Wastewater Treatment Plants (WWTPs) reduce the levels of sewage’ toxic elements, improving the quality of effluents before returning to the environment. However, most of WWTPs remove organic matter and pathogens without specific treatment for the elimination of contaminants. This study used ecotoxicity tests with aquatic organisms from different trophic levels (microalgae, microcrustacean, and fish) and measured biomarkers of cell detoxification and damage in fish (Danio rerio) to evaluate the efficiency of two WWTPs located in Southern Brazil (Navegantes WWTP - Rio Grande, and Mato Grande WWTP – Canoas) in toxicity removal. Samples of receiving waterbodies and effluents (raw and treated) resulted in toxicity for the aquatic organisms used in this study. However, the toxicity of treated effluent in both WWTPs was lower than raw effluent, regardless of the type of treatment, whether expressed as lethality or as sublethal effects (biomarkers), including the Integrated Biomarker Response (IBR) approach. The use of toxicity tests associated with the application of biomarkers were suitable tools to indicate the efficiency of treatment processes in removing the toxicity from the effluents. As expected WWTP treatment with activated sludge (Mato Grande) produces a better quality of the effluent to be discharged in the water bodies compared to the WWTP treatment with stabilization ponds (Navegantes); nevertheless, the toxicity of the receiving water bodies depends on its intrinsic characteristics and other activities occurring around, being challenging to relate to WWPTs discharges.