Anthropogenic pressures in estuaries may impair not only the fitness of organisms and the evolutionary processes necessary to the survival, but also the management of exploited marine resources. In order to assess these impacts, phenotypic and genotypic data pertaining to young-of-the-year (YOY) sole (Solea solea) were screened in differentially contaminated North East Atlantic estuaries ranging from Portugal (Mondego) to the English Channel (Seine). YOY sole inhabiting each estuary was found being phenotypically distinct from each other; each of them being impacted by pollution when comparing observed phenotypic data with published literature. According to the strong pollution in the Seine estuary, the corresponding YOY sole sample showed significantly lower body mass, size and condition factor compared to other samples. Using fifteen genetic markers, the Mondego estuary demonstrated low, but significant levels of genetic differentiation with most of the samples. Using neutrality tests, two loci were found to be putatively under directional selection (Soso7 and Soso23), but only locus Soso7 demonstrated significant positive heterozygosity-fitness correlation (HFC) for body size and body mass, suggesting a possible ongoing adaptive process. The candidate locus MT associated to a detoxifying metallothionein gene did not show significant genetic differentiation, but (i) significant deficit in heterozygote in the Seine estuary as already reported in other coastal samples impacted by metallic contaminants, and (ii) significant positive HFC with body mass were found. Selective rather than demographic processes better explain an observed genetic structure in YOY sole and are predominantly associated with the heavily contaminated Seine estuary whose nursery function and capacity are degraded.