This paper compares empirical and theoretical site response using several different reference depths/conditions at the Garner Valley Downhole Array (GVDA). Empirical transfer functions (ETFs) from small amplitude ground motions are compared with 1D linear-viscoelastic theoretical transfer functions (TTFs) calculated using shear wave velocity (Vs) profiles obtained from both invasive and non-invasive seismic testing. A previous study at the GVDA demonstrated that suites of non-invasive Vs profiles produced TTFs that better matched ETFs between bedrock and the surface than TTFs developed from invasive Vs profiles. However, comparisons for other reference depths/conditions were not considered. This study shows that suites of non-invasive Vs profiles at the GVDA also produce more accurate TTFs than those from invasive Vs profiles for all reference depths/conditions, and that estimates of the fundamental site frequency from horizontal- to-vertical spectral ratios can be used as an effective metric to determine an appropriate reference condition in forward site response analysis.