Given the effects of steep dips and large lateral variations in seismic velocity beneath the Vancouver Island continental shelf, seismic processing and travel time inversion are inadequate to obtain a detailed velocity model of the subsurface. Therefore, seismic full waveform inversion is applied to multichannel seismic reflection data to obtain a high-resolution velocity model beneath the Tofino fore-arc basin under the continental shelf off Vancouver Island margin. Seismic velocities obtained in this study help in understanding the shallow shelf sediment structures, as well as the deeper structures associated with accreted terranes, such as Pacific Rim and Crescent terranes. Shallow high velocities, as large as ∼5 km/s, were modeled in the mid-shelf region at ∼1.5–2.0 km depth. These coincide with an anticlinal structure in the seismic data, and possibly indicate the shallowest occurrence of the volcanic Crescent terrane. In general, seismic velocities increase landward, indicating sediment over-consolidation related to the compressional regime associated with the ongoing subduction of the Juan de Fuca plate and the emplacement of Pacific Rim and Crescent accreted terranes. Seismic velocities show a sharp increase about 10 km west of Vancouver Island, possibly indicating an underlying transition to the Pacific Rim terrane. A prominent low velocity zone extending over 10 km is observed in the velocity model at 800–900 m below the seafloor. This possibly indicates the presence of a high porosity layer associated with lithology changes. Alternatively, this may indicate fluid over-pressure or over-pressured gas in this potential hydrocarbon environment.