During the MW 7.1 Hector Mine earthquake, peak ground velocities recorded at sites in the central San Bernardino basin region were up to 2 times larger and had significantly longer durations of strong shaking than sites just outside the basin. To better understand the effects of 3D structure on the long-period ground-motion response in this region, we have performed finite-difference simulations for this earthquake. The simulations are numerically accurate for periods of 2 sec and longer and incorporate the detailed spatial and temporal heterogeneity of source rupture, as well as complex 3D basin structure. Here, we analyze three models of the San Bernardino basin: model A (with structural constraints from gravity and seismic reflection data), model F (water well and seismic refraction data), and the Southern California Earthquake Center version 3 model (hydrologic and seismic refraction data). Models A and F are characterized by a gradual increase in sediment thickness toward the south with an abrupt step-up in the basement surface across the San Jacinto fault. The basin structure in the SCEC version 3 model has a nearly uniform sediment thickness of 1 km with little basement topography along the San Jacinto fault. In models A and F, we impose a layered velocity structure within the sediments based on the seismic refraction data and an assumed depth-dependent Vp/Vs ratio. Sediment velocities within the SCEC version 3 model are given by a smoothly varying rule-based function that is calibrated to the seismic refraction measurements. Due to computational limitations, the minimum shear-wave velocity is fixed at 600 m/sec in all of the models. Ground-motion simulations for both models A and F provide a reasonably good match to the amplitude and waveform characteristics of the recorded motions. In these models, surface waves are generated as energy enters the basin through the gradually sloping northern margin. Due to the basement step along the San Jacinto fault, the surface wave energy is confined to the region north of this structure, consistent with the observations. The SCEC version 3 model, lacking the basin geometry complexity present in the other two models, fails to provide a satisfactory match to the characteristics of the observed motions. Our study demonstrates the importance of using detailed and accurate basin geometry for predicting ground motions and also highlights the utility of integrating geological, geophysical, and seismological observations in the development and validation of 3D velocity models.