The Hatshepsut temple in Egypt is a masterpiece of ancient architecture. Just as distinct as the temple itself is the rock formation it is carved into, and recurring rock falls in the vicinity have raised concerns regarding the temple’s safety under progressing erosion and seismic activity. Due to the material characteristics (brittle carbonate rock), high stresses could lead to rapid crack propagation, and vibra-tion-based measures may be suitable precursors for imminent rock falls. This paper describes a two-day measurement campaign on the rock towers as a preliminary study prior to the implementation of a long-term seismic station. Next to operational modal analysis, horizontal-to-vertical spectral ratios, and standard spectral ratios are evaluated to cross-validate the resonance behaviour. To the author’s knowledge, this is the first study where stochastic subspace identification (SSI) is applied for the estimation and automated tracking of natural frequencies, mode shapes, and damping ratios in rock formations. One of the advantages of this method is the inherent uncertainty quantification, meaning for each vibration record, the mean values and the standard deviations are estimated for each modal parameter, giving deep insights into the reliability of the vibration-based monitoring of rock formations.