The adoption of the International Convention for the Control and Management of Ships’ Ballast Water and Sediments (BWMC) in 2004 (herewith the Convention) has sought to prevent the spread of harmful aquatic organisms and pathogens in the ballast water and sediments of ships, threatening marine ecosystems worldwide. The Convention sets out the various requirements and the various steps vessels owners / operators and port States need to undertake in order to effectively manage ballast water and sediments. However, there are still open issues and uncertainty, including the scientific and practical challenges of sampling of ballast tanks and monitoring compliance with the Convention’s standards. In order to monitor compliance with the Convention’s standards, documented management practices can be inspected for appropriateness and inspection of vessel log books can give an indication that practices have been implemented. However, sampling is the most effective way to ensure compliance with standards set out in the Convention. To check compliance with the D-1 (exchange) standard, vessel log books should be inspected and sampling can be used to check for anomalies in the composition of the ballast water (e.g. salinity). D-1 compliance is intended as an interim step until treatment systems are more widely available – although, some ports may require exchange as well as treatment in the long term. Compliance with the D-2 (performance) standard following treatment of the ballast water requires the sampling of biological, chemical and physical parameters. Whether checking compliance to the D-1 or D-2 standards, there are significant sampling challenges. These include the logistics of gaining vessel access; having multiple sample methods available to suit ballast tank access restrictions; getting a representative sample; sample analyses; sample interpretation and; what to do if a sample fails? In addition to this, local requirements can present further challenges (e.g. small time windows for bacterial analysis). This paper will highlight the difficulties of sampling ballast tanks in practice, drawing from national and international experiences, and will also comment more broadly on the sampling process and governance – such as regional differences and the role of port State control. Drawing on protocols adopted by other states will help to facilitate a more efficient, consistent and organised implementation of the Convention to the shipping community worldwide.