As important socio-economic zones, deltas are increasingly threatened by floods under global climate change. Understanding the response of arterial traffic systems to flood risks in sensitive delta area is vital for the operation of the regional economy and society. This study examined the impacts of the temporal and spatial changes in rainfall on flood risks in traffic systems in the Yangtze River Delta in China. We constructed a framework for assessing flood risk in the arterial traffic system under changing rainfall regimes. Thirteen representative spatial indices enabled calculation of hazard, exposure, and vulnerability, producing associated flood risk values. Results show an increase, during 1960–2017, in rainfall-related flood risks for the arterial traffic system in the Yangtze River Delta. In particular, the proportion of areas with medium and high risk levels increased over 20 %. These results suggest a strong correlation between increasing flood risks and the spatial and temporal patterns of changing rainfall regimes under global climate change. Changes in rainfall, therefore, are important in assessing and managing the risks posed by floods, in the Yangtze River delta and other similar urbanized sensitive river deltas.