To investigate the effect of the shallow, low-velocity sediments on the seismic wave field in the northern San Francisco Bay, we modeled tangential component displacement seismograms recorded during the 18 August 1999 MW 4.6 Bolinas, California, earthquake. The modeling indicates that the velocity structure of Pleistocene horizons in the San Francisco Bay is important for simulations of weak ground motions for Bay Area earthquakes. Models including the Pleistocene sediments generate the 1-sec-period surface waves observed at several stations. Modeling of Treasure and Yerba Buena Island records requires structures approximately an order of magnitude higher in spatial resolution than the current 3D velocity models for the region. This pair of sites, located only 2 km apart in the bay, records a sixfold difference in peak ground acceleration during the Bolinas earthquake. Three transects are forward modeled using 1D frequency-wavenumber integration and 2D finite-difference methods. Generally the ground motions are characterized by a direct shear wave (S0), a midcrustal reflection (S1), a near-receiver multiple (S2), and surface waves. The direct S0 arrival at all six stations requires a faster model than GIL7, the model routinely used to estimate earthquake source parameters using the Berkeley Digital Seismic Network. In addition, the timing of S1 indicates the possibility of a dipping midcrustal interface. S2 can be matched with a single strong impedance contrast at 3 km depth. A thin (200-m) surface layer of weathered rock and sediments simulates the surface waves that follow S2 at the Richmond Field Station site. However, the surface waves at Treasure Island and the Berkeley sites are longer in duration and higher amplitude than at Richmond and require 2D structure. A simple shallow uniform basin model for the San Francisco Bay consisting of stiff sediments (shear-wave velocity, β = 400 m/sec; thickness ∼100 m) over weathered rock (β = 1.5 km/sec) of the Franciscan assemblage produces surface waves in the 0.02-2 Hz passband at Treasure Island and the Berkeley sites.