Fluid-fracture surface interaction, caused by different mechanisms, is one of the underlying reasons for permeability reduction over long period of time in different georesources, such as deep geothermal systems and shale gas/oil reservoirs. The sensitivity of the ultrasonic signatures (e.g., frequency content, velocity, amplitude, and attenuation) to the changes in fracture aperture caused by fluid-fracture surface interactions can be considered as a probe for flow-induced fracture aperture evolution. Flow-through tests on an artificially fractured phyllite specimen from a geothermal reservoir along with the concurrent measurements of ultrasonic signatures of P- and cross-polarized S-waves demonstrated the sensitivity of ultrasonic signatures to the evolution of fracture aperture/permeability under a constant state of stress (i.e., constant pore and confining pressures). In particular, the closure of the fracture and the decrease of permeability led to an increase of the P-wave velocity, a decrease of the P-wave attenuation, and an increase of the S-wave amplitude. In addition, time evolution of the time-frequency maps of the transmitted ultrasonic waves revealed that partitioning of the frequency content slightly changes because the fracture aperture/permeability is altered. Specifically, alterations in hydraulic aperture are reflected in the changes of time-frequency partitioning, whereas under constant hydraulic aperture, the time-frequency partitioning is unaltered.