It is timely to raise cyber security awareness while attacks on maritime infrastructure have not yet gained critical momentum. This paper analyses vulnerabilities in existing shipborne systems and a range of measures to protect them. It discusses Information Technology network flaws, describes issues with Industrial Control Systems, and lays out major weaknesses in the Automated Identification System, Electronic Chart Display Information System and Very Small Aperture Terminals. The countermeasures relate to the concept of “Defence-in-depth”, and describe procedural and technical solutions. The maritime sector is interconnected and exposed to cyber threats. Internet satellite connections are feasible and omnipresent on vessels, offshore platforms and even submarines. It enables services that are critical for safety and rescue operations, navigation and communication in a physically remote environment. Remote control of processes and machinery brings benefits for safety and efficiency and commercial pressure drives the development and adaptation of new technologies. These advancements include sensor fusion, augmented reality and artificial intelligence and will lead the way to the paradigm of “smart” shipping. Forecasts suggest unmanned, autonomous ships in international waters by 2035. This paper is the starting point for future research, to help mapping out the risks and protect the maritime community from cyber threats.