Marine shipping, responsible for about 80% of global trade by volume, also contributes 3% of global greenhouse gas (GHG) emissions. In line with the International Maritime Organization’s (IMO) net-zero strategy, Canada has set ambitious GHG reduction targets for its marine sector. Given the sector's reliance on fossil fuels and the urgent need for decarbonization, marine operators are particularly interested in near-term alternatives like biodiesel and renewable diesel for achieving interim targets by 2030. However, significant gaps remain in understanding the supply feasibility of these fuels in the Canadian context, including feedstock availability, market fluctuations, and biofuel policies. This research evaluates biodiesel and renewable diesel supply chain vulnerabilities in Canada to support marine operators’ decision-making from a supply feasibility perspective. This thesis addresses these gaps by developing a comprehensive vulnerability assessment framework for biodiesel and renewable diesel supply chains, combining a suite of systems analysis methods. Inspired by the Drivers, Pressures, States, Impacts, Response (DPSIR) framework, this study identifies and defines key pressures and state indicators for both alternatives. Causal loop diagrams (CLDs) are developed to map how these pressures can influence the reliability and consistency of fuel supply through the measurement of state indicators. Strategy mapping analysis, using graph theory and complex network theory, further highlights the interconnection of international and domestic supply chains and the vulnerable supply chain processes, such as feedstock supply and end-user demand. To ground the conceptual assessment framework in real-world application, this thesis explores four regional case studies of Canadian biodiesel and renewable diesel supply chains, assessing the unique regional supply challenges faced by marine operators. For instance, in the Arctic, extreme cold can cause biodiesel to gel, making renewable diesel a more reliable, though costly, alternative for marine operators. In the Atlantic, market fluctuations driven by competitive demand from other sectors and global influences raise concerns about domestic supply availability for government operators and create significant cost uncertainties for commercial operators. These case studies clarify how these factors shape regional fuel preferences, inform strategies for adopting alternative fuels, and strengthen consistent and reliable fuel supply in Canada.