An accepted solution to the environmental problems related to a ship's ballast water has been the adoption and proper utilization of approved onboard ballast water plans and management systems (BWMS). On 8 September 2017, the International Maritime Organization Ballast Water Management Convention comes into force, and under this Convention, ships engaged in international trade must have an approved BWMS aboard to discharge ballast water, reducing species transfer. In response to enormous global concern about this problem, the overwhelming majority of the BWMS, approved currently for use by International Maritime Organization (IMO) and United States Coast Guard, utilize two main technologies (electro-chlorination or ultraviolet irradiation) as their principle mode of disinfection, often used in combination with filtration. However, both technologies have been questioned regarding their practically, efficiency, and possible environmental impacts upon discharge. This review article aims to explore some questions about these two technologies, drawing attention to some current uncertainties associated with their use. Also, it draws attention to some technical obstacles and regulatory impediments related to the new development of green biocide technology, which largely has been ignored, despite its potential as a simpler, cleaner and effective technology.