surface phytoplankton derived from satellite chlorophyll-a (Chl-a) is studied using Lagrangian metrics computed from High-Frequency Radar currents. The combination of complementary Lagrangian diagnostics, including the Lagrangian divergence along fluid trajectories, provides an improved description of the 3D flow geometry which facilitates the interpretation of two non-exclusive physical mechanisms affecting phytoplankton dynamics and patchiness. Attracting small-scale fronts, unveiled by backwards Lagrangian Coherent Structures, are associated to negative divergence where particles and Chl-a standing stocks cluster. Filaments of positive divergence, representing large accumulated upward vertical velocities and suggesting accrued injection of subsurface nutrients, match areas with large Chl-a concentrations. Our findings demonstrate that an accurate characterization of small-scale transport processes is necessary to comprehend bio-physical interactions in coastal seas.