Environmental selection in disturbed habitats are expected to erode diversity. However, habitat disruption can also unlock the evolutionary potential of populations by breaking ecological barriers and opening populations up to introgression of novel genotypes. We investigate a natural aquatic system historically exposed to a mosaic of anthropogenic stressors (heavy metals, acidification) and give evidence that localized disturbance can maintain levels of genetic diversity typically seen at regional and even cross-continent spatial scales. Using nuclear and mitochondrial genetic markers, and a population genetic survey of species of the Daphnia pulex complex from contaminated and control lakes, we show that contaminated lakes harbour high levels of haplotype and nucleotide diversity. Despite the geographic proximity and joint watershed of many lakes, the observation of shared multi-locus genotypes among populations is rare. Yet the observation and dominance of hybrid genotypes in three highly stressed habitats favours the hypothesis that ecological transitions can trigger hybridization and the emergence of novel asexual (obligately parthenogenetic) clones.