In the present research, magnetic rhamnolipid-Co/Al layered double hydroxide (MR-LDH) was synthesized to uptake methylene blue (MB) and reactive orange 16 (RO16) from aqueous solution. The main parameters, including pH, adsorbent dosage, contact time, and initial analyte concentration, were optimized to achieve the best adsorption efficiency. Accordingly, the elimination of MB on MR-LDH is improved in the basic medium due to the electrostatic interactions between the negative charge of MR-LDH and the positive charge of MB dye. In contrast, the acidic medium (pH = 3) was favored for RO16 adsorption because of hydrogen bonding between the protonated form of azo dye and protonated hydroxyl groups at the surface of MR-LDH. The calculated maximum adsorption capacities for MB and RO16 were 54.01 and 53.04 mg/g at 313 K, respectively. The Langmuir model, which assumes monolayer adsorption on the adsorbent surface, provides the best explanation for the adsorption of both dyes (R² = 0.9991 for MB and R² = 0.9969 for RO16). Moreover, the pseudo-second-order kinetic model best described the adsorption process for MB (R² = 0.9970) and RO16 (R² = 0.9941). The proposed adsorbent maintains stable adsorption performance for four consecutive cycles. After each adsorption process, MR-LDH is easily separated by an external magnet. The findings show that MR-LDH was found to be an excellent adsorbent for the removal of both cationic and anionic organic dyes from aqueous solutions.