Marine heatwaves along the coast ofWestern Australia, referred to as Ningaloo Niño, have had dramatic impacts on the ecosystem in the recent decade. A number of local and remote forcing mechanisms have been put forward, however little is known about the depth structure of such temperature extremes. Utilizing an eddy-active global Ocean General Circulation Model, Ningaloo Niño and the corresponding cold Ningaloo Niña events are investigated between 1958-2016, with focus on their depth structure. The relative roles of buoyancy and wind forcing are inferred from sensitivity experiments. Composites reveal a strong symmetry between cold and warm events in their vertical structure and associated large-scale spatial patterns. Temperature anomalies are largest at the surface, where buoyancy forcing is dominant and extend down to 300m depth (or deeper), with wind forcing being the main driver. Large-scale subsurface anomalies arise from a vertical modulation of the thermocline, extending from the western Pacific into the tropical eastern Indian Ocean. The strongest Ningaloo Niños in 2000 and 2011 are unprecedented compound events, where long-lasting high temperatures are accompanied by extreme freshening, which emerges in association with La Niñas, more common and persistent during the negative phase of the Interdecadal Pacific Oscillation. It is shown that Ningaloo Niños during La Nina phases have a distinctively deeper reach and are associated with a strengthening of the Leeuwin Current, while events during El Niño are limited to the surface layer temperatures, likely driven by local atmosphere-ocean feedbacks, without a clear imprint on salinity and velocity.