Ballast water serves as a prevalent vector for aquatic invasive species transport in the Laurentian Great Lakes region. The International Maritime Organization (IMO) currently requires ballast water exchange for cargo ships entering the St. Lawrence Seaway, which serves to limit introduction of species from outside of the Great Lakes. Regulations within the Great Lakes, however, are inconsistent with Canada requiring that vessels built before 2009 must install ballast water management systems (BWMS) by 2030, while vessels built after 2009 must install BWMS by 2024. In the United States, there is currently no BWMS regulation for vessels trading exclusively in the Great Lakes. Even with no regulation, BWMS are currently in use in the Great Lakes region, and while not required, do use the numeric IMO discharge standards, designed for saltwater, as a target for treatment. These discharge standards use size class as their definition of organisms, with less than 10 µm being the microorganism size class. Fecal indicators such as Escherichia coli, Enterococci spp. and Vibrio cholerae are used to assess whether BWMS treatments meet these discharge standards. BWMS treatments are in general successful in disinfecting this size class, however there is often not sufficient concentration of fecal indicators in uptake water to challenge the system and make meaningful conclusions about the treatment. The Lake Superior Research Institute has been researching BWMS since 1998 and in 2020 have established a research and development plan to inform regulators of whether market ready BWMS are able to effectively achieve discharge standards when operated in the Great Lakes region. Here we describe the current state of BWMS in the Laurentian Great Lakes, along with challenges with microbial discharge standards.