The search for alternatives to petroleum-based hydrocarbon fuels for marine propulsion systems is driven primarily by environmental factors. This article formulates the requirements that alternative fuels must meet and identifies the most promising: hydrogen, ammonia, and methanol. The article analyzes the existing experience of using these fuels in marine propulsion systems, identifying the problems and necessary upgrades to marine engines. The article describes existing methods for producing hydrogen, ammonia, and methanol, outlining their advantages and disadvantages. It is noted that most existing technologies for producing alternative fuels require significant energy inputs and are accompanied by harmful emissions into the atmosphere. Therefore, when assessing the energy efficiency of using alternative fuels, it is necessary to consider energy and environmental factors in both the use and production of fuel. Directions for further scientific research in the field of alternative fuels for marine propulsion systems are outlined. The goal of this research is to develop an approach that ensures an objective assessment of the environmental impact of switching to alternative fuels. The study concluded that the use of hydrogen, ammonia, and methanol in marine propulsion systems offers potential for reducing the carbon footprint of maritime transport, although it may increase NOx emissions. The actual environmental impact should be assessed across the entire fuel life cycle—from raw material extraction to combustion. Current production technologies for these fuels are too energy-intensive and economically unviable, and marine engines require significant modernization. Expanding their use is only possible with further improvements in fuel production technologies and internal combustion engine operating processes.