I would say the best way to track the injected amendment into the ground or an aquifer is to use a chemical tracer along with the amendment injection. If the injected tracer has a conductivity contrast with the environment, it would be easy to see the trajectory of the injection by Electrical Resistivity Imaging (ERI) survey using time lapse method. Resistivity measurements are often fast surveys (when the array setup on the ground is completed) and time lapse measurements can be done within matter of minutes.
In most cases of remediation or amendments, the petrophysical properties of the study area would be changed due to the amendment. I cases that amendment leads to a new mineral phase formation or biofilm formation (biofilm is any group of microorganisms in which cells stick to each other and often these cells adhere to a surface), the best methods would be those that are sensitive to changes in porefluid-grain interface. Studies have shown that Spectral Induced Polarization (SIP) is sensitive to both mentioned factors.
It is hard to determine if longterm changes are related to biological activities with only geophysics; however, a simple soil sampling would help to prove such an assumption that changes detected by geophysics are related to a biological activity. Such changes can be seen by permanent installation of geophysical instruments at a site or conducting frequent measurements over a long period of time.