As part of a structural restoration project in 2010, I conducted a 3D ground-penetrating radar (GPR) survey at the Great Church of St. Sophia to investigate the foundations of the present structure. I inferred from the time slices the geometry of the foundation remnants of the previous structure that existed at the same site, mixed with the landfill, which I know exists at the site from the construction history of the current structure. I further delineated the geometry of the cistern, which I discovered beneath the inner narthex during a previous 2D reconnaissance GPR survey. The cistern is approximately 60 m long and 5 m wide at a depth of 1 m below the ground level. I also discovered a water pipe that approaches the cistern in the perpendicular direction from the outer court of the church grounds. The cistern may be connected with this pipe to the Great Cistern of the Byzantine period, approximately 500 m away from the church grounds.