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Urban flooding disrupts traffic networks, affecting mobility and disrupting residents’ access. Flooding events are predicted to increase due to climate change; therefore, understanding traffic network’s flood-caused disruption is critical to improving emergency planning and city resilience. This study reveals the anatomy of perturbed traffic networks by leveraging high-resolution traffic network data from a major flood event and advanced high-order network analysis. We evaluate travel times between every pairwise junction in the city and assess higher-order network geometry changes in the network to determine flood impacts. The findings show network-wide persistent increased travel times could last for weeks after the flood water has receded, even after modest flood failure. A modest flooding of 1.3% road segments caused 8% temporal expansion of the entire traffic network. The results also show that distant trips would experience a greater percentage increase in travel time. Also, the extent of the increase in travel time does not decay with distance from inundated areas, suggesting that the spatial reach of flood impacts extends beyond flooded areas. The findings of this study provide an important novel understanding of floods’ impacts on the functioning of traffic networks in terms of travel time and traffic network geometry.