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The purpose of this present study was to use the growth rates, RNA–DNA ratio and morphometric (Fulton’s K) condition indices measured on 0-group juveniles European flounder, as a means of comparing the quality of estuarine nursery habitats. The Seine estuary, heavily impacted by manmade modifications and one of the most contaminated in Europe, was compared to two smaller estuaries considered as clean (low domestic, agricultural and industrial effluents). Indicators of human disturbance (sediment chemical contaminants) as well as biotic data (macrobenthos abundances) were used to establish between-site differences in environmental quality. The abundance of macrobenthos (potential preys for juvenile) was high and not significantly different among the three estuaries confirming the important role played by estuaries as feeding grounds. Sediment metal concentrations (Cd, Cr, Cu, Pb, Zn) were significantly higher in the Seine than in the Canche and Authie estuaries. Otolith growth was closely related to somatic fish growth, and we used daily otolith increments from the previous 10 days before capture as an indicator of 0-group flounder recent growth (RG). RG did not vary significantly among flounders from the Canche and Authie estuaries and individuals from the Seine had slower RG. RNA–DNA ratio and K values were also significantly lower in individuals from the Seine compared to those of the Authie or the Canche. Pollution (e.g. metal contaminants) is the most likely cause of growth and condition differences among estuaries. The results of this study suggest that habitat-specific fish growth and condition are useful proxies for habitat quality since they integrate the effect of multiple environmental factors. [ABSTRACT FROM AUTHOR]