AbstractHydrometeorological phenomena have increased in intensity and frequency in last decades, with Europe as one of the most affected areas. This accounts for considerable economic losses in the region. Regional adaptation strategies for costs minimization require a comprehensive assessment of the disasters’ economic impacts at a multiple‐region scale. This article adapts the flood footprint method for multiple‐region assessment of total economic impact and applies it to the 2009 Central European Floods event. The flood footprint is an impact accounting framework based on the input–output methodology to economically assess the physical damage (direct) and production shortfalls (indirect) within a region and wider economic networks, caused by a climate disaster. Here, the model is extended through the capital matrix, to enable diverse recovery strategies. According to the results, indirect losses represent a considerable proportion of the total costs of a natural disaster, and most of them occur in nonhighly directly impacted industries. For the 2009 Central European Floods, the indirect losses represent 65% out of total, and 70% of it comes from four industries: business services, manufacture general, construction, and commerce. Additionally, results show that more industrialized economies would suffer more indirect losses than less‐industrialized ones, in spite of being less vulnerable to direct shocks. This may link to their specific economic structures of high capital‐intensity and strong interindustrial linkages.