A three-dimensional numerical flow model for the Zhoushan Archipelago waters using FVCOM is developed to simulate the complex flow field in high-pile wharf foundation zones. The model employs direct numerical simulation with high-resolution ~1.0 m grid to resolve flow patterns around pile structures. Key findings reveal a dual-scale flow retardation effect: (1) macro-scale velocity reduction (70–85%) across the entire pile group area, and more critically (2) extreme localized velocity attenuation (90–98%) due to individual pile sheltering effects. This research identifies a self-amplifying sedimentation mechanism where: (i) hydrodynamic weakening creates localized deposition hotspots with 30–50% higher accumulation rates than surrounding areas, (ii) newly formed sediment deposits further enhance piles’ flow-blocking capacity by 15–25%, and (iii) the intensified sheltering effects accelerate subsequent sedimentation.