Waterproof dam concrete’s permeability stability in goaf waterlogged environments critically impacts coal mine safety and groundwater sustainability. Underwater immersion, weak infiltration pathways are formed at the joint interfaces of the composite structure (concrete-concrete), potentially triggering water damage incidents. Optimization research on interface anti-seepage performance is urgently required. This study focuses on the composite structure of waterproof concrete dams, analyzing permeability modification by nano SiO2/TiO2/Al2O3 at varying percentages on bi-material specimens post-immersion. Gas permeability, Liquid-measured porosity test, Ultrasonic velocity, and SEM were performed to evaluate the permeability evolution and interface stability of nanomaterial-modified concrete after different days of water immersion. Results indicate that post 14-day immersion, the permeability of ordinary concrete monomer specimens (OC) and bi-material specimens (C-C) increased to 0.236×10-5μm2 and 0.760×10-3μm2, respectively, corresponding to degradation levels of 220.5% and 88.5%. Moreover, the permeability of C-C remained two orders of magnitude higher than that of OC, and their degradation followed a three-stage pattern: rapid amplification, moderate development, and gradual stabilization. Nanomaterial incorporation suppressed permeability deterioration, particularly the 0.5% TiO2 group, showing optimal performance. Post-immersion, the 0.5%TiO2 group showed 0.236×10-3μm2 permeability, representing a 69.0% improvement relative to the C-C. Other groups demonstrated modification effects of 55.9% for 0.5%Al2O3, 52.6% for 1.0%Al2O3, 42.1% for 1.0%TiO2, and 24.4% for 0.5%SiO2, while the addition of 1.0%SiO2 exhibited no significant improvement. Liquid-measured and ultrasonic tests showed the 0.5% TiO2 group had 16.4% lower porosity and 14.2% higher wave velocity post-immersion. SEM analysis demonstrated that nano-TiO2 effectively suppressed the expansion of interface cracks, and image binarization processing revealed a 49.6% reduction in fracture surface porosity in the 0.5%TiO2 group, resulting in a denser interface microstructure and enhanced permeability stability. This study establishes key technical foundations for optimizing composite structural materials for waterproof concrete dams, thereby enhancing permeability stability in underground storage facilities and related engineering structures.