Natural hazards including floods can trigger catastrophic failures in interdependent urban transport network-of-networks (NoNs). Population growth has enhanced transportation demand while urbanization and climate change have intensified urban floods. However, despite the clear need to develop actionable insights for improving the resilience of critical urban lifelines, the theory and methods remain underdeveloped. Furthermore, as infrastructure systems become more intelligent, security experts point to the growing threat of targeted cyber-physical attacks during natural hazards. Here we develop a hypothesis-driven resilience framework for urban transport NoNs, which we demonstrate on the London Rail Network (LRN). We find that topological attributes designed for maximizing efficiency rather than robustness render the network more vulnerable to compound natural-targeted disruptions including cascading failures. Our results suggest that an organizing principle for post-disruption recovery may be developed with network science principles. Our findings and frameworks can generalize to urban lifelines and more generally to real-world spatial networks.