Despite many efforts for pollution abatement in aquatic ecosystems, there are still some cases of high accumulation of industrial pollutants due to past activities. In Flix reservoir (Ebro River, Spain), there are around 200,000-360,000 tons of industrial pollutants with a high concentration of heavy metals and organochlorides due to the activity of an organochlorine industry during more than half a century. This exceptional amount of pollutants provides a good opportunity (and need) to analyse their effects on fish populations under natural conditions, which is rarely available to ecotoxicologists. We compared the reproductive traits and prevalence of diseases and parasites at this impacted area with a neighbouring upstream reservoir unaffected by the pollution (reference sites) and also to downstream sites. Deformity, eroded fin, lesion and tumour (DELT) anomalies and ectoparasites were clearly more frequent at the impacted area for several fish species (common carp, roach and pumpkinseed). A significant negative impact of Flix reservoir on condition (eviscerated and liver weights, adjusted for fish size with analysis of covariance) and reproductive traits (gonadal weight and number of mature eggs, adjusted for fish size) was also detected for several fish species. The responses to the pollutants were species-specific, and common carp (Cyprinus carpio) was the species with the clearest effects on fitness-related traits at the impacted area, despite also being among the most tolerant to pollution.