During the Canterbury earthquake sequence, the observed level of ground motion on the soft soils of Christchurch was very strong and highly variable. Many studies are now emerging that analyse the amplification effect of these soft soils, usually by estimating a frequency-dependent amplification function relative to a rock outcrop station, or ‘reference site’. If the rock outcrop has its own amplification due to weathering or topographic effects, then the calculated amplification for the soil sites can be compromised. This study examines ten seismic stations in Canterbury to determine the best reference site for Christchurch, using the horizontal-to-vertical spectral ratio (HVSR) method for S-wave shaking. More broadly, this study uses HVSR to expand existing knowledge of the dynamic characteristics of seismic stations in the Canterbury area. Most rock stations show their own local amplification effects that reduce their individual ability to be used as reference stations. The recently installed Huntsbury station (HUNS) appears to be the best reference site for Christchurch, but this will need to be verified when more records become available. In the meantime, the D13C temporary station is currently the best reference station for site effect studies in both Christchurch and Lyttelton.