Elevated concentrations of contaminants have negative impacts on aquatic organisms and their parasites. Changes in parasite infections have been proposed as a technique for monitoring the health of aquatic ecosystems. Furthermore, alterations in physiological responses (biomarkers) of organisms have also been used to delineate ecosystem quality. Lake Heritage is situated along the Crocodile River in Muldersdrift, Gauteng, South Africa and is subject to contamination by acid mine drainage. Clarias gariepinus is a well‐studied bioindicator species and host to numerous endo and ectoparasites. The aims of this study were to delineate the health status of Lake Heritage through a multifaceted approach by comparing the water quality, biomarker responses and parasite biodiversity of C. gariepinus, compared to unexposed laboratory‐reared fish. Physical and chemical water quality parameters were determined with a hand‐held probe, test kits and element analysis with ICP‐MS. Biomarker responses in the gill, liver and muscle tissues from C. gariepinus were assessed for total protein, metallothioneins, superoxide dismutase and reduced glutathione concentrations and activities of acetylcholinesterase and catalase. Results for water quality variables showed higher pH, nitrate, hardness and copper levels compared to the South African Target Water Quality Guidelines. Catalase activity, and concentrations of superoxide dismutase and reduced glutathione showed a response in C. gariepinus to the water quality. Ectoparasites had lower prevalence and mean intensity than endoparasites. However, there were no differences in the physiological responses between infected and uninfected hosts. The study shows that the eutrophic conditions in Lake Heritage cause biomarker responses in the host when compared to host fish in laboratory conditions.