Paraíba do Sul River is located at a very densely inhabited region of Brazil crossing the three most industrialized states of the country (São Paulo, Minas Gerais and Rio de Janeiro states). As a result, industrial and farming residues as well as urban sewage are frequently disposed without appropriate treatment. The current study aimed at investigating the water quality in three reservoirs along the Paraíba do Sul River (Ilha dos Pombos, Santa Cecília and Santa Branca), through physiological, morphological, biochemical, and genetic biomarkers. The bioindicator chosen was the catfish Pimelodus maculatus, sampled during the dry (June 2008) and rainy (February 2009) seasons. Also, some water physicochemical parameters were analyzed from the sampling sites, but displayed no alterations according to the Brazilian Agency for Water Quality Legislation. Branchial carbonic anhydrase activity was inhibited in the dry season, while renal carbonic anhydrase activity was inhibited in the rainy season in the Santa Branca reservoir, indicating disturbance of osmoregulatory and acid–base regulation processes. Histopathological alterations were observed in the gills (neoplasic and tissue hyperplasia processes) and liver (necrosis), indicating serious damage to the functional integrity of these organs. A high incidence of melanomacrophage centers was observed in the liver, suggesting an intense immune response in all reservoirs. Acetylcholinesterase and catalase activity showed also differences corroborating some morphological results. Likewise, the induction of the micronucleus and DNA damage indicate genotoxicity, but mainly in the Santa Branca reservoir. Thus, the health status of P. maculatus warrants caution in the use of the water from the 3 reservoirs for direct human consumption, particularly after the accidental spill of endosulfan in November 2008, three months before the rainy season sampling.