The sodium alginate-H3BO3 (SA-H3BO3) is traditionally used as bioremediation method for wastewater treatment in recirculating aquaculture system. Even though this method has many advantages (e.g., high cell loading) for immobilization, the remove of ammonium is not very effective. In this study, a modified method was built by adding polyvinyl alcohol and activated carbon into SA solution, and then crosslinked with saturated H3BO3-CaCl2 solution for creating new beads. Moreover, response surface methodology was utilized for optimizing the immobilization based on Box-Behnken design. The removal rate of ammonium in 96 h was taken as the primary performance criterion to characterize the biological activity of immobilized microorganisms (i.e., Chloyella pyrenoidosa, Spirulina platensis, Nitrifying bacteria, and Photosynthetic bacteria). Based on the results, the optimal parameter of immobilization as follows: the concentration of SA was 1.46%, the concentration of polyvinyl alcohol was 0.23%, the concentration of activated carbon was 0.11%, the crosslinking time was 29.33 h, and the pH was 6.6.