A “Well-to-Propeller” Life Cycle Assessment of maritime transport was performed with a European geographical focus. Four typical types of vessels with specific operational profiles were assessed: a container vessel and a tanker (both with 2-stroke engines), a passenger roll-on/roll-off (Ro-Pax) and a cruise vessel (both with 4-stroke engines). All main engines were dual fuel operated with Heavy Fuel Oil (HFO) or Liquefied Natural Gas (LNG). Alternative onshore and offshore fuel supply chains were considered. Primary energy use and greenhouse gas emissions were assessed. Raw material extraction was found to be the most impactful life cycle stage (~90% of total energy use). Regarding greenhouse gases, liquefaction was the key issue. When transitioning from HFO to LNG, the systems were mainly influenced by a reduction in cargo capacity due to bunkering requirements and methane slip, which depends on the fuel supply chain (onshore has 64% more slip than offshore) and the engine type (4-stroke engines have 20% more slip than 2-stroke engines). The combination of alternative fuel supply chains and specific operational profiles allowed for a complete system assessment. The results demonstrated that multiple opposing drivers affect the environmental performance of maritime transport, a useful insight towards establishing emission abatement strategies.