The current study aimed to assess changes in phytoplankton composition and productivity along an oligotrophic gradient in relation to changes in sea surface temperature (SST). Phytoplankton pigments, nutrients, and physical water column properties were studied along a longitudinal transect in the Mediterranean Sea (MED) in May–June 2013, covering its western (wMED) and eastern (eMED) basins. Pigments were used to determine phytoplankton taxonomic composition and taxon specific carbon fixation, whereas beam attenuation was used to calculate particulate organic carbon (POC). Nitrate, phosphate, and silicate concentrations integrated over 0–125 m declined from wMED to eMED (on average 13, 9, and 2 fold lower in eMED compared with wMED, respectively) and correlated inversely with SST (16.2–23.0 °C) for the whole transect in the Mediterranean Sea.