Surface modification of silica-coated magnesium ferrite nanoparticles (MgFe 2 O 4 @SiO 2 NPs) by 3-aminopropyltriethoxysilane (APTES) shows enhanced selectivity for the removal of Congo Red (CR) from both single and binary aqueous dye solutions. Before coating the surfaces of amine-functionalized magnesium ferrite nanoparticles (MgFe 2 O 4 −NH 2 NPs) with silica, control studies of the adsorption of cationic, neutral, and anionic dyes were performed using both single and binary dye systems. The studies found that the MgFe 2 O 4 −NH 2 nanoadsorbent favors the adsorption of indigo carmine (IC) and CR in single dye solutions (>90% removal efficiencies). However, MgFe 2 O 4 −NH 2 NPs preferentially adsorb CR in binary dye solutions. Interestingly, the selectivity of CR over IC depends on the initial concentration of IC/CR in the IC/CR binary systems. A further enhancement in the selective removal of CR in both single and binary dye solutions was achieved by coating the MgFe 2 O 4 −NH 2 NPs with silica followed by modification with APTES (i.e., APTES-modified MgFe 2 O 4 @SiO 2 NPs). The highly selective adsorption capacity for CR on the APTES-modified MgFe 2 O 4 @SiO 2 nanoadsorbent was attributed to the mixture of polar functional groups (i.e., −OH and −NH 2 ) on the surface of the nanoadsorbent, which facilitates adsorbent−adsorbate interactions such as electrostatic and hydrogen-bonding interactions, which are amplified for CR with its more numerous polar functional groups (i.e., amine, azo, and sulfonate groups). From the results, the APTES-modified MgFe 2 O 4 @SiO 2 nanoadsorbent offers an effective, inexpensive, and reusable/sustainable system for the selective removal and remediation of Congo Red from wastewaters.