Strong surface tides flowing over the Australian North West Shelf and through the Indonesian Archipelago generate large-amplitude internal tides that dominate the internal ocean temperature and velocity variability in the Indo-Australian Basin. On a global and regional scale, these waves are important due to their influence on vertical mixing affecting water mass properties, and on momentum budgets where frictional and wave-mean flow interactions alter the mean circulation. Here we use a combination of in-situ observations, satellite altimetry data, and a 3D ocean circulation model to demonstrate the spatial and seasonal variability of the internal tides in the region. We present a method for extracting these modulations from an internal-tide resolving regional 3D ocean model validated using observations. It is shown that internal tides reaching the Australian North West Shelf from Indonesia are modulated by seasonal changes in the strength of the Indonesian Throughflow and eddy structures in the Indo-Australian basin. These seasonal modulations lead to internal tides on the shelf that are still oscillatory, but only weakly correlated with the local surface tide forcing.