Physical factors induced by the turbulent flow play a crucial role in regulating marine ecosystems. Here we show that the combination of complementary Lagrangian diagnostics provides an improved description of the flow geometry, which facilitates the interpretation of non-exclusive physical mechanisms affecting phytoplankton composition, dynamics and patchiness. The influence of small-scale dynamics (O(3.5-25) km, i.e. spanning upper submesoscale and mesoscale processes) on phytoplankton in surface waters derived from satellite chlorophyll-a (Chl a) is studied using Lagrangian metrics computed from High-Frequency Radar currents over the Ibiza Channel. Attracting small-scale flow structures are associated to filaments of accumulated negative divergence where particles and Chl a standing stocks cluster. Regions of accumulated positive divergence, representing large accumulated upward vertical velocities and suggesting accrued injection of subsurface nutrients, match areas with large Chl a concentrations. Furthermore, the influence of other accumulated dynamical properties of the flow on phytoplankton composition over a filament, originated in a region where Atlantic Water and resident Mediterranean Water are mixed, is studied combining in-situ observations obtained during the SHEBEX cruise (May 2015) and Altimetry-derived Lagrangian computations. We find that fluid parcels presenting high values of Lagrangian Turbulent Kinetic Energy and Vorticity are related to areas of large presence of diatoms as compared with the abundance of flagellates. Our findings suggest that an accurate characterization of the Lagrangian flow properties is necessary to comprehend bio-physical interactions in the ocean.