The accurate calculation of ground motions for future large earthquakes depends on detailed knowledge of three-dimensional (3D) geologic structure and the earthquake source process, as well as sufficient computational resources. In this article we describe the results of finite-difference simulations for the 1989 Loma Prieta, CA, earthquake, with a 3D seismic velocity model for the San Francisco Bay region and a heterogeneous slip model of the source. Additionally, we explore the sensitivity of the synthetics to the major geologic structures in the velocity model. The San Francisco Bay region (particularly the Loma Prieta region) is a unique area for the study of 3D wave propagation because of the pronounced lateral velocity contrasts across the strike-slip faults of the region. Understanding the effects of such long wavelength structure is doubly important when considering a source located close to such a contrast. Our simulations show that the lateral velocity contrast across the San Andreas Fault (SAF) would be expected to substantially affect the propagation of elastic waves radiated from a source in the Loma Prieta region. Indeed, we find that the refraction of energy by the SAF serves to reduce ground motions at stations located along the San Francisco Peninsula, and the Quaternary and Tertiary alluvial basins of the San Francisco Bay region are found to amplify and extend the duration of ground motions in Santa Clara Valley, Livermore Valley, and San Pablo Bay. We find that the 3D model as currently defined accurately describes the spatial variation of peak ground velocity for frequencies less than 0.5 Hz, which suggests that this model may be used to estimate ground motions for future earthquake scenarios.