Abstract The objective of this study was to evaluate the effect of thorium (Th) bioaccumulation on the metabolism of silver catfish ( Rhamdia quelen) through biochemical parameters of the muscle (glycogen, glucose, lactate, protein, and ammonia). In addition, lipidic peroxidation levels (TBARS), catalase (CAT) and glutathione- S-transferase (GST) in the gills and in hepatic and muscular tissues were also analyzed. Cytogenetic parameters were studied through the evaluation of nuclear abnormalities in red blood cells. Silver catfish juveniles were exposed to different waterborne Th levels (in μg L −1): 0 (control), 25.3 ± 3.2, 69.2 ± 2.73, 209.5 ± 17.6, and 608.7 ± 61.1 for 15 days. The organs that accumulated the highest Th levels were the gills and skin. The increase of waterborne Th concentration corresponded to a progressive increase of Th levels in the gills, liver, skin and kidneys, with the highest accumulation in the gills and skin. Metabolic intermediates in the muscle were altered by Th exposure, but no clear relationship was found. CAT and GST activities in the hepatic and muscular tissues of this species suggest that the enzymatic activities can be stimulated at the lowest Th levels and inhibited at the higher levels (mainly in 608.7 μg L −1). The results of the cytogenetic assay contribute to this hypothesis because the higher toxicity in blood samples was found in juveniles exposed to 69.2 and 209.5 μg L −1 Th.