Islands all over the world face common challenges connected to energy costs and greenhouse gas emissions. Thus, islands have been identified as perfect sites for implementing and testing innovative solutions to boost the green energy transition towards a sustainable and clean energy system. The supply of clean water is a major issue that affects small islands, and desalination, particularly Reverse Osmosis, represents a valid solution to this challenge. In this research, an energy system model is used to analyse long-term water and energy supply strategies of the tourist island of Favignana, Italy. The model is built with the Open Source long-term energy modelling tool OSeMOSYS at an hourly resolution. It considers both the potential synergies offered by Reverse Osmosis Desalination and the use of water storage to store the excess electricity when needed. The indirect emissions for the maritime transportation of goods and fuels (i.e., water and diesel) to the island are also accounted for. Different energy policies are compared to understand how a carbon tax, a limit on emissions and no policy would impact the long-term energy strategy of the island. The results show that a carbon tax that covers also the maritime transportation sector would lead to the lowest overall cumulative emissions. They additionally reveal that the contribution of emissions for maritime transportation of goods and fuels is relevant and cannot be neglected if a full decarbonisation has to be achieved. On the technological side, investment in a desalination plant is the most viable option in all cases. Finally, for the first time, OSeMOSYS is applied with hourly resolution and the results are compared with those obtained with lower time resolution showing that inaccuracies are found both for overall values and for the dispatching strategies.