The spatial and temporal variations of the microphytoplankton communities were examined during four oceanographic cruises conducted between July 2005 and March 2007 aboard the RV ‘Hannibal’. Water thermal stratification started in May–June, and a thermocline established at 20 m depth, but ranged between 25 m during July and more than 30 m during September. The high concentrations of chlorophyll-a were observed during the May–June semi-mixed conditions and were mainly correlated with the concentrations of phosphate, suggesting a potential limitation by this nutrient. The Bacillariophyceae were dominant in the coastal samples, whereas they declined in the offshore area, most likely due to silicate shortage. Cyanobacteriae developed over semi-mixed conditions and at the thermocline depth. Relatively constant abundance of dinoflagellates was observed during the sampling periods from the coast to the offshore area, mainly explained by the high diversity species of this group. The results suggest that some phytoplankton taxa are generally adapted to specific hydrological conditions, whereas the dinoflagellates did not seem to follow this trend. Our findings have important biogeochemical implications in relationship with the export fluxes of the particulate matter throughout the water column.