To assess anthropogenic impacts of point-source and diffuse discharges on fish populations of the Waikato River, compare responses to different discharges and identify potential sentinel fish species, we sampled wild populations of brown bullhead catfish (Ameiurus nebulosus, (LeSueur, 1819)), shortfin eel (Anguilla australis Richardson, 1848), and common bully (Gobiomorphus cotidianus McDowall, 1975) in the Waikato River. Sites upstream and downstream of: geothermal; bleached kraft mill effluent (BKME); sewage and thermal point-source discharges were sampled. At each site, the population parameters, relative abundance, age structure and individual indices such as: condition factor; and organ (gonad, liver, and spleen) somatic weight ratios; and number and size of follicles per female were assessed. Indicators of fish residence and in some cases exposure to contaminants in discharges were analyzed. Bile chemistry of brown bullhead and shortfin eel was assayed, liver and muscle metal levels were analyzed for brown bullhead and shortfin eel respectively, and stable isotopes of C and N in common bully were measured. Bile, metal and isotopic signatures gave strong evidence that fish had been resident at sites for some time before sampling. Signatures of bile and metal contaminants showed contamination was localised to discharge areas. Gradients in stable isotopes in common bully showed evidence of changes in water sources and anthropogenic effects along the river. Biochemical variables, hepatic ethoxyresorufin-O-deethylase (EROD) and plasma steroids indicated exposure and response of brown bullhead and shortfin eel to pulp and paper contaminants at the BKME site. Physiological (blood) variables showed fish largely responded in a predictable way to elevated water temperatures at discharge sites at time of sampling, however total haemoglobin of brown bullhead and common bully blood failed to increase at the BKME site despite elevated temperatures and low dissolved oxygen. Growth rates, condition factor, age structure, and gonadosomatic index (GSI) suggest that discharges with significant heat or nutrients benefit brown bullhead despite physiological impairment at the BKME site. Shortfin eel individuals also benefited from heated water discharges. No consistent impacts on common bully health were obvious at individual discharge sites, or cumulatively along the river due to the gradual deterioration in water quality downstream. Common bully individuals also benefited from heat in discharges but lack of juveniles at sites where numerous juvenile brown bullhead were found, suggest that unlike brown bullhead populations, common bully populations were not responding with significant recruitment. Although I found little evidence of toxic effects of discharges on shortfin eel, caution is required in assessing the potential of contaminants to impact eel populations due to the life history of shortfin eel, and exploited nature of populations. For example, reproductive damage suffered by adult eels may not immediately manifest itself in the effected population due to temporal delays in gonadal maturation, and recruitment, and single panmictic populations supplementing recruitment of impacted populations. Distinct changes in population parameters at each of the paired sites and changes in individual variables showed that fish responded to discharges. The range of responses in species suggests different sensitivity to contaminants and amount of benefit which each species receives from heat in discharges. In these terms shortfin eel would be the most resistant, then brown bullhead and lastly common bully. Interpretation of population-level impacts at the geothermal and BKME discharge sites is made difficult due to benefits of additional heat. There is also the possibility that detection of sub-lethal or chronic effects on sensitive juvenile life-stages may be being hidden by compensatory density population responses. Responses and life history of common bully made them the preferred indicator species of the three species sampled, and supported overseas examples using small-bodied fish species as sentinels.