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 distribiution 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 distribiution. 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  1x1x1  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,  proves  that  this  novel  method  not  only can  be used  for  ballast  water  treatment,  but  is  also  effective  for  drinking  water  purification.