The paper presents the results of a study of the physical and chemical characteristics of the binding of single-walled carbon nanotubes (SWNT) with typical enzymes of the antioxidant system of the fish Danio rerio. The enzymes chosen as target proteins were superoxide dismutase 1 (SOD1), glutathione peroxidase 8 (Gpx8) and catalase (CAT). Virtual molecular structures of target enzymes and SWNT were modeled and optimized. Three main types of SWCNTs have been studied: chair conformation (chirality n = m = 7, repeats =9, length ≈22 Å); “zigzag” conformation (chirality n = 7, m = 0, repeats =6, length ≈21 Å; “chiral” conformation (chirality n = 7, m = 3, repeats =1, length ≈37 Å. Comparisons of annotated amino acid residues binding with the prediction of the molecular cavity with amino acid residues conjugated with SWNTs was carried out using UniProt DB and PrankWeb. For all proteins except Gpx8, the topology of amino acid residues potentially involved in binding to nanotubes was accurately localized, ranged from 13 to 30. Molecular interactions between proteins and SWNT s were predicted using the molecular docking method using AutoDock software. The study showed that the formation of generally stable SWNT–enzyme complexes with fairly low binding energy values for each. Combinations of SWNT–enzyme complexes range from –13.41 to ‒18.09 kcal/mol. The potential biological effects of the studied carbon nanotubes on the biochemical and physiological systems of D. rerio fish are discussed. The presented approach is promising for studying pathophysiological models of cytotoxicity.