Hydrogels are potential adsorbents for removing contaminants from aqueous solutions. To enhance adsorption efficiency, multi-walled carbon nanotubes (MWCNTs-COOH) can be encapsulated within them. In this study, chitosan hydrogels cross-linked with epiclon (5 and 10 w/w%) through amide linkages were prepared. The hydrogels were modified with 0.3 and 0.5 w/w% MWCNTs-COOH. FT-IR, TGA, FE-SEM, and swelling measurements were used to characterize the hydrogels. FE-SEM confirmed a three-dimensional porous nanostructure. Maximum swelling occurred at 40 �C and pH 4.0. Aflatoxin B1 was chosen as a model to evaluate the hydrogel’s ability to remove toxic compounds from aqueous media. Adsorption isotherm studies showed the process follows the Langmuir model. The adsorption capacity of the nanocomposite hydrogel was about 7% higher than that of hydrogels without MWCNTs-COOH at pH 4.8. Enhanced adsorption was observed with the higher epiclon content. The adsorption efficiency (94%) confirmed the hydrogel’s effectiveness for toxic compounds with polar functional groups.