Nuclear accident-derived radionuclide dispersion poses critical challenges to marine ecological sustainability and human–ocean interdependence. While existing studies focus on hydrodynamic modeling of pollutant transport, the link between nuclear safety and sustainable ocean governance remains underexplored. This study investigates radionuclide diffusion patterns in semi-enclosed bays using a high-resolution coupled hydrodynamic particle-tracking model, explicitly addressing threats to marine ecosystem stability and coastal socioeconomic resilience. Simulations revealed that tidal oscillations and topographic constraints prolong pollutant retention by 40% compared to open seas, elevating local concentration peaks by 2–3× and intensifying bioaccumulation risks in benthic organisms. These findings directly inform sustainable marine resource management: the identified high-risk zones enable targeted monitoring of fishery resources, while diffusion pathways guide coastal zoning policies to decouple economic activities from contamination hotspots. Compared to Fukushima’s open-ocean dispersion models, our framework uniquely quantifies how semi-enclosed geomorphology exacerbates localized ecological degradation, providing actionable metrics for balancing nuclear energy development with UN Sustainable Development Goals (SDGs) 14 and 3. By integrating hydrodynamic specificity with ecosystem vulnerability thresholds, this work advances science-based protocols for sustainable nuclear facility siting and marine spatial planning.