We present an empirical model for describing the temporal variability of the internal tide, that uses seasonal harmonics to temporally modulate the amplitude of the fundamental tidal harmonics. 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 (non-stationary) harmonic model for the Indo-Australian Basin Region. The non-stationary model described up to 15 \% more baroclinic sea surface height and isotherm displacement variance than the fixed-amplitude harmonic model at some observation 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 produced by multiple generation sites. Application of the seasonal harmonic model demonstrates that temporal shifts in the standing wave locations coincide with seasonal variations in density stratification, particularly within 2 - 3 internal wave lengths from strong generation sites. It is shown that the variance fraction of internal tide signal explained by seasonal modulations is largest in standing wave node regions. This result helps explain the contrasting skill of the seasonal harmonic model at two moorings that were separated by only 38 km. Output of the harmonic model also demonstrates that the seasonally-evolving, southward propagating $M_2$ internal tide from Lombok Strait had a smaller amplitude in October when shear from the Indonesian Throughflow was strongest. Further applications for a regional internal tide climatology database are discussed.