A new three-dimensional (3-D) model shows seismic velocities beneath the Puget Lowland to a depth of 11 km. The model is based on a tomographic inversion of nearly one million first-arrival travel times recorded during the 1998 Seismic Hazards Investigation in Puget Sound (SHIPS), allowing higher-resolution mapping of subsurface structures than previously possible. The model allows us to refine the subsurface geometry of previously proposed faults (e.g., Seattle, Hood Canal, southern Whidbey Island, and Devils Mountain fault zones) as well as to identify structures (Tacoma, Lofall, and Sequim fault zones) that warrant additional study. The largest and most important of these newly identified structures lies along the northern boundary of the Tacoma basin; we informally refer to this structure here as the Tacoma fault zone. Although tomography cannot provide information on the recency of motion on any structure, Holocene earthquake activity on the Tacoma fault zone is suggested by seismicity along it and paleoseismic evidence for abrupt uplift of tidal marsh deposits to its north. The tomography reveals four large, west to northwest trending low-velocity basins (Tacoma, Seattle, Everett, and Port Townsend) separated by regions of higher velocity ridges that are coincident with fault-bounded uplifts of Eocene Crescent Formation basalt and pre-Tertiary basement. The shapes of the basins and uplifts are similar to those observed in gravity data; gravity anomalies calculated from the 3-D tomography model are in close agreement with the observed anomalies. In velocity cross sections the Tacoma and Seattle basins are asymmetric: the basin floor dips gently toward a steep boundary with the adjacent high-velocity uplift, locally with a velocity “overhang” that suggests a basin vergent thrust fault boundary. Crustal fault zones grow from minor folds into much larger structures along strike. Inferred structural relief across the Tacoma fault zone increases by several kilometers westward along the fault zone to Lynch Cove, where we interpret it as a zone of south vergent faulting overthrusting Tacoma basin. In contrast, structural relief along the Seattle fault zone decreases west of Seattle, which we interpret as evidence that the N-S directed compression is being accommodated by slip transfer between the Seattle and Tacoma fault zones. Together, the Tacoma and Seattle fault zones raise the Seattle uplift, one of a series of east-west trending, pop-up structures underlying Puget Lowland from the Black Hills to the San Juan Islands.