Abstract: A method and apparatus in which water is magnetically treated to kill microorganisms such as bacteria colonies in water systems, thereby reducing the requirements and cost of watersystem maintenance and the quantity of toxic chemical treatments released to the environment. The method includes removing a volume of water from a bacterially or microorganism contaminated environment, magnetically treating the water, then returning the treated water back to the environment. The apparatus includes a permanent magnet of alternating polarity to form a magnetic field through which the water is treated and passed.