The vulnerability of guided transport systems exposed to natural disasters is demonstrated in particular through the part of incidents on international railway networks due to intense weather conditions. Moreover, in the future, the frequencies of natural hazards will likely be intensified by climate change, increasing the consequences on transport systems and thus on railway mobility. The concept of resilience brings a new way of analyzing the impacts of natural risks on technical systems according to a systematic approach. Resilience can be defined as the capacity, for a system, to absorb changes and to persist beyond a disturbance. This approach offers the opportunity to investigate the complex interactions between a transport system and a natural hazard by analyzing the failures caused by cascade effect within the system. All these failures can be determined by using a combination of dependability and safety methods: the functional analysis, the failure mode and effects analysis and the event tree analysis. This methodology allows to build a tool based on the identification of the scenarios of successive failures that allows to assess related costs and repair times. The Prague subway flooding in 2002 is considered as a case study application of this tool.