The main questions which will be addressed in this paper are; which ballast water treatment system (BWTS) should be fitted to a fleet of small general cargo ships that are trading in Northern Europe, including the Baltic Sea, and how will the implementation of the Ballast Water Management Convention (BWMC, herewith “the Convention”) will affect the engine room crew? There is a large capital cost in the purchasing and fitting of such a system, and as the vessels in question have some special requirements, such as operating in very cold weather and having small engine rooms, the correct system must be chosen. As the small engine room crew, consisting of a chief engineer and an oiler, must be able to operate, maintain and repair the system, the chosen system will impact on their working life while onboard these vessels. To answer the research questions, all the chief engineers employed by the Company and a number of shore superintendents from other shipping companies, involved in the management of small general cargo ships were surveyed using questionnaires. Their responses were then analysed and conclusions drawn from this analysis. The criteria required to choose a ballast water treatment system was narrowed down during the research, and then used to find the most suitable system for the company vessels. A small number of systems currently in production from well-known manufacturers were evaluated during this process. Following evaluation of the systems using the responses from the respondents, the most suitable system for the company vessels was identified and chosen. The need for training was also identified to successfully operate and maintain the system, and to reduce any additional stress that may be experienced by the crew due to the BWMC. The research also contains a review of the BWMC, and a comparison with measures brought in by the United States Coast Guard (USCG), which include the transfer of harmful aquatic organisms and pathogens, (HAOP) by merchant vessels from area to area by other methods that are ignored by the BWMC. It also considers the long-term health effects on the crew and marine ecosystem from treated ballast water using some types of treatment systems. The report of the survey provides scope for a more informed decision making process when choosing a BWTS for a small general cargo vessel. However, in addition, the process can be applied to any type of vessel as many of the issues encountered will be the same regardless of size and trading pattern.