The Albuquerque–Belen and Socorro basins reside in the central Rio Grande rift and partially overlie the midcrustal Socorro magma body (SMB), the inflation of which contributes to ongoing seismicity and localized uplift of the region. Rayleigh‐wave dispersion measurements extracted from ambient noise cross correlation of seismic data collected from the Sevilleta seismic array in the southern Albuquerque and northern Socorro basins were inverted to obtain Rayleigh‐wave phase‐velocity maps at 3–7 s. Tomography results indicate large () lateral variations in Rayleigh‐wave phase velocities at this period range. Rayleigh‐wave velocities were inverted utilizing a nonlinear Monte Carlo Markov chain method to obtain a 3D S‐wave velocity in the uppermost 10 km of the crust. At shallow depths (), S‐wave velocity models show low‐velocity () anomalies in the Rio Grande rift axis, mainly due to Cenozoic rift sediments, and relatively higher () velocities in the local mountain ranges could be due to older or volcanic rocks. At 8–10 km depth, this relationship is inverted, and higher S‐wave velocities () are generally more present beneath the rift axis than beneath the surrounding ranges. We suggest that the elevated S‐wave velocities () could be related to a large (30 km by 12 km) granitic pluton found below the sediment cover in Consortium for Continental Reflection Profiling (COCORP) reflection profiles in the Abo Pass survey (line 2A). The low S‐wave velocities could be related to structural changes in moderate‐to‐high‐grade metamorphism of midcrustal rocks and upper‐crustal extension from ongoing uplift of the northern part of midcrustal SMB.