Recently, destruction and disturbance of marine ecosystem have been caused by adventive aquatic organisms. To solve the problems, water treatment technique is necessary to remove aquatic organisms efficiently. In this study, magnetic separation system for continuous removal of the aquatic organisms using superconducting magnet which generates strong magnetic field was developed. The jar tests to remove aquatic organisms using permanent magnet showed that nearly 100% of separation efficiency was achieved by aggregation of aquatic organisms using ferromagnetic particles and flocculants. Cost and waste reduction by lowering agent dosages was examined for practical application of magnetic separation system, and continuous processing equipment was designed by simulation and experiment using superconducting magnet.