A new hydrogel, based on chitosan crosslinked with 2-chlorophenyl-bis(6-amino-1,3-dimethyluracil-5-yl) methane, (2Clph-BU-Cs), has been successfully created. Various instrumental techniques such as elemental analysis, FTIR, SEM, and XRD were used to prove its structure. Its removal efficiency for anionic Congo red (CR) dye under different conditions for industrial wastewater treatment was studied. For optimizing the conditions to maximize CR dye removal, the impacts of temperature, contact time, pH, and initial concentration of the dye on adsorption capacity were investigated. The removal of the dye was pH-dependent, with a much higher value achieved at pH 4 than at pH 7 and 9. The maximum adsorption capacity of the hydrogel was 93.46 mg g−1. The model of adsorption process was fitted to the pseudo-second-order kinetic model. The intraparticle diffusion demonstrated the multi-step nature of the adsorption process. The thermodynamic results showed that the adsorption process was endothermic because of the positive value of enthalpy (43.70 kJ mol−1). The process of adsorption at high temperatures was spontaneous, according to the values of ∆G0. An increase in randomness was seen in the value of ∆S°. Generally, the investigated hydrogel has the potential to be used as a promising effective reusable adsorbent for industrial wastewater remediation.