The widespread use of pesticides results in a growing contamination of the aquatic environment. The effects of (1) a simple mixture of a glyphosate-based formulation and AMPA (Aminomethylphosphonic acid -- a primary metabolite of glyphosate) and of (2) a more complex mixture of herbicides (glyphosate/AMPA/mecoprop/acetochlor/2,4D) were explored on the molecular and physiological responses of the European flounder Platichthys flesus, considering a long-term and environmentally realistic contamination. Molecular responses were identified using suppression subtractive hybridization on liver samples: the level of gene transcription was significantly different between contaminated fishes vs control ones for 532 sequences, after a 62-day contamination. Among them, 222 sequences were identified by homology with data-based sequences; they encoded several metabolic pathways including: methionine and lipid metabolism, immunity, protein regulation, coagulation and energetic metabolism. Expression pattern of nine transcripts in the liver was confirmed by real-time PCR. The molecular study underlined that potential markers of liver injury were expressed for both mixtures, in particular betaine homocysteine methyl transferase and chemotaxin. Physiological responses were analysed considering blood parameters and condition factor; after the two months contamination period; no significant physiological difference was detected between contaminated and control fish.