Transport greenhouse gas emissions are mainly caused by the use of fossil fuels, e.g., gasoline and diesel. This case study for the Netherlands calculates how alternative fuels, e.g., electricity, hydrogen or biofuels, contribute to policy aims to decarbonize transport. Alternative fuels, produced in various ways, have different carbon (CF), land (LFs) and water footprints (WFs). This study assesses CFs, LFs and WFs for fuels (kgCO2e/m2/m3 per GJ), showing differences among fuels dependent on primary energy sources. It calculates CFs, LFs and WFs for four scenarios with different fuels. The biofuel scenario is not attractive. CFs slightly decrease, while LFs and WFs increase enormously. The electricity scenario has small CFs and the smallest LFs and WFs, but this is only when using wind or solar energy. If storage is needed and hydrogen is produced using wind energy, CFs double from 3055 to 7074 kg CO2e, LFs increase from 15 106 to 43 106 m2 and WFs from 3 106 to 37 106 m3 compared to the electricity scenario. The case study shows that wise fuel choices contribute to policy aims to decarbonize transport, although LFs and WFs are also important to consider. These case study results are relevant for sustainable transportation transitions worldwide.