The San Andreas fault (SAF) is one of the most studied strike‐slip faults in the world; yet its subsurface geometry is still uncertain in most locations. The Salton Seismic Imaging Project (SSIP) was undertaken to image the structure surrounding the SAF and also its subsurface geometry. We present SSIP studies at two locations in the Coachella Valley of the northern Salton trough. On our line 4, a fault‐crossing profile just north of the Salton Sea, sedimentary basin depth reaches 4 km southwest of the SAF. On our line 6, a fault‐crossing profile at the north end of the Coachella Valley, sedimentary basin depth is ∼2–3  km and centered on the central, most active trace of the SAF. Subsurface geometry of the SAF and nearby faults along these two lines is determined using a new method of seismic‐reflection imaging, combined with potential‐field studies and earthquakes. Below a 6–9 km depth range, the SAF dips ∼50°–60° NE, and above this depth range it dips more steeply. Nearby faults are also imaged in the upper 10 km, many of which dip steeply and project to mapped surface fault traces. These secondary faults may join the SAF at depths below about 10 km to form a flower‐like structure. In Appendix D, we show that rupture on a northeast‐dipping SAF, using a single plane that approximates the two dips seen in our study, produces shaking that differs from shaking calculated for the Great California ShakeOut, for which the southern SAF was modeled as vertical in most places: shorter‐period (T<1  s) shaking is increased locally by up to a factor of 2 on the hanging wall and is decreased locally by up to a factor of 2 on the footwall, compared to shaking calculated for a vertical fault.