Renewable fuels contribute to net zero emissions by replacing fossil fuels in the transportation sector. Nevertheless, there are significant environmental concerns associated with renewable energy development, including land and water usage. This research explores the use of land and water related to large-scale renewable fuel production. We develop a multi-objective mathematical model to determine the optimal supply chain design for the EU's future renewable fuel demand in the transportation sector. We propose a flexible, multi-period, and multi-stage supply chain design that can accommodate multiple feedstocks and multiple products and that takes the seasonality of the resources into account. We consider economic and environmental impacts by minimizing total system costs, land use, and water use. Based on the analysis of the results, we gain insights into conflicting objective functions and the associated trade-offs and synergies to assist decision-makers in selecting an appropriate framework and gaining a better understanding of future opportunities and impacts of renewable fuel production. The outcome demonstrates that, despite not being a desirable alternative in terms of water and land usage, the utilization of energy crops as raw material has economic benefits. As shown by the results, the burden of such a supply chain lies with renewable electricity requirements that could be the capacity bottleneck and require investments. We find that we could achieve a nearly optimal value of land use and water use by increasing total cost by only 10%.