For smooth implementation of the IMO Ballast Water Management Convention that is to come into effect in the near future, IMO and Member States are working on the development of various technologies and establishment of legislative action. Ballast water treatment systems are essential, yet difficult technologies, as they need not only to treat living organisms, but also define whether they are viable or not, count the number of viable organisms, and present quantitative results of the concentration of active substances. Despite the fact that the Convention is looming in the near future, the issues mentioned above obstruct the setup of consensual technologies for performance reliability of the treatment system and analysis method of efficacy test results. This paper considers the unsolved issues of the ballast water treatment technologies, and presents guidelines to solve these issues.