The paleogeography of New Guinea indicates fluctuating periods of flooding and emergence since the Jurassic, which are inconsistent with estimates of global sea level change since the Eocene. The role of deep Earth dynamics in explaining these discrepancies has not been explored, despite the strongly time-dependent geodynamic setting within which New Guinea has evolved. We aim to investigate the role of subduction-driven mantle flow in controlling long-wavelength dynamic topography and its manifestation in the regional sedimentary record, within a tectonically complex region leading to orogeny. We couple regionally refined global plate reconstructions with forward geodynamic models to compare trends of dynamic topography with estimates of eustasy and regional paleogeography. Qualitative corroboration of modelled mantle structure with equivalent tomographic profiles allows us to ground-truth the models. We show that predicted dynamic topography correlates with the paleogeographic record of New Guinea from the Jurassic to the present. We find that subduction at the East Gondwana margin locally enhanced the high eustatic sea levels from the Early Cretaceous (∼145 Ma) to generate long-term regional flooding. During the Miocene, however, dynamic subsidence associated with subduction of the Maramuni Arc played a fundamental role in causing long-term inundation of New Guinea during a period of global sea level fall.