To assess the ecological risk of phosphorus release from sediments in deep reservoirs and ensure water quality safety in the Danjiangkou Reservoir, the core water source area for the South-to-North Water Diversion Project, a three-dimensional risk index model coupling AD (active driver), MP (mobility potential), and ES (environmental stress) was innovatively developed. By integrating the diffusive gradients in thin-films, high-resolution peeper techniques, and machine learning, this research systematically reveals the spatiotemporal patterns and multidimensional driving mechanisms of sediment phosphorus release risk in deep reservoirs. Results show a low risk across the reservoir during the dry season. In the wet season, however, the deep enclosed bays and the deep inflow river mouth areas shift into ultra-high-risk hotspots. During this period, increased external inputs coupled with anaerobic conditions induced by thermal stratification enhance the amplification of AD and ES indices. This forms a dual risk mechanism characterized by “hypoxia stress and external enrichment,” elevating overall risk. Random forest analysis identifies DO_bottom (bottom dissolved oxygen) as the most critical factor, with a threshold effect observed. High risk of sediment phosphorus release is triggered directly by DO_bottom less than 3.5 mg/L. Notably, concentration of DGT_P>0.35 mg/L can still cause moderate risk even under aerobic conditions. Nonlinear interactions between DO_bottom-DGT_P and DO_bottom-ΔT are identified as core drivers of risk escalation. The former interaction primarily reflects biochemical synergy, while the latter underscores physicochemical coupling. Regarding inhibition mechanisms, shallow areas maintains high DO_bottom and weak stratification due to strong mixing, significantly mitigating MP risk. The transition zone forms a dual inhibitory barrier through the simultaneous reduction of both AD and MP. This study reveals the spatial mechanism whereby “topographic confinement-water depth gradient-external input” regulate AD, MP, and ES through cascade effects, providing a scientific basis for precise control of endogenous phosphorus in deep reservoirs.