In view of compliance with increasingly stringent environmental legislation imposed by regional, national, and supranational (e.g., European Union) authorities, innovative environmental technologies for the treatment of dye-contaminated effluents are necessary in the color industry. In this study, effluents of an industrial dye producer were subjected to distinct treatment trains following an initial qualitative characterization. The effectiveness of ozonation and a treatment using white rot fungi (WRF) and their enzymes were compared with respect to parameters such as residual color, toxicity on human cells, and genotoxicity. A combined ozonation/WRF process was also investigated. The effluent exhibited significant toxicity that was reduced by only 10% through ozonation, whereas the fungal treatment achieved a 35% reduction. A combined treatment (ozone/WRF) caused an abatement of the toxicity by more than 70%. In addition, the initial genotoxicity of the effluent was still present after the ozone treatment, while it was completely removed through the fungal treatment.