Urban stormwater runoff pollution has emerged as a pressing concern, with heavy metals emerging as a primary contaminant. This poses a significant threat to the ecological environment and human health. As an effective management measure, heavy bioretention systems are often subject to different degrees of wet and dry alternation, resulting in changes in the accumulation patterns of heavy metals in the system. In this study, a simulation system was constructed and experimental groups with varying dry and wet alternation cycles were established. We then proceeded to analyze the morphological transformations of Cd²⁺ and Pb²⁺ using the continuous extraction method, thereby unveiling the mechanism behind changes in the bioefficacy of heavy metals under dry and wet alternation. The results demonstrated that wet-dry alternation significantly altered the morphological distribution of heavy metals. Specifically, the exchangeable states of Cd²⁺ and Pb²⁺ decreased by 3%-7% and 2%-3%, respectively, during the drought period. However, these metals increased by 1%-4% after rewatering. The bioavailability of Cd and Pb exhibited an increase in response to short-term wet-dry alternation, while long-term drought resulted in a decrease. This study elucidates the regulatory principles that govern the alterations in the morphology and bioavailability of heavy metals under conditions of wet and dry alternation. This provides a theoretical basis for controlling heavy metal pollution in urban storm-water and optimizing bioretention systems.