The release of heavy metals into the environment as a result of industrial and agricultural activities represents one of the century’s most significant issues. Cobalt is a hazardous metal that is employed in a variety of industries. In this study, response surface methodology (RSM) combined with Box–Behnken design (BBD) was utilized to optimize the Co(II) ion removal from synthetic wastewater by the brown macroalga Padina pavonica. The influence of three factors, namely algal inoculum size, pH, and initial metal concentration, was assessed in optimization studies. RSM proposed a second-order quadratic model with a p-value of <0.0001 and R2 of 0.984 for P. pavonica. According to the data related to RSM optimization, the maximum percentage of Co(II) removal of 84.3% was attained under the conditions of algal inoculum size of 5.98 g/L, pH of 6.73, and initial Co(II) concentration of 21.63 mg/L. The experimental data from the biosorption process were fitted well with the Langmuir, Freundlich, and Temkin isotherm models. The maximal Co(II) adsorption capacity was estimated using the Langmuir model to be 17.98 mg/g. Furthermore, the pseudo-second-order kinetic model was shown to have the best fit for Co biosorption by P. pavonica, showing that the mechanism of Co(II) biosorption was chemisorption controlled by surface biosorption and intra-particle diffusion. Thermodynamic parameters were also investigated to evaluate the Gibbs free energy for the Co(II) ion, which was positive, showing that the biosorption process is nonspontaneous and exothermic, and the cobalt biosorption rate decreases with increasing temperature. Algal biomass was characterized by Fourier transform infrared spectroscopy, scanning electron microscopy, and energy dispersive spectroscopy. These analyses revealed the biosorbent’s diverse functional groups and porous, rough appearance. Therefore, P. pavonica can be used to implement sustainable, eco-friendly, and acceptable solutions to water pollution problems.