Water quality greatly influences the population density of aquatic biota, including parasites. In order to evaluate the relationship between fish parasites and water quality in Kashmir Himalayas, we assessed helminth parasite densities in Schizothorax niger Heckel, 1838 (an endemic cyprinid fish of Kashmir) from three lakes, namely Anchar, Manasbal and Dal, which reflected the varied stages of eutrophication. The overall prevalence of helminth infections was higher in the hypertrophic Anchar Lake (prevalence = 18.6%) compared to Manasbal Lake, which was the least eutrophied (prevalence = 6.4%). Furthermore, mean prevalence of monoxenous and heteroxenous parasites was higher in lakes containing higher levels of water degradation (Anchar and Dal). The mean number of helminth species per fish host was the highest in the hypertrophic lake (1.3 ± 0.3) in comparison to the least eutrophic lake (0.2 ± 1.5). Variability of calculated infection indices (prevalence, mean intensity and mean abundance) revealed that helminth parasite composition in the fish was affected by the lakes' environmental stress (degraded water quality). Therefore, data on the density of helminth parasites in fish can provide supplementary information on the pollution status of a water body.