An anti-fouling system for offshore drilling structures which injects metallic ions into seawater pumping systems. An ion generator may be positioned at various positions including the strainer basket of one or more of the seawater pumps or at various positions in the system. As well, ion generators may be skid mounted and/or otherwise centrally located and connected by controllable valves to various treated water injection points, whereby the flow rates are determined and ion concentrations are maintained at desired levels throughout the system, regardless of different pumping rates.