Flooding events can produce significant disturbances in underground transport systems within urban areas and lead to economic and technical consequences, which can be worsened by variations in the occurrence of climate extremes. Within the framework of the European project RESCCUE (RESilience to cope with Climate Change in Urban arEas—a multi-sectorial approach focusing on water), climate projections for the city of Barcelona manifest meaningful increases in maximum rainfall intensities for the 2100 horizon. A better comprehension of these impacts and their conditions is consequently needed. A hydrodynamic modelling process was carried out on Barcelona Metro Line 3, as it was identified as vulnerable to pluvial flooding events. The Metro line and all its components are simulated in the urban drainage models as a system of computational link and nodes reproducing the main physical characteristics like slopes and cross-sections when embedded in the current 1D/2D hydrodynamic model of Barcelona used in the project RESCCUE. This study presents a risk analysis focused on ensuring transport service continuity in flood events. The results reveal that two of the 26 stations on Metro Line 3 are exposed to a high risk of flooding in current rainfall conditions, and 11 of the 26 stations on Metro Line 3 are exposed to a high risk of flooding in future rainfall conditions for a 20-year return period event, which affects Metro service in terms of increased risk. This research gives insights for stakeholders and policymakers to enhance urban flood risk management, as a reasonable approach to tackle this issue for Metro systems worldwide. This study provides a baseline for assessing potential flood outcomes in Metro systems and can be used to evaluate adaptation measures’ effectiveness.