An automatic heat exchanger flushing and maintenance system includes a heat exchanger having coolant circulation passages and raw water circulation passages disposed in thermal contact with the coolant circulation passages, an engine disposed in fluid communication with the coolant circulation passages, a raw water inlet conduit disposed in fluid communication with the raw water circulation passages of the heat exchanger, a flush fluid supply disposed in fluid communication with the raw water circulation passages of the heat exchanger, at least one flush fluid valve disposed between the flush fluid supply and the raw water circulation passages of the heat exchanger and a valve controller disposed in communication with the at least one flush fluid valve and operable to open and close the at least one flush fluid valve.