Hydrophobic organic contaminants (HOC) (i.e. PAHs and PCBs) were measured in the water column and in Eurytemora affinis samples from the Seine Estuary collected from November 2002 to February 2005. Results showed seasonal variations of both total PCB and PAH levels in the suspended particulate matter (SPM) and in the copepods with maximum levels during winter times. PAH and PCB concentrations in the SPM ranged from 499 to 5819ngg(-1) and from 58 to 463ngg(-1), respectively. Phenanthrene, pyrene and benzo[b+j+k]fluoranthene (B[b+j+k]F) were the predominant PAH compounds in the water column, while CB 101, 118, 153 and 138 were the most abundant PCB congeners. PCBs and PAHs bioaccumulated by E. affinis (EA) varied between 383 and 1785ngg(-1) and 165-3866ngg(-1). CB101, 153, 138 and B[b+j+k] were, respectively, the major compounds of PCB and PAH fingerprints in EA. Thereby, the copepods could reach high accumulation factor (ACF) (91000 for PCBs and 17000 for PAHs). The principal component analyses of contaminant concentrations and environmental parameter datasets distinguished two groups of copepods. The winter time cluster, with high percentage of adult copepods, which bioaccumulated the highest PCB and PAH body-burdens, and the second cluster with juveniles showing the lowest HOC concentrations. Thus, PAH and PCB concentrations in EA exhibited significant correlations with the percentage of adults making up the samples.