This paper shows a detailed, advanced procedure to implement cost–benefit analyses (CBAs) in order to assess the effectiveness of flood mitigation measures. The town of Lodi (North of Italy) has been selected as a case study for the research work, as it was hit by a large flood in 2002 for which several data are available. In order to compute the benefits, in terms of avoided damage with the mitigation measure in place, micro-scale damage models developed within the Flood-IMPAT + project were used. The great amount of input data for such models comes from results of a two-dimensional river modelling, for what concern the hazard parameters, and from open-source database, to evaluate the vulnerability and the exposure of the hit area. The research highlights that technological-advanced, high-performance hydraulic models allow taking into account a variety of hazard scenarios, with reasonable computational time, supporting the proper accounting of the probabilistic nature of risk in CBAs. Nonetheless, such high-resolution tools support the implementation of micro-scale damage assessment models, which can provide information on the distribution of benefits in the investigated area, increasing the effectiveness of CBAs for policy making.