Background: Invasion by different kinds of ballast water microorganisms is one of the most important marine environment problems around the world; therefore preventing the invasion of these unwanted and harmful stowaways is one of the main strategies of responsible agencies. Some of these methods such as ocean exchange, heating, filtration, hydro cyclones, UV irradiation and chemical treatment, have various problems such as technical deficiency, high costs, lack of safety and environmental side effects. Materials and Methods: A novel system of treatment by Gamma irradiation is designed to irradiate the blast water uniformly and effectively. To determine the dose distribution as a function of distance from the irradiation source, the MNCP code was used. The systems used for source implant in this simulation were Paterson-Parker, Paris and Network systems. In each system, Sivert-integral and inverse square law were used in MATLAB program to determine the dose distribution. Results: Results of initial laboratory tests on offshore water samples of Siri Island indicated that the appropriate dose for deactivation of organisms of water samples is approximately one kGy. It has been demonstrated that the dose can be provided by twenty five 100,000 Ci line sources of 60Co in a triangle implant arranged in a 1x1 x1 m3 cubic shape water pipe. In order to increase efficiency and radiation safety, water passed from two other coaxial and bigger cubes, after passing from the first cube. A one meter thick wall of concrete around the cubes was adequate to shield the system completely. Conclusion: The main advantages of this system such as high efficiency, safety, reliability, minimum environmental adverse effects, prove that this novel method not only can be used for ballast water treatment, but is also effective for drinking water purification.