India's National River Linking Project (NRLP) is a large-scale inter-basin water transfer scheme designed to address water scarcity and excesses by connecting surplus basins to deficit ones across the country. However, such large-scale hydrological alterations pose serious ecological risks. This study examines the potential role of river interlinking on the distribution and dynamics of freshwater invasive alien species and their interactions with native biodiversity across Indian river basins. We modelled the distribution of 15 naturalised freshwater IAS using species distribution models based on bioclimatic variables. These maps were then overlaid with basin-level freshwater biodiversity and threatened-species data, as well as the proposed river-linking network. The results reveal strong positive correlations between IAS richness and overall as well as threatened freshwater biodiversity, with biodiversity hotspots such as the Krishna, Godavari, Mahanadi, Brahmaputra, and Western Ghats basins being most at risk. The proposed interlinking routes are expected to act as ecological corridors, enabling biotic exchange among previously isolated basins. Such increased connectivity could accelerate biological invasions, disrupt migratory routes, alter hydrological regimes, and undermine ecosystem resilience. The findings emphasise the urgent need to incorporate invasion ecology and biodiversity safeguards into NRLP plans to prevent irreversible ecological damage.