Monitoring time‐lapse changes in subsurface physical properties of the near‐surface critical zone is increasingly important with respect to climate change, environmental conservation/remediation, geohazard mitigation, and geotechnical engineering activities. Innovative controlled‐source cross‐well seismic monitoring surveys combined with full waveform inversion analysis enable us to map small and highly localized changes by repeatedly scanning the subsurface between borehole sensors at depth. In the Kanto Basin, Japan, we successfully monitor the dynamic transient fluid‐flow effects of the subsurface injection of microbubble water, which is of interest for soil contamination remediation and preventing earthquake liquefaction. The fluid migration is detected by observing P‐wave velocity changes (∼1%) within a very thin (∼1 m) sediment layer at a depth of ∼25 m. The injected microbubble water of the differential physical properties (temperature) is observed to follow geological and hydrologic preferential fluid‐flow paths rather than diffusing equally in all directions away from the injection well.