A dilatational step-over between the right-lateral Hayward and Rodgers Creek faults lies beneath San Pablo Bay in the San Francisco Bay area. A key seismic hazard issue is whether an earthquake on one of the faults could rupture through the step-over, enhancing its maximum possible magnitude. If ruptures are terminated at the step-over, then another important issue is how strain transfers through the step. We developed a combined seismic reflection and refraction cross section across south San Pablo Bay and found that the Hayward and Rodgers Creek faults converge to within 4 km of one another near the surface, about 2 km closer than previously thought. Interpretation of potential field data from San Pablo Bay indicated a low likelihood of strike-slip transfer faults connecting the Hayward and Rodgers Creek faults. Numerical simulations suggest that it is possible for a rupture to jump across a 4-km fault gap, although special stressing conditions are probably required (e.g., Harris and Day, 1993, 1999). Slip on the Hayward and Rodgers Creek faults is building an extensional pull-apart basin that could contain hazardous normal faults. We investigated strain in the pull-apart using a finite-element model and calculated a ∼0.02-MPa/yr differential stressing rate in the step-over on a least-principal-stress orientation nearly parallel to the strike-slip faults where they overlap. A 1- to 10-MPa stress-drop extensional earthquake is expected on normal faults oriented perpendicular to the strike-slip faults every 50–500 years. The last such earthquake might have been the 1898 M 6.0–6.5 shock in San Pablo Bay that apparently produced a small tsunami. Historical hydrographic surveys gathered before and after 1898 indicate abnormal subsidence of the bay floor within the step-over, possibly related to the earthquake. We used a hydrodynamic model to show that a dip-slip mechanism in north San Pablo Bay is the most likely 1898 rupture scenario to have caused the tsunami. While we find no strike-slip transfer fault between the Hayward and Rodgers Creek faults, a normal-fault link could enable through-going segmented rupture of both strike-slip faults and may pose an independent hazard of M ∼6 earthquakes like the 1898 event.