An oceanographic cruise conducted during June 2008 in the Gulf of Gabes revealed the existence of different water masses; the Modified Atlantic Waters (MAW) circulated in the upper 100 m in the offshore area, the Mixed Mediterranean Water (MMW) was confined to the inshore region and the Ionian Water (IW) was in deep offshore water. The thermal stratification was indicated by the vertical profiles of temperature generated from a coast-offshore section. Phosphorus limitation was induced by the thermal stratification as shown by the high N/P ratio. Heterotrophic and mixotrophic dinoflagellates were the major contributors to total phytoplankton biomass. Ciliates were less abundant and dominated by tintinnids. Small planktonic copepods (≤1.45 mm) contributed to 93.64% of total copepod abundance in the inshore area as a result of the high density of Oithona similis, Oithona nana, Clausocalanus furcatus and Euterpina acutifrons in this area characterized by warm and salty MMW. In fact, small copepods were significantly correlated to both temperature and salinity. Small copepod fraction prevailed also in the MAW contributing to 71.05% of total copepod abundance as a result of the dominance of O. nana and C. furcatus. Nonetheless, the large copepod Nannocalanus minor was more adapted to the deep IW where it contributed to 44.05% of total copepod abundance. Invasive species were encountered in the offshore region intruded by the Atlantic waters. The Atlantic copepods were scarce and less abundant reflecting the weakening of the Atlantic flow in the eastern basin of the Mediterranean.