Locating groundwater in deep-seated karst aquifers is inherently difficult. With seismic methods, we studied the upper epikarst and the underneath low-permeability volume (LPV) of several karst systems located in the southern Quercy and Larzac regions of France and found that refraction tomography was effective only in the epikarst and not in the LPV. We evaluated a 3D case study using a combination of surface records and downhole receivers to overcome this limitation. This 3D approach unveiled a set of elongated furrows at the base of the epikarst and identified heterogeneities deep inside the LPV that may represent high-permeability preferred pathways for water inside the karst. To achieve the same result when no borehole was available, we studied seismic amplitudes of the wavefield, recognizing that wave-induced fluid flow in low-permeability carbonates is a driving mechanism of seismic attenuation. We developed a workflow describing the heterogeneity of the LPV with spectral attributes derived from surface-consistent decomposition principles, and we validated its effectiveness at benchmark locations. We applied this workflow to the 3D study and found a low-amplitude signal area at depth; we interpreted this anomaly as a water-saturated body perched above the aquifer.