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The adverse effect of climate change continues to expand, and the risks of flooding are increasing. Despite advances in network science and risk analysis, we lack a systematic mathematical framework for road network percolation under the disturbance of flooding. The difficulty is rooted in the unique three-dimensional nature of a flood, where altitude plays a critical role as the third dimension, and the current network-based framework is unsuitable for it. Here we develop a failure model to study the effect of floods on road networks; the result covers 90.6% of road closures and 94.1% of flooded streets resulting from Hurricane Harvey. We study the effects of floods on road networks in China and the United States, showing a discontinuous phase transition, indicating that a small local disturbance may lead to a large-scale systematic malfunction of the entire road network at a critical point. Our integrated approach opens avenues for understanding the resilience of critical infrastructure networks against floods.