The complex mixtures of contaminants released in wastewater treatment plant (WWTP) effluents are a major source of pollution for aquatic ecosystems. The present work aimed to assess the environmental risk posed by WWTP effluents by applying a multi-biomarker approach on caged rainbow trout (Oncorhynchus mykiss) juveniles. Fish were caged upstream and downstream of a WWTP for 21 days. To evaluate fish health, biomarkers representing immune, reproductive, nervous, detoxification, and antioxidant functions were assayed. Biomarker responses were then synthesized using an Integrated Biomarker Response (IBR) index. The IBR highlighted similar response patterns for the upstream and downstream sites. Caged juvenile females showed increased activities of innate immune parameters (lysozyme and complement), histological lesions and reduced glycogen content in the hepatic tissue, and higher muscle cholinergic metabolism. However, the intensity of the observed effects was more severe downstream of the WWTP. The present results suggest that the constitutive pollution level of the Meuse River measured upstream from the studied WWTP can have deleterious effects on fish health condition, which are exacerbated by the exposure to WWTP effluents. Our results infer that the application of IBR index is a promising tool to apply with active biomonitoring approaches as it provides comprehensive information about the biological effects caused by point source pollution such as WWTP, but also by the constitutive pollutions levels encountered in the receiving environment.