Nanoplastic contamination is emerging as a significant threat to groundwater security on small islands, where freshwater lenses serve as primary water supplies. Existing groundwater management frameworks are largely based on salinity intrusion and do not account for the distinct transport behavior of nanoplastics. This study formulates a multi-physics numerical model incorporating variable-density groundwater flow, salt transport, and nanoplastic migration processes to investigate nanoplastic transport in idealized strip-island aquifers under pumping conditions. The model is calibrated using laboratory-scale data and evaluated at the field scale. Results show that nanoplastic migration is controlled not only by advection–dispersion processes but also by particle-specific interactions, leading to transport dynamics fundamentally different from those of dissolved salts. In particular, the higher effective dispersivity of nanoplastics causes earlier breakthrough at extraction wells and the formation of broader contaminant transition zones. Pronounced scale effects are observed: while laboratory simulations exhibit rapid upward coning and contamination, field-scale simulations indicate attenuated coning and stabilization over substantially longer timeframes. Sensitivity analysis identifies nanoplastic dispersivity as the dominant parameter influencing well contamination risk. These findings demonstrate that safe extraction strategies based solely on salinity thresholds may underestimate contamination risks and that well placement and pumping design must account for nanoplastic transition zones. The study provides a process-based framework for adapting groundwater management to emerging nanoplastic pollution in vulnerable island environments.<span></span>