Currently, regional flood research often lacks a synergistic assessment of both flood occurrence risk and flood duration, limiting the comprehensive understanding needed for sustainable disaster risk reduction. To address this gap, this study applies advanced machine learning approaches to assess flood hazards in the Yangtze River Delta, one of China’s most economically and environmentally significant regions. Specifically, XGBoost is employed to evaluate flood occurrence risk, while LSTM is used to predict flood duration. A novel flood risk index (FRI) is proposed to quantify the integrated risk by combining these two dimensions, supporting more sustainable and effective flood risk management strategies. Furthermore, SHAP analysis is conducted to identify the most critical factors contributing to flooding. The results demonstrate that XGBoost delivers strong predictive performance, with average precision, recall, F1-score, accuracy, and AUC values of 0.823398, 0.831667, 0.827090, 0.826435, and 0.871062, respectively. Areas with high flood risk, long duration, and elevated FRI values are mainly concentrated in major river basins and coastal zones. The range of flood risk spans from 0.000073 to 0.998483 (mean: 0.237031), flood duration from 0.223598 to 2.077040 (mean: 0.940050), and FRI from 0 to 0.934256 (mean: 0.091711). Cities with over 40% of their areas falling in medium to high FRI zones include Suzhou (48.99%), Jiaxing (48.07%), Yangzhou (46.87%), Suqian (44.19%), Changzhou (43.43%), Wuxi (43.20%), Lianyungang (42.21%), Yancheng (40.88%), Huai’an (40.73%), and Bengbu (40.06%). SHAP analysis reveals that elevation and rainfall are the most critical factors influencing flood occurrence, underscoring the importance of integrating environmental variables into sustainable flood risk governance.
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