Waterborne transport contributes to around 14% of the overall greenhouse gas emissions of transport in the European Union and it is among the most efficient modes of transport. Nonetheless, considering the aim of making the European Union carbon-neutral by 2050 and the fundamental role of waterborne transport within the European economy, effort is needed to reduce its environmental impact. This paper provides an assessment of research and innovation measures aiming at decreasing waterborne transport’s CO2 emissions by assessing European projects based on the European Commission’s Transport Research and Innovation Monitoring and Information System (TRIMIS). Additionally, it provides an outlook of the evolution of scientific publications and intellectual property activity in the area. The review of project findings suggests that there is no single measure which can be considered as a problem solver in the area of the reduction of waterborne CO2 emissions, and only the combination of different innovations should enable reaching this goal. The highlighted potential innovations include further development of lightweight composite materials, innovative hull repair methods, wind assisted propulsion, engine efficiency, waste heat electrification, hydrogen and alternative fuels. The assessment shows prevalence of funding allocated to technological measures; however, non-technological ones, like improved vessel navigation and allocation systems, also show a great potential for the reduction of CO2 emissions and reduction of negative environmental impacts of waterborne transport.