Due to the great exploitation of maritime traffic, care must be taken to the protection of the marine environment. It has been proven that worldwide transported ballast waters alongside with freights have a very negative impact on the marine environment. However, ballast waters are essential for almost every commercial vessel to maintain the required stability. It is highly probable that there are numerous organisms and pathogens in the transported ballast. When organisms and pathogens reach into a new marine environment through ballast water, they become a threat to all indigenous organisms of that environment. This paper will describe the legal regulations of the different maritime organizations in the world which are dealing with this issue. In addition, there are also described methods which are being used to prevent the spread of harmful organisms with the ballast waters. The emphasis will be on shipboard ballast treatment systems, and ballast water sediments will also be described. All relevant treatment methods will be described, regulations for obtaining the necessary approvals by the authorities as well as application in practice of ballast water treatment plants.