The maritime emission regulations and incentives require and motivate the selection of different types of energy systems, fuels, and abatement options. In early-stage ship design, the design space of possible combinations can be significant. Therefore, a selection tool has been developed to find the most satisfactory combination of abatement options at minimum costs that at least meet the emission requirements. This decision problem is studied from a general perspective to develop a universal selection tool to enable a widespread application in the maritime industry. The selection tool contains datasets with decision parameters of different energy systems, fuels, and abatement options. The energy systems, including reference fuels, can be selected and assessed on their annual economic and environmental performance. Both upstream and operational emissions are considered and, in addition, the external costs of the emissions are quantified. The abatement options, including fuels, have different effects on fuel consumption and emissions. Moreover, interaction effects occur when combining alternatives. The identified problem is a combinatorial optimisation problem and the objective space is constrained by the emission and compatibility constraints. It is formulated as a multi-objective optimisation problem, whereby the annual internal (investment plus operational) costs and external costs are simultaneously minimised. The external costs can serve as a balancing approach for emission reduction. Furthermore, it can encourage the reduction of the overall environmental impact beyond the regulatory emission constraints. A genetic optimisation algorithm is integrated into the selection tool, which optimises the combinations of abatement options that are subject to the applicable constraints. The functioning of the methodology is evaluated by case studies for the NAVAIS subjects: a battery-electric road ferry and a diesel-electric workboat, both for European waters. The results can provide useful insights into the concept design space of feasible combinations that comply with emission regulations.