The purpose of this study was to compare the toxicity of two major municipal effluents subjected to different treatment processes: a physico-chemically treated effluent (high-risk effluent) and a biofiltered/UV-disinfected effluent (low-risk effluent). Juvenile fathead minnows were exposed to increasing concentrations of the high-risk and low-risk effluents in semi-static conditions for 16 weeks at 25 °C. At the end of the exposure period, juveniles were collected for immunocompetence (leukocyte density and phagocytosis), oxidative stress (catalase and superoxide dismutase activity) and DNA damage (COMET assay) assessments. The data revealed that DNA damage was the most sensitive biomarker, with increases at concentrations between 3.5% and 5%, and that the treatment processes had no influence on the intensity of genotoxic effects. A greater increase in oxidative stress enzymes was observed with the high-risk effluent as compared to the low-risk effluent, suggesting that oxidative stress was dependent on the treatment process applied. At the immunocompetence level, a biphasic pattern of response was found in both the high-risk and low-risk effluents. Indeed, in fish exposed to the low-risk effluent, an initial increase in leukocyte density and phagocytosis activity was followed by a subsequent decrease in these effects with increasing concentrations of the effluent. In the high-risk effluent, the initial increase and subsequent drop in leukocyte density occurred at lower concentrations while phagocytosis activity increased only at the highest concentration. In conclusion, the occurrence of DNA damage was not affected by the 2 types of effluents; however, oxidative stress and immunocompetence were more strongly influenced by the high-risk effluent than the low-risk one.