In this study, the effect of aligning nano-particles in the porous silica gel structure on the selectivity of adsorption was studied. Nano-magnetite particles were embedded into silica gel in order to produce nano-composite. By doing so, the agglomeration of nano-particles could be reduced and subsequently provided higher effective active sites for adsorption to take place. When the nano-particles in the gel matrix are aligned, it is expected to enhance the adsorption. Adsorption of Cu2+ and Cd2+ were conducted in both single ion system and binary mixture of the two to determine the adsorption performance using aligned and non-aligned gel composites. Improved selectivity of Cu2+ was observed in both single and binary system when aligned gel nano-composite was used compared to the non-aligned gel nano-composite. For copper and cadmium in single system, the removal percentage was enhanced from 23.6% to 36% and 15% to 16% respectively when the aligned gel was used instead of non-aligned nano-composite. Similarly for binary system, copper and cadmium removal percentage was enhanced from 15.7% to 21.3% and 6.3% to 10.2% respectively, when the aligned gel was used. This proved that when the nano-particles in the gel matrix are aligned, improvement in the performance of the gel nano-composite as adsorbent can be achieved. As for selective adsorption, it was noted that the removal percentage of copper was higher compared to cadmium in all cases performed. It was found that the magnetic field of the aligned gel increased the selectivity towards cadmium ions. Thus, the magnetic alignment of the aligned gel played a significant role where the selectivity of ions to be adsorbed could be controlled.