This paper presents a comprehensive literature review on the safety and risk assessment of storing and transferring hydrogen, ammonia, and methanol at port facilities. It examines regulations, safety standards, and guidelines that address the hazards and risks associated with alternative fuels in maritime operations. The paper also examines comprehensive documents from the European Maritime Safety Agency (EMSA), which offer critical insights and in-depth analyses on the application, safety, and environmental implications of these alternative fuels. Additionally, this review encompasses articles from scientific databases over the past decade, focusing on risk assessment studies related to the safe use of hydrogen, ammonia, and methanol as alternative marine fuels. The aim is to identify scientific gaps and harmonization challenges in the application of these fuels. By providing a comprehensive understanding of key safety concerns, this paper highlights the necessity for further research and regulatory alignment to ensure the safe implementation of hydrogen, ammonia, and methanol as marine fuels.