A nitrogen-doped magnetic graphene oxide (NMGO) was synthesized and applied as an adsorbent to remove Cu(II) and Cr(VI) ions from aqueous solutions. The individual and combined effects of various factors (A: pH, B: temperature, C: initial concentration of metal ions, D: CaCl2, and E: humic acid [HA]) on the adsorption were analyzed by a 25-1 fractional factorial design (FFD). The results from this study indicated that the NMGO had higher adsorption capacities for Cu(II) ions than for Cr(VI) ions under most conditions, and the five selected variables affected the two adsorption processes to different extents. A, AC, and C were the very important factors and interactions for Cu(II) adsorption. For Cr(VI) adsorption, A, B, C, AB, and BC were found to be very important influencing variables. The solution pH (A) was the most important influencing factor for removal of both the ions. The main effects of A-E on the removal of Cu(II) were positive. For Cr(VI) adsorption, the main effects of A and D were negative, while B, C, and E were observed to have positive effects. The maximum adsorption capacities for Cu(II) and Cr(VI) ions over NMGO were 146.365 and 72.978 mg/g, respectively, under optimal process conditions.