This study investigated the impact of micropollutants on fish health from Segredo hydroelectric reservoir (HRS) along the Iguaçu River, Southern Brazil, contaminated by urban, industrial, and agricultural activities. This is the first comprehensive study assessment in the river after the severe drought in the 2020s in three fish species from different trophic levels Astyanax spp. (water column depth/omnivorous), Hypostomus commersoni (demersal/herbivorous), and Pimelodus maculatus (demersal/omnivorous). Animals, water, and sediment samples were collected from three distinct sites within the reservoir: Floresta (upstream), Iratim (middle), and Station (downstream). The chemical analysis revealed elevated concentrations of metals (Al, Cu, Fe) and the metalloid As in water, or Cu, Zn, and As in sediment, surpassing Brazilian regulatory limits, while the organic pollutants as DDT, PAHs, PCBs, and PBDEs were found under the Brazilian regulatory limits. The metal bioaccumulation was higher in gills with no significant differences among sites. The species Astyanax spp. and H. commersoni displayed variations in hepatosomatic index (HSI) and P. maculatus in the condition factor index (K) between sites, while adverse effects due to micropollutants bioaccumulation were observed by biochemical, genotoxic, and histopathological biomarkers. The principal component analysis and integrated biomarker response highlighted the upstream site Floresta as particularly inhospitable for biota, with distinctions based on trophic level. Consequently, this multifaceted approach, encompassing both fish biomarkers and chemical analyses, furnishes valuable insights into the potential toxic repercussions of micropollutant exposure. These findings offer crucial data for guiding management and conservation endeavors in the Iguaçu River.