The invention disclosed provides an apparatus and method for filtration and disinfection of ship's ballast water, such as sea water, based on hydrodynamic cavitation. The apparatus comprises a vortex diode with a tangential entry port and an axial outlet port with single or multiple bleeding holes. The disinfected water may be re-circulated through the system for additional disinfection or released from the tank into the surrounding waterways. The disinfection of seawater/ship's ballast water is achieved through filtration and hydrodynamic cavitation and the method does not involve use of any chemicals or any chemical reaction. The invented apparatus and method is simple, eco-friendly and can be fitted on to existing intake and discharge systems of any ship with minor modifications. It poses no risk to the health of the ship's crew unlike chemical methods and requires no special skill or additional manpower for its operation. The apparatus and method is capable of effectively sterilizing hazardous organisms contained in ballast water stored in a ballast tank.