A water treatment system including a filter, an aerator, a hydrogen absorption manifold, a first treatment container, a second treatment container, a magnetron, a boiler, a superheater, a fractional distillation separator and a condenser. The filter is adapted for removing chloride ions and transmutated chlorine ions, while the hydrogen absorptive manifold is designed for absorbing hydrogen ions and reducing the pH of the water. The magnetron alters the spin of an electron in an outer shell of an atom contained in the water so that a solution added to the water coats selective elements causing them to precipitate from the water. The boiler and superheater may be utilized to convert the water to a superheated steam, while the fractional distillation separator is adapted for condensing and separating elements, including radioactive elements, from the superheated steam. A method for treating contaminated water using the water treatment system is also provided.