ABSTRACT The Waikato River is the longest river in New Zealand and is exposed to range of anthropogenic stressors. This study investigated the effects of three major point-source discharges on resident shortfin eels Anguilla australis along the river. Shortfin eels were caught from sites upstream and downstream of discharges of bleached kraft mill effluent (BKME) from pulp and paper manufacture, sewage, and a thermal power plant. At each site, population parameters (relative abundance and age structure) and individual metrics of health such as condition factor and organ (gonad, liver, and spleen) to somatic weight ratios were measured. Blood, biochemical (hepatic 7-ethoxyresorufin-O-deethylase or EROD) and chemical markers (bile chemistry and trace elements in flesh) were also measured. Measures of exposure and response to discharges confirmed that the shortfin eels were resident at the sites sampled. The discharges had few negative impacts on individual eel health and positive responses were seen to warm water discharge. However, resident shortfin eels were immature so reproductive responses could not be determined. In conclusion, shortfin eels in this study showed few responses to the effects of the discharges except for increased resin acids, bile polycyclic aromatic hydrocarbons, and EROD at the BKME site.