Abstract We employ differential adjoint tomography to suppress the effects of uneven noise sources and image the upper crust S wave velocity structure of San Gabriel Basin, Chino Basin and San Bernardino Basin in the northern Los Angeles. A Sequential Subdomain Inversion strategy is implemented to address regional imbalance of sensitivity kernel coverage and improve resolution in the region with suboptimal data coverage. Our results align well with known structures and reveal some undiscussed details in this region. Beyond delineating upper crustal structure, we analyzed the relationship between velocity anomalies and regional seismicity. Diffuse low‐velocity anomalies detected at the Fontana Seismicity region provide evidence for fluid migration. The high‐velocity channel within the San Jose Fault zone indicates that the fault acts as a water barrier. We also identified a concentrated low‐velocity anomaly between 0.8 and 4 km depth beneath Puddingstone Reservoir, potentially indicating groundwater seepage.