Nowadays, the treatment of dyes and pigments was considered a serious challenge in the world. In this work, a novel high-performance magnetic bio-based κ-carrageenan-kaolinite hydrogel (CKAlFe) was designed, characterized, and used for the simultaneous adsorption of Alizarin red and Congo red dyes from an aqueous solution. The morphological characterization revealed the successful preparation of non-rigid and plate-like CKAlFe adsorbent with the microporosity structure, in which the κ-carrageenan forms the amorphous part and kaolinite clay, Al2O3, and Fe3O4 are involved in the crystalline part of the structure. It was found as an efficient adsorbent with maximum adsorption capacities of 26.9 and 33.5 mg/g toward Congo red and Alizarin red molecules respectively. The adsorption capacity of CKAlFe was decreased in acidic media. The adsorption kinetics followed the pseudo-second-order kinetic model. The intra-particle diffusion controlled the adsorption rate at low initial concentrations, while the transfer rate of molecules from solution to the surface of CKAlFe played this role at higher concentrations. Also, the adsorption isotherm followed the extended Langmuir isotherm model. The thermodynamic study demonstrated that Congo red and Alizarin red binary adsorption onto CKAlFe was endothermic and spontaneously occurred, while Alizarin red molecules required more energy than Congo red to be adsorbed and a higher fraction of the active sites were occupied by Congo red molecules. The mechanism study showed that multiple interactions including π-π stacking, electrostatic interaction, dipol-dipol H bonding, and Yoshida H bonding can be involved in the adsorption process of studied dyes onto CKAlFe. Besides, the isosteric enthalpy of adsorption revealed that the adsorption type varied from physical to chemical process, increasing the amount of adsorbed dyes. The prepared magnetic hydrogel is highly capable of being used in drug delivery for selectively detection, hyperthermia/thermal ablation, and different products already on the market.