This thesis aims at exploring different sources of uncertainty related to the economic analysis of the flood risk. It embraces several fields of knowledge in order to determine how the selection of strategies used to model flood hazard and assess the vulnerability of a territory may affect damage potential estimations. We measured the variability of damage estimations as a function of the datasets, methods, models and scales considered to: analyse the probability of floods (hydrology); model and map flood hazard (hydraulics); assess the vulnerability and susceptibility of properties to floods (civil engineering, geography and environmental economics). The methods and analyses developed here should bring support for practitioners in the investigation of uncertainties, determination of evaluation priorities and optimisation of the distribution of resources between the different modules of the evaluation process. In order to explore a second level of complexity of flood risk evaluations, we developed a method for analysing the systemic vulnerability of infrastructure networks, in relation with their resilience.