Loma Prieta aftershock data recorded in the Marina District of San Francisco clearly show a large amplification in ground motion and a much longer duration of shaking relative to the response recorded at nearby rock sites for frequencies between 1 and 10 Hz. Some of the amplification can be explained by the difference in impedance between the Marina sites and the rock sites; however, 1D models underpredict the amplification in the range 1 to 3 Hz and cannot account for the increased durations. The available geologic information within the Marina District indicates lateral variations in sediment thickness and composition. Our previous experience with modeling wave propagation in these types of basin environments has shown that these structures can greatly amplify and prolong the duration of the signals observed at sites within the basin. In this study, the seismic response of the Marina basin is modeled with a 3D finite-difference wave field simulation technique. Results from the numerical simulations at the basin sites indicate that the large amplitude arrivals following the direct S wave are surface waves traveling at relatively slow apparent velocities. In general, the surface waves contain the strongest recorded motions and produce the long duration of shaking observed at these sites. In addition, spectral ground motions from the 3D basin models do fairly well in reproducing the observed spectral amplification near 1 Hz that is characteristic of the basin sites. The simulation results suggest that focusing effects due to the geometry of the basin structure itself have a significant impact in determining the resonant periods at these basin sites.