New data are presented from non-destructive structural investigations in the Istanbul Yerebatan (Basilica) Cistern (placed in the top 10 sites in Turkey on the UNESCO World Heritage List) for restoration purposes. Degradation identified is discussed in relation to past earthquakes. Istanbul has housed many civilizations and searching for the traces of earthquakes in historical sites in a city which has experienced many large earthquakes during this process will assist in illuminating the past. It is possible to see traces of these earthquakes in the Yerebatan (Basilica) Cistern, serving as the largest enclosed water storage in Istanbul for nearly 1000 years. In line with this aim, research was completed with the high-resolution ground penetrating radar (GPR) method on both the floor and internal side walls of the cistern which is undergoing restoration. In this study, deformation was determined in the layers of water insulation on the floor of the cistern and it was understood these deformations were associated with degradation in the 336 columns acting as supports for the cistern. Drilling in anomalous sites determined by GPR screening identified traces of repairs and it was concluded that the degradation causing anomalies may be related to past earthquakes.