The invention relates to a method and system for treating water within a water system to control one or more of scaling, corrosion, bacteria and algae. In particular, the invention relates to methods and systems for applying a superimposed time-varying frequency electromagnetic wave comprising both AC and DC components in a pulsating manner to water within a water system, such as, for example, cooling water systems, cooling towers, boiler systems and water storage systems. The method and the system of the invention significantly reduce capital costs and require very low energy, they avoid environmentally unfriendly final products, and are able to result in various treatment effects simultaneously.