jats:titleAbstract</jats:title>jats:pWe present a new 3‐D seismic structural model of the eastern Indonesian region and its surroundings from full‐waveform inversion (FWI) that exploits seismic data filtered at periods between 15–150 s. jats:italicSASSY21</jats:italic>—a recent 3‐D FWI tomographic model of Southeast Asia—is used as a starting model, and our study region is characterized by particularly good data coverage, which facilitates a more refined image. We use the spectral‐element solver jats:italicSalvus</jats:italic> to determine the full 3‐D wavefield, accounting for the fluid ocean explicitly by solving a coupled system of acoustic and elastic wave equations. This is computationally more expensive but allows seismic waves within the water layer to be simulated, which becomes important for periods ≤20 s. We investigate path‐dependent effects of surface elevation (topography and bathymetry) and the fluid ocean on synthetic waveforms, and compare our final model to the tomographic result obtained with the frequently used ocean loading approximation. Furthermore, we highlight some of the key features of our final model—jats:italicSASSIER22</jats:italic>—after 34 L‐BFGS iterations, which reveals detailed anomalies down to the mantle transition zone, including a convergent double‐subduction zone along the southern segment of the Philippine Trench, which was not evident in the starting model. A more detailed illumination of the slab beneath the North Sulawesi Trench reveals a pronounced positive wavespeed anomaly down to 200 km depth, consistent with the maximum depth of seismicity, and a more diffuse but aseismic positive wavespeed anomaly that continues to the 410 km discontinuity.</jats:p>