We have studied the possibility of advanced water purification by using a high-gradient superconducting magnetic separation (HGSMS) with magnetic activated carbon. The purpose of this system is a high-speed removal of humic acid, other persistent organic matters and ammonia nitrogen from raw water without secondary wastes. We synthesized two types of magnetic adsorbents. One is a magnetic mesoporous activated carbon (MMPC) for humic acid and other organic matters, and the other is an oxidized magnetic activated carbon (Ox-MAC) for ammonia nitrogen. By means of expanding micro-pores by heat treatment, the humic acid was able to be efficiently absorbed by MMPC. About 80% of ammonia nitrogen can be adsorbed from 0.8 mg/L of ammonium chloride solution by Ox-MAC due to the acid functionalities fixed on the surface. Since the adsorbed humic acid and ammonia nitrogen are easily released from the adsorbents by heating in atmosphere at low temperatures, these adsorbents are reusable. By using HGSMS, MMPC with a large magnetization of about 16.4 can be collected from the solution by 99.95% at a high speed flow velocity of 1 m/s and relatively low magnetic fields under 2 T. These results show that the HGSMS with the magnetic activated carbon may be a good candidate for a new advanced water purification system with a high speed treatment and no secondary wastes.