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Several biomarkers are currently used to determine chronic exposure of fish to environmental contaminants. In studies to assess the effects of pulp mill effluent on winter flounder (Pleuronectes americanus), body and hepatosomatic indices (HSIs), histopathology, levels of hepatic detoxifying enzymes, mixed function oxygenases (MFO), muscle acetylcholinesterase (Ache) and selected parasite abundance were compared in samples taken near a paper mill (sulphite-bleaching) and a number of reference sites. Our studies revealed a number of significant (P < 0.05) differences between samples taken near the paper mill and reference sites. Flounder captured at two locations near the mill were greater in length and weight, had elevated HSIs and more lesions in the liver and spleen while an acanthocephalan, Echinorhynchus gadi, located in the digestive tract, was lower than at more distant sites. Activity of MFO and Ache were similar at most sites and might be a reflection of the fish's foraging behaviour and consequently intermingling of populations from different locations during summer. These results support the view that several biomarkers should be utilised when assessing the health of fish living in habitats degraded by pollutants.