Observed amplification and reverberation of ground motions in the Heathcote Valley during the 2010-2011 Canterbury Earthquake Sequence highlighted the lack of data on the subsurface velocity structure of sedimentary basins across New Zealand. A similar lack of data applies to the Hamilton Basin, a deep, predominantly alluvial, basin in the Waikato Region. In response, 13 deep shear wave velocity profiles have been measured in this study. Dispersion data obtained through active and passive methods were inverted with fundamental frequencies deduced from the horizontal-to-vertical spectral ratio method and a suite of layering ratios in the absence of detailed geological information. Potential for amplification is inferred from the large impedance contrasts at the soil-basement interface in the developed Vₛ profiles. The fundamental site period is over 5s in the Te Rapa and Gordonton depressions in the northern basin, where basement rock is up to 1400m deep. As basement shallows towards the south, fundamental periods shorten. Complex wave propagation occurs towards the southeastern basin influenced by ignimbrite deposition interspersed within the alluvial sediments of the Tauranga Group. Despite the variation in basement structure, velocities associated with lithology changes tend to be relatively consistent, allowing for the use of a four-unit velocity structure to represent basin deposits. The peat bogs which dominate the surficial landscape have significantly low shear wave velocities (28-38m/s), which presented unique difficulties in near surface velocity resolution. The soft near surface soil deposits across the basin have Vₛ₃₀ values ranging from 166-234m/s and four class E sites have been identified. Based on the new Vₛ profiles, a refined fundamental frequency-depth correlation was developed for the region. The results in this thesis are intended to inform site response analysis and seismic risk assessment.