The European inland waterway transport consumes about 6.2 TWh of fossil diesel per year. To reduce greenhouse gas (GHG) emissions in accordance with the European reduction goals, the fossil diesel must be substituted by alternative energy carriers. The direct use of electricity (battery-based), e-hydrogen and e-methanol are identified as most suitable for this large-scale (retrofit) transition. The remaining emissions and costs are assessed from a Well-to-Wake perspective using a modular modelling framework which has been set up within the European innovation action project SYNERGETICS. The GHG emissions of the examined alternatives range from 20 to 380 gCO2e(fossil)/kWh for the year 2020. Although there will not be net zero supply paths, the GHG emissions can be significantly reduced compared to fossil diesel with 350 gCO2e(fossil)/kWh. Unlike for fossil diesel, the remaining GHG emissions will be dominated by the Well-to-Tank part. Thus, well-chosen supply paths become even more important in the future. In fact, a full Well-to-Wake perspective should be applied where possible. The costs range from 0.25 to 0.60 EUR/kWh for the year 2020, compared to 0.05 EUR/kWh for fossil diesel. Hence, effective policies and regulations are needed to tackle this cost difference. Battery-electric powered vessels show lower nitrogen oxide (NOx) and particulate matter (PM) emissions than those powered by fossil diesel. However, e-hydrogen and e-methanol vessels have higher NOx and PM emissions due to the more complex supply paths. Bio-based options lack sustainable biomass capacities.