A study was conducted to ascertain the influence of a thermal discharge on the health and parasites of a coastal cold-water flatfish, the winter flounder (Pleuronectes americanus), a species sensitive to environmental change. Flounder were sampled in spring 1998 and 1999 beneath the plume and at reference sites north and south up to 1 km from the discharge. Species diversity and estimates of abundance of macroscopic algae, invertebrates, and fish were also recorded. After capture by scuba divers, a comparison of condition factor, organ indices, blood values, histology, and parasites was made between groups of fish from the discharge and reference sites. Diversity and abundance of algae, invertebrates, and fish were considerably greater beneath the plume than at the reference sites. The thermal water had no apparent effect on flounder taken beneath the plume, but it affected both its ecto- and endoparasites. Prevalence and mean abundance of Cryptocotyle lingua metacercariae were significantly greater, whereas Trichodina jadranica and Gyrodactylus pleuronecti were less on the gills of fish sampled beneath the plume than at the reference sites. Four endoparasites, i.e., Ceratomyxa drepanopsettae, Steringophorus furciger, Macvicarius soleae, and Lecithaster gibbosus were significantly more abundant in the reference samples. These results suggest that environmental change affected transmission of the parasites of winter flounder exposed to the thermal effluent.