We present models of the three-dimensional (3D) seismic attenuation structure, both Qp and Qs, for a 16 km2 area centered on the San Andreas Fault Observatory at Depth (SAFOD). The P- and S-wave t*-values used in the inversion were determined from local earthquake data recorded by seismic network and portable array stations within the Parkfield region by inverting arrival spectra for source parameters, t*, and site response. Two techniques for determining the site response, the joint and alternating methods, were compared and it was found that the alternating method significantly underestimated site response variations. The t*-values were inverted to obtain 3D frequency-independent Qp and Qs models using 3DVp and Vs models and associated event locations. A shallow low-Q area (Qp and Qs about 50–75) on the southwest edge of both models is attributed to the low-velocity Cenozoic sedimentary rocks that overlie the Salinian basement rock. A high-Q feature (Qp and Qs about 250 to 300) abuts this area and is interpreted as the Salinian basement. Adjacent to the San Andreas fault (SAF) trace, on its southwest side, there is a low-Q feature (Qp and Qs about 50–80) attributed to a wedge of sedimentary rocks; uniformly low Qp- and Qs-values suggest that the wedge is fluid rich. A low-Q basin feature (Qp and Qs about 50–75) on the northeast side of the SAF is interpreted as a fluid rich zone. Beneath this area there is a high-Q feature (Qp and Qs about 220–300), which may be caused by crack closure due to increased pressure with depth in the rocks of the Franciscan formation. Given these high Q-values, it seems unlikely that this area acts as a fluid pathway for fluids entering the fault zone from the east into the seismogenic zone of the SAF.