An experimental study of the fundamental period of vibration of geologic strata above multiple impedance contrasts is presented for the Canterbury Plains, a deep, complex sedimentary basin on the South Island of New Zealand. Microtremor Horizontal-to-Vertical Spectral Ratio (mHVSR) analysis was used at 152 locations to investigate the fundamental period of the strata above three significant impedance contrasts in the region: the Riccarton Gravel, the Banks Peninsula volcanic (BPV) rock, and the deep graywacke basement bedrock. Up to three mHVSR peaks were observed in many of the mHVSR curves, with the long-period (2–7 s) peaks controlled by the BPV and/or the underlying bedrock. As the thickness of the BPV increases, the response of the geologic strata above the basement bedrock was masked by the shallower BPV, effectively changing the definition of what constitutes the reference condition (i.e. engineering bedrock) for site response analyses. The mHVSR peaks matched the long-period amplification peaks observed in the response spectra calculated from ground motions recorded during the Canterbury Earthquake Sequence events, underscoring the importance of the identification and consideration of deep impedance contrasts in site classification.