Abstract: The present invention concerns a water injection system for EOR comprising in the direction of water flow: a water intake; a biocide tank for injecting a dose of biocide into the flow of water, a fine filtration unit able to retain particles of a size of 0.1 ?m or higher, a biofilm sensor in continuous contact with the water flow, a water injection line; as well as a method for removing a biofilm or controlling the formation of a biofilm on the surface of the pipes or the filtering elements of said water injection system wherein said method comprises the following steps: measuring the biofilm growth, response R of the biofilm sensor, comparing R with a reference value Ro, if R is higher than Ro, injecting a dose of biocide into the flow of water from the biocide tank.