Aliphatic and polycyclic aromatic hydrocarbons (AHs and PAHs, respectively) were analyzed in the dissolved fraction (<0.7 μm) of surface water and in various particulate/planktonic size fractions (0.7–60, 60–200, 200–500 and 500–1000 μm) collected at the deep chlorophyll maximum, along a North-South transect in the Mediterranean Sea in spring 2019 (MERITE-HIPPOCAMPE campaign). Suspended particulate matter, biomass, total chlorophyll a, particulate organic carbon, C and N isotopic ratios, and lipid biomarkers were also determined to help characterizing the size-fractionated plankton and highlight the potential link with the content in AHs and PAHs in these size fractions. Ʃ28AH concentrations ranged 18–489 ng L−1 for water, 3.9–72 μg g−1 dry weight (dw) for the size fraction 0.7–60 μm, and 3.4–55 μg g−1 dw for the fractions 60–200, 200–500 and 500–1000 μm. AH molecular profiles revealed that they were mainly of biogenic origin. Ʃ14PAH concentrations were 0.9–16 ng L−1 for water, and Ʃ27PAH concentrations were 53–220 ng g−1 dw for the fraction 0.7–60 μm and 35–255 ng g−1 dw for the three higher fractions, phenanthrene being the most abundant compound in planktonic compartment. Two processes were evidenced concerning the PAH patterns, the bioreduction, i.e., the decrease in concentrations from the small size fractions (0.7–60 and 60–200 μm) to the higher ones (200–500 μm and 500–1000 μm), and the biodilution, i.e., the decrease in concentrations in plankton at higher suspended matter or biomass, especially for the 0.7–60 and 60–200-μm size fractions. We estimated the biological pump fluxes of Ʃ27PAHs below 100-m depth in the Western Mediterranean Sea at 15 ± 10 ng m−2 day−1, which is comparable to those previously reported in the South Pacific and Indian Ocean.