A variety of methods are utilized to reinvestigate the physical relationship between the seismic response of Treasure Island (TI) and Yerba Buena Island (YBI) in California. These islands are a soil (TI) and rock (YBI) site pair separated by 2 kin. The site pair has been used previously by researchers to identify soil response to earthquake shaking. Linear regime ground motions (M(W)4.0-M(W)4.6 and PGA: 0.014-0.017 g) recorded in the TI vertical array indicate a coherent wavefield in the sediments and an incoherence between the rock and sediments. Our analyses show that the greatest change in the wavefield occurred between the rock and soil layers, corresponding to a significant impedance contrast. The waveforms change very little as they propagate through the sediments, indicating that the site response is a cumulative effect of the entire soil structure and not a result of wave propagation within individual soil layers. In order to highlight the complexity of the site response, correlation analysis was used to demonstrate that the rock and soil ground motions were not highly coherent between the two sites. YBI was, therefore, shown to be an inappropriate reference site for TI. One-dimensional (1D) vertical wave propagation and inverse techniques were used to differentiate between 1D site response and more complex site behavior. Both 1D methods (vertical wave propagation and inverse transfer functions) proved incapable of capturing the site response at TI beyond the initial four seconds of motion. Finite difference waveform modeling, based on a two-dimensional velocity structure of the northern San Francisco Bay was needed to explain the linear site response at TI as horizontally propagating surface waves trapped in the bay sediments. A simplified velocity structure for the San Francisco Bay including a single 100 m basin layer (constant shear-wave velocity of 400 m/s) over a 1.5 km/s layer of Franciscan bedrock was able to trap energy in the basin and produce surface waveform ringing similar to that observed in the TI data. Due to surface waves propagating in the San Francisco Bay sediments, any.1D model will not fully characterize site response at TI. All 1D models will fail to produce the late arriving energy observed in the ground motions.