Condition indices and metal bioaccumulation of early life stages of juvenile flounder (5–10cm) were determined in three anthropogenic estuaries (the Scheldt, Seine and Loire) and compared to a reference site (the Canche). Significant correlations were found between metal concentrations in sediment and (i) fish liver for Cd, Cu, Ni, Pb, V and Zn and (ii) fish gills for Cd and Mn. Metal accumulation in juvenile flounder from the three anthropogenic estuaries coincided with significantly lower Fulton’s K indices (from 0.99±0.03 to 1.06±0.01mgmm−3) compared to those from the Canche estuary (from 1.02±0.01 to 1.13±0.01mgmm−3). This discrepancy in fish condition index increased with fish size and therefore, strongly depends on the time juvenile spend in estuary. Muscle lipid contents and Triacylglycerol to Sterol ratios were significantly lower in fish collected in the Scheldt (lipid content: 21.3±3.6%), Seine (17.9±19.8%) and Loire (19.5±2.4%) estuaries compared to those originating from the Canche (38.3±4.6%). This study highlights that combined measures of both fish metal contents and condition indices gives a relevant assessment of juvenile fish health growing in anthropogenic estuaries.