The five-mile-long Elizabeth Tunnel, which crosses the San Andreas fault (SAF) zone near Lake Hughes, California, is part of the Los Angeles Aqueduct (LAA) that delivers water from Owens Valley to the City of Los Angeles. Geologic characterization of the Elizabeth Tunnel alignment is focused on developing a better understanding of fault displacement hazards at the SAF crossing to support design of both short- and long-term strategies to increase the earthquake resilience of the City’s water supply system. The results of this study define a fault zone that is wider and more complex at the surface than at tunnel depth. A 750-ft transect of deep, angled core borings, located ~ 100 ft west of, and parallel to the tunnel alignment, penetrated a wide zone (>550 ft) of fault-damaged granitic and gneissic rocks containing a few thick fault zones that can be correlated confidently between borings as well as a multitude of very thin faults and shears throughout the rock mass. Fault rocks are predominantly defined as coherent cataclasites and ultracataclasites, as opposed to incoherent clay gouge, even at this relatively shallow sampling depth. Integrating geomorphic, geologic, petrographic, and geophysical data defines a steeply south-dipping SAF that splays upward and increases in complexity toward the surface, and provides the basis for engineering design considerations at this critical SAF crossing.