As part of a multidisciplinary investigation of the structure and tectonics of the Queen Charlotte Basin and underlying crust, deep multichannel seismic reflection and coincident crustal refraction data were collected in 1988. Energy from the reflection air-gun array source was recorded at land sites at offsets appropriate to record crustal refraction and wide-angle reflection data. Refraction data recorded in a broadside geometry provide good three-dimensional coverage of western Hecate Strait. These data are modelled using tomographic inversion techniques to determine the three-dimensional velocity structure of the crust in this region. The one-dimensional average velocity increases rapidly with depth to 6.5 km/s at 7 km depth. Velocities from 7 to at least 12 km depth remain approximately constant and are associated with rocks of the Wrangellia terrane. Significant lateral velocity variations, including large differences in near-surface velocities attributable to surface features, relatively low velocities representing interbedded Tertiary sediments and volcanics, and a deep high-velocity anomaly that may represent the root of an igneous intrusion, are mapped. Wide-angle reflections from the Moho are used to determine the thickness of the crust. The Moho is at 29 km depth beneath the east coast of the Queen Charlotte Islands. This is deeper than the Moho observed below Queen Charlotte Sound and as deep as, or deeper than, that below Hecate Strait. Crustal thinning during Tertiary extension was thus greatest beneath the surface expression of the Queen Charlotte Basin, leaving the crust under the islands considerably thicker than under the basin. In an alternate or additional explanation, compression at the continental margin during the last 4 Ma may have been taken up by thickening or underplating of the continental crust beneath the islands. If the Pacific plate is subducting beneath the islands, the Moho observations constrain the slab to dip greater than 20–26°.