Graphene Oxide has shown outstanding performance in the application of adsorption, but these adsorbents are still limited due to some factors. Assembling 2-dimensional (2D) nanomaterials into 3-dimensional (3D) macrostructure (microbead, hydrogel, aerogel, sponge) is a promising alternative to solve the limitation. This paper embedded GO into the two natural polysaccharide polymers (agarose and sodium alginate) to form a 3D-adsorbent. GO-Alg and GO-Agar microbeads were synthesized using the crosslinking method. Analysis techniques such as FT-IR, FESEM-EDX, XRD, and zeta potential were used to characterize the GO-containing microbeads. Adsorption parameters such as adsorbent dosage, pH, contact time, initial ion concentration, and temperature were optimized. Langmuir isotherm and pseudo-first-order kinetic model well fit into the experiment data. The maximum adsorption capacity (qmax) obtained was 120.37 mg.g−1 for removing methylene blue solution. Thermodynamic parameters such as ∆G˚, ∆H˚, and ∆S˚ were determined, and the process was considered endothermic and spontaneous. Reusability results showed good regeneration of GO-Alg microbead up to eight consecutive adsorption-desorption cycles without a significant drop in removal efficiency (> 96%). The application of GO-Alg microbead for MB removal on a packed-bed reactor was investigated in different experimental conditions, and 1 mL.min−1 flow rate with 15 cm bed height revealed a better result. The application of fluidized-bed adsorption was performed to solve the limitation of packed-bed adsorption, and the result showed better adsorption performance than packed-bed using the same operating condition.