The aim of this work is to characterize and evaluate the retention of Cu2+ and Ni2+ from single and binary systems by alginate-Moroccan clay bio-composite with the utilization of calcium chloride as a cross-linking agent, using the ionotropic gelation method. The bio-nanocomposite was characterized by using a variety of techniques (SEM, EDX, XRD, and pHPZC). The efficiency of the adsorbent was investigated under different experimental conditions by varying parameters such as pH, initial concentration, and contact time. To demonstrate the adsorption kinetics, various kinetic models were tried and assessed, including pseudo-first-order, pseudo-second-order, intraparticle diffusion, and Elovich models. The research results show that the adsorption process of Cu2+ and Ni2+ metal ions follows a pseudo-second-order kinetic model, and the corresponding rate constants were identified. To evaluate the parameters related to the adsorption process in both single and binary systems, different mathematical models of isotherms, such as Langmuir, Freundlich, Temkin, and Dubinin-Radushkevich, were investigated. The correlation coefficients obtained showed that the most suitable isotherm for describing this adsorption process is the Langmuir model. The process is considered to be physical and endothermic, as suggested by the positive values of ΔH° and ΔS°, indicating increased randomness at the solid/liquid interface during Cu2+ and Ni2+ adsorption. Furthermore, the spontaneity of the process is confirmed by the negative values of ∆G°. The bio-nanocomposite beads demonstrated a maximum adsorption capacity of 370.37 mg/g for Ni2+ and 454.54 mg/g for Cu2+ in the single system. In the binary system, the maximum adsorption capacities were observed to be 357.14 mg/g for Ni2+ and 370.37 mg/g for Cu2+. There is significant evidence for the use of alginate-Moroccan clay bio-nanocomposite as a cost-effective alternative adsorbent for the efficient removal of metal ions in single and binary systems.