Detecting and quantifying water flow structures in heterogeneous karst through geophysical imagery of karst structures, is open to large uncertainties. Here we determine that subterranean flow-induced seismic signal originating in karst subsurface water pathways such as fractures, conduits and caves can be detected as persistent frequencies on spectrograms. Conducting passive seismic surveys on two karst sites with shallow and deep conduits show that these frequencies are site dependent, and differ from what might be expected from surface water flow in rivers. We applied an amplitude-based location method to locate this flow-induced micro-tremor. Numerical simulation of the elasto-acoustic wave propagation in a simplified karst model shows that resonance plays an important role, excited by specific frequencies in the flow-related seismic spectrum. This study introduces a novel approach for detecting the flowing structures in karst by directly imaging the source itself rather than inferring flow pathways through geophysical imaging of karst structures. Waveform data is available from the GEOFON data centre, under network code 3V.