In the presented work, magnetic alginate (MA) beads were prepared and activated with epichlorohydrin and then functionalized with agmatine ligands (MA-A). The materials were analyzed by FTIR, SEM, XRD, and BET methods. The adsorption capacity of the MA-A for U(VI) was 451.4 mg/g. The Langmuir isotherm model well described the experimental data for the adsorption of U(VI) ions. The second-order kinetic model data proposed that the adsorption of U(VI) ions preferred the chemisorption mechanism. The adsorption enthalpy of the MA-A beads for U(VI) ions was 35.4 kJ/mol. After seven cycles of use, the adsorption capacity of MA-A beads was not significantly changed for U(VI) ions. Finally, the functionalization of MA beads with agmatine ligand can be a good candidate for applications for environmental technologies to remove metal ions.