A method and a modular system for performing a sterilizing treatment of ballast waters (12) onboard of a ship (10), for reducing and/or removing the contents of invasive living micro-organisms. A water loading pump (13) and a water preliminary filtering stage (14) are operatively connected to a plurality of ballast water storing tanks (11); a UV sterilizing apparatus (18) for the ballast water is submerged into the ballast water in each water storing tank (11), and is operatively connected to a local control unit (QE). Each UV sterilizing apparatus (18) comprises a UV radiation source (28). The ballast water (12) inside each storing tank (11) is recirculated although the UV radiation source (28), for a required time and mixed with the ballast water inside the water storage tank (11) to enable the living micro-organisms to be substantially reduced or eliminated, during the navigation.