Emissions of nitrogen oxides (NOx) from marine propulsion systems have gained public interest resulting in emission limits as defined by the International Maritime Organization (IMO) with IMO Tier III, especially for vessels operating in Emission Control Areas (ECA). The reduction of greenhouse gas emissions is also increasingly important for marine propulsion. Minimizing NOx while reducing climate impact calls for technologies such as the gas engine with aftertreatment systems, preferably with the ability to run on alternative fuels. A proven technology for reducing NOx in marine engines is the Selective Catalytic Reduction (SCR) aftertreatment system. It is also possible to avoid engine raw emissions by shifting the combustion process to lower temperature levels. Hydrogen is an alternative fuel with combustion properties enabling premixed operation at significantly higher air-fuel ratio than natural gas (NG) and thus, reducing raw NOx emissions. The study uses a systematic approach to compare emissions and efficiency of a lean-burn gas engine with a natural gas and a mild conversion hydrogen setup, utilizing two different strategies: combustion of NG with the assumption of an SCR catalyst and high raw NOx emissions and combustion of pure hydrogen using the NOx reduction potential of higher excess air. The scope of the study makes it possible to illustrate engine concepts for future applications in the displacement class of 4.8 L per cylinder. The highest efficiency of 45.3% was achieved with the natural gas engine and SCR. The concept with the lowest Global Warming Potential (GWP) was the hydrogen fueled engine under the prerequisite of using green hydrogen, accompanied by a reduction in efficiency of 0.6% compared to the efficiency optimum of NG with SCR. Assuming the use of gray hydrogen, the GWP was 48% and 52% higher than with NG and NG with SCR, respectively, at the efficiency-optimal operating points.