The Hayward Fault System is considered the most likely fault system in the San Francisco Bay Area, California, to produce a major earthquake in the next 30 years. To better understand this fault system, we use microseismicity to study its structure and kinematics. We present a new 3D seismic-velocity model for the eastern San Francisco Bay region, using microseismicity and controlled sources, which reveals a ???10% velocity contrast across the Hayward fault in the upper 10 km, with higher velocity in the Franciscan Complex to the west relative to the Great Valley Sequence to the east. This contrast is imaged more sharply in our localized model than in previous regional-scale models. Thick Cenozoic sedimentary basins, such as the Livermore basin, which may experience particularly strong shaking during an earthquake, are imaged in the model. The accurate earthquake locations and focal mechanisms obtained by using the 3D model allow us to study fault complexity and its implications for seismic hazard. The relocated hypocenters along the Hayward Fault in general are consistent with a near-vertical or steeply east-dipping fault zone. The southern Hayward fault merges smoothly with the Calaveras fault at depth, suggesting that large earthquakes may rupture across both faults. The use of the 3D velocity model reveals that most earthquakes along the Hayward fault have near-vertical strike-slip focal mechanisms, consistent with the large-scale orientation and sense of slip of the fault, with no evidence for zones of complex fracturing acting as barriers to earthquake rupture.