Shallow coal mining in gully regions has resulted in significant subsidence hazards and increased the risk of surface water inflow into mining panels, compromising the sustainability of surface water management and underground resource exploitation. In this study, the chain disaster process caused by shallow coal seam mining and heavy rainfall is quantitatively analyzed. The findings reveal that shallow coal seam mining leads to the formation of caved and fractured zones in the vertical direction of the overlying rock. The fractured zone can be further classified into a compression subsidence zone and a shear subsidence zone in the horizontal direction. The shear subsidence zone is responsible for generating compression and shear deformations, intercepting rainfall runoff, and potentially triggering landslides, necessitating crack landfill treatments, which are critical for promoting sustainable mining practices. The HEC-RAS program was utilized to integrate annual maximum daily rainfall data across different frequencies, enabling the establishment of a dynamic risk assessment model for barrier lakes. Numerical simulations based on unsaturated seepage theory provide insights into the infiltration and seepage behavior of rainfall in the study area, indicating a significant increase in saturation within lower gully terrain. Precipitation infiltration was found to enhance the saturation of the shallow rock mass, reducing matric suction in unsaturated areas. Finally, the disaster chain is discussed, and recommendations for managing different stages of risk are proposed. This study offers a valuable reference for the prevention and control of surface water damage under coal mining conditions in gully regions.