Abstract Subsurface structures play important roles in seismic ground motion, crustal hydrology, stability of the built environment, and more. Constraining temporal changes of subsurface shear wave velocity (VS) can provide useful information to all these topics and the growing field of hydrological monitoring with seismic velocity. Using borehole records at Garner Valley, CA, we estimate seasonal subsurface VS variations from impulse response functions (IRFs) of earthquake data (2005–2018) along with IRFs and cross-correlation of cross-hole experiment data (2015–2018). The inferred VS variations are up to ∼25% in the top 6 m and ∼10% at 2–5 m in depth. The VS variations correlate strongly with the water table depth changes, suggesting that the changes are mostly due to fluctuations of pore pressure in the shallow material. The shallow velocity changes alter the near-surface conditions, can affect seismic hazard estimation, and may be improperly attributed to deeper processes without careful analysis.