The surface of silica spheres was modified using 3-mercaptopropyl trimethoxysilane (MPTMS) with an acid catalyst and a base catalyst. Large aggregation was observed for the spheres modified with an acid catalyst. The spheres modified with an acid catalyst (ACS) show aggregated spheres. However, no aggregation was observed for the spheres modified with a base catalyst (BCS). Aqueous lead solutions with 625 and 1663 ppm were used to test the removal of lead ions. Various amounts of modified spheres were treated to the lead solutions. The lead concentration drastically decreased with the increase of the amount of the spheres. The lead removal efficiency for the BCS is much more effective than that of ACS. For more-quantitative analysis of the residual lead concentration, inductive coupled plasma-mass spectrometry (ICP-MS) was employed. As the amount of spheres increased, the lead concentration drastically decreased. The lowest concentration of 1.2 ppb was obtained, which indicates that the lead ion can be completely removed from the aqueous system.