To elucidate tidally related variations of hydrophobic organic contaminant (HOC) bioavailability and the impact of these contaminants on estuarine ecosystems, both PCB and PAH concentrations were investigated in the dissolved phase and in the suspended particulate material (SPM) of the Seine Estuary. Both PAH and PCB highest levels were observed in surface and bottom water when SPM remobilizations were maximum, in relation to higher speed currents. In parallel, acetylcholinesterase (AChE) and glutathione-S-transferase (GST) activities were investigated in the copepod Eurytemora affinis. Significant decreasing AChE levels were measured during the tidal cycle and between surface and bottom copepods related to salinity and to HOC concentration variations. Significant increasing GST levels were also observed when HOC concentrations in the water column were the highest. This study underlined the need to standardize sampling procedures for biomonitoring studies in order to avoid interfering factors that could modify biomarker responses to chemical exposure.