This study utilized ambient seismic noise tomography to investigate correlations of hydrogeological systems with heterogeneous porosity with the internal velocity structure of karst aquifers using the Floridan Aquifer System (FAS) as an example. We conducted a seismic signal analysis with 30 days of vertical component seismic data acquired within the Santa Fe River Sink‐Rise system (Sink‐Rise System), using power spectral density estimates and frequency‐wavenumber analysis to identify any noise source biases. Empirical Green's functions were derived through phase cross‐correlations and phase‐weighted stacking. The functions allowed extraction of group velocity dispersion measurements, which were inverted to generate 2D tomographic images at various periods. Tomographic images show multiple layers with varying group velocities that aligned with known hydrogeological features of the FAS, including its base, low‐porosity and low‐permeability dolostone semiconfining units characterized by elevated velocities, and zones of elevated porosity from karstification with reduced seismic velocities. Our results show how ambient seismic noise can be used to evaluate aquifer physical properties, identify unknown features, and identify the location and continuity of aquifer units.