This study deals with the development of a clean process for the remediation of waters polluted with the dyes methylene blue (MB) and methyl orange (MO). Magnetic adsorbents have been synthesized in order to develop an extraction process assisted by a magnetic field to avoid extra separation techniques. To follow an “ecoconception” approach, magnetic beads containing magnetite were prepared with sodium alginate. Alginates are natural polysaccharides present in marine seaweed. Batch experiments were carried out as a function of initial pH solution, mass of adsorbent, initial dye concentration, salinity and desorption. An optimum adsorption was observed at pH 7 and 4 for MB and MO, respectively. The maximum adsorption followed the Langmuir, Freundlich and Dubinin Radushkevich isotherms with a value of 10,851.64 mg of MB per gram of adsorbent, whereas MO presented a value of 58,411.21 mg/g. Electrostatic interactions are suggested as the driving adsorption forces based on the equilibrium, salinity and desorption results. Salinity has a negative impact on MB due to competing ions and a positive effect on MO, due to shielding of equally charged groups. Acetone was the most efficient eluent for MO and HCl for MB. This present work highlights the potential use of magnetic beads in the elimination of dyes from wastewater as a low-cost and environment friendly purification technique.