One cationic surfactant with a wide spectrum of microbiocidal activity is benzethonium chloride (BEC). Despite being widely used, the toxicity data on vertebrate organisms are limited. Therefore, we aimed to evaluate within this study the acute toxicity of BEC on the gills and kidneys of Cyprinus carpio (European carp). An alteration of the antioxidant enzymes activities (glutathione reductase, glutathione peroxidase and glutathione S-transferase) was noticed after 96 h of exposure, along with an elevation of lipid peroxidation and decreased concentration of reduced glutathione, which confirmed that BEC was able to induce toxicity to these tissues. These metabolic effects were correlated with unspecific structural changes observed in gills and kidneys, having moderate degree of severity (such as an increase of melanomacrophages aggregation incidence and cytoplasm vacuolation of goblet cells in collecting tubules) and generally being compatible with life for the exposure time studied. The most severe structural effects were observed in gills after 96 h, noticing a lamellar aneurysm, hemorrhages and lamellar epithelium disruption due to the blood vessels and pillar cells damages and increased blood flow inside the lamellae. By our research we can confirm the utility of biochemical and histological analyses in the fish organs as tools for monitoring the water quality and ecotoxicological potential of chemicals.