This study investigated the potential utility of poly (sodium N-undecanoyl-L-leucyl-valinate) (poly-L-SULV), poly (sodium N-undecanoyl-L-leucyl-alanate) (poly-L-SULA), and poly (sodium N-undecanoyl-glycinate) (poly-SUG) molecular micelles (MMs) as chelators for heavy metal (Cd, Cr, Cu, Co, and Ni) ion remediation of kaolinite clay using D-optimum experimental design. D-optimum experimental design was employed to simultaneously investigate the influence of design variables such as the buffer pH, chelator concentration, and centrifuge speed to evaluate the optimum conditions and to reduce the time and cost of metal ion remediation. The partition coefficients of the metal ion concentrations between the kaolinite clay and chelator equilibrium were also evaluated. In addition, the influence of metal ion concentrations on the remediation capability of the chelators was evaluated by conducting remediation studies at four different (10 ppm, 40 ppm, 60 ppm, and 80 ppm) metal ion concentrations. In general, the results of the remediation efficiency and partition coefficients obtained in this study are highly metal ion dependent and also dependent upon the chelator used for the remediation. Specifically, the remediation efficiency of the molecular micelles was found to be comparable to or better than the corresponding remediation efficiency obtained when SDS or EDTA was used for the remediation. However, at optimum conditions, poly-SULV and poly-L-SULA molecular micelle chelators demonstrated superior remediation efficiencies for Cr, with remediation efficiency of 99.9 ± 8.7% and 99.1 ± 0.7%, respectively.