The mesoscale (10–100 km, days–weeks) plays a key role in the Ocean's ecosystem structure and dynamics. This work compares the pico–nanoplankton patterns observed in the Alboran Sea (Western Mediterranean) during three oceanographic cruises. We analyse its response to different expressions of mesoscale circulation associated with the three major hydrodynamic features in the basin; namely the Northwestern Alboran Front (NWAF, surveyed in OMEGA-1 cruise), the Almeria–Oran Front (AOF, surveyed in OMEGA-2 cruise) and the Western Alboran Gyre (WAG, surveyed in BIOMEGA cruise). The first two surveys were carried out under the most typical quasi-stationary twin gyre conditions of the Alboran Sea, whereas the third cruise was performed after an eastward migration of the WAG. The analysis of pico and nanoplankton populations was carried out using flow cytometry. The patchiness observed in the three cruises indicates an association of phytoplankton peaks with the main frontal structures: abundances were higher in the NWAF/upwelling area in OMEGA-1, at the Mediterranean side of the AOF in OMEGA-2, and at a tongue of recent Atlantic Water west of the WAG in BIOMEGA. However, a more detailed analysis reveals that different factors explain the origin of the phytoplankton biomass in each front/cruise. Mixing processes at the Strait of Gibraltar and the subsequent advection of water properties into the Western Alboran Sea were the mechanisms responsible for the abundances observed in the NWAF. The highest concentrations observed in the AOF were related to the intrusion of Mediterranean Surface Waters to the north of the front. During the migrating WAG the phytoplankton distribution was influenced by the formation of a new gyre. The relation between phytoplankton and mesoscale dynamics is further explored in terms of vertical velocity diagnosis. In all cases, intense vertical motion is negatively correlated with the abundance of phytoplankton populations. This resulted from the intense geostrophic background flow associated with large vertical velocities, which drove low residence times of water mass properties and hence a weak biological response. Fast-repeated surveys made during the OMEGA-1 and OMEGA-2 cruises reveal that the surveyed hydrographic features are subjected to significant temporal variability. In this case, the impact on the biology is most evident at taxa level.