The spatial distribution of chlorophylls and carotenoids was recorded throughout the Gulf of Gabes (South Ionian Sea) in March 2007, and was related to patterns of the physical structure and the nutrient concentrations. Two distinctwater masseswere identified based on the temperature and salinity (T–S) analysis: a cool and less salty Modified Atlantic Water (MAW) and a saltier Mediterranean Mixed Water (MMW). There was no significant difference in the mean nitrogen and phosphate concentrations between MMW and MAW, although the silica values were significantly higher in MAW. The Integrated chlorophyll a mean value was about 4 mg m−2, with a maximum of 13 mg m−2 at MAW stations. Higher Chlorophyll a records in typical MAW stations were mainly due to chlorophytes, which contributed up to 58% of the pigments concentrations in the MAWand about 46% in theMMW. The contribution of chlorophytes to total Chlorophyll a was found to be relatively stable throughout the water column. The contribution of diatoms, which were twofold higher in the MMW than in the MAW, did not exceed 17% of chlorophyll a and was mainly due to subsurface maxima. The chlorophytes, pelagophytes, prymnesiophytes and cryptophytes all together accounted for more than 77% of total chlorophyll a in the MAWand about 67% in the MMW. There were statistically significant differences between MMW and MAW in the pigment contribution of cyanobacteria and pelagophytes. These two taxa accounted for 13% and 24% of chlorophyll a respectively in the MAWand MMW indicating that these differences concerned phytoplankton classes at relatively low contributions to total chlorophyll a.