We present an empirical model of the seasonal variability of the internal tide using seasonal harmonics to modulate the amplitude of the fundamental tidal constituents. Internal tide data, from both long-term, in-situ moorings and a mesoscale- and internal tide-resolving ocean model, are used to demonstrate the performance of the seasonal harmonic model for the Indo-Australian Basin Region. The seasonal model describes up to 15 % more of the observed (baroclinic) sea surface height variance than a fixed-amplitude harmonic mode at the mooring sites. The ocean model results demonstrate that the study region, which includes the Australian North West Shelf (NWS), Timor Sea and southern Indonesian Islands, is dominated by standing wave interference patterns due to the presence of multiple generation sites. The seasonal harmonic model reveals that temporal shifts in the standing wave patterns coincide with seasonal variations in density stratification. This shift is particularly evident within distances of 2 - 3 internal wave lengths from strong generation sites. The fraction of the variance of the internal tide signal explained by seasonal modulations is largest in standing wave node regions, contributing to differences in predictive skill of the seasonal harmonic model at two moorings separated by only 38 km. Output of the harmonic model also demonstrated that the seasonally-evolving M2 internal tide propagating southward from Lombok Strait had a small amplitude in October when shear from the Indonesian Throughflow was strongest.