The Salar de Atacama in northern Chile accumulated halite during the Pliocene and Quaternary under conditions that alternated between a saline lake and a dry salt flat. Hidden beneath its uninterrupted flat surface is the Salar fault system. The halite deposits provide a high-resolution history of deformation. Contours on the ca. 5 Ma base of the halite unit in the southern salar, defined in a deep oil-exploration borehole and traced through reflection seismic lines, reveal that net reverse offset across the Salar fault system is down-to-the-east by ∼900 m; of that total, 200 m occurred during the Quaternary and 700 m during the Pliocene. Distributions, thicknesses, and geometries of eight stratigraphic sequences within the halite unit reveal a history of episodic faulting and demonstrate that faulting during approximately half the 5 m.y. interval, including the Holocene, did not generate fault scarps. We suggest that deposition caused by evaporation of ground water brines in the salt flat, rather than either dissolution or deflation, has smoothed the topography of the dry lake bed across the active fault zone. For the case of west-directed groundwater flow, we propose that the east-facing Salar fault system focuses groundwater flux along the eastern flank of the fault, which enhances halite precipitation in the downthrown block during desiccated stages and counteracts fault-driven topographic relief. The realization that a seismic risk may exist even though the Salar fault system is hidden leads to the appreciation that similar unrecognized seismic risks may exist in more populous arid basins.