© 2015 Elsevier Ltd. Isolated carbonate build-ups (ICBs) represent attractive hydrocarbon exploration targets. They are often seen as long-term transgressive features, but their distribution within basins and growth history can be difficult to predict as they respond to the interplay between various tectonic, eustatic and oceanographic parameters. Here we use a 3D seismic megasurvey (18,000km2) combined with well data to understand the timing and mechanisms of formation of tropical Quaternary ICBs in NW Australia. At present the ICBs are typically 1-30km wide and form clusters of ~150 build-ups, developing 2-85km from the edge of a 650km-wide continental shelf. Our results demonstrate that the structural evolution of the margin had a major impact on the distribution of the ICBs. Main period of fault activity commenced during the latest Miocene-Early Pliocene, corresponding to the initial collision of the Australian Plate with Banda Arc. Fault activity increased from Late Pliocene and peaked during the Early Pleistocene. It was associated with flexural reactivation of structural highs (uplift) and lows (subsidence) along the shelf-margin. Seismic evidence of moat channel and drift deposits suggest that contour current activity intensified during the late Early Pleistocene (ca. 1MaBP). Despite potentially good conditions for carbonate production (basement highs and warm water ocean currents), ICBs did not form until the Mid Pleistocene (ca. 0.582-0.8MaBP). This age corresponds to the onset of major sea level fluctuations associated with repeated, high-amplitude (+120m) rapid deglacial rises and slow falls. Thus, we infer that the NW Australia ICBs formed due to: (1) structural shaping of the margin; (2) oceanographic changes, and most importantly, (3) onset of repeated high-amplitude transgressions reactivating the carbonate production along isolated highs following 4th-5th order lowstand exposures and allowing catching-up carbonate morphologies to develop.