Sometime after the 8-9th century, the overground area of the Basilica started to be used as an artisan quarter after a fire destroyed the octagon in 726 and the university's activities ceased during the Iconoclastic period. During the late middle ages (16th century) and the early modern period, small houses were built on top of the cistern (Müller-Wiener, 1977, p. 284).

Apparently the cistern was forgotten after the conquest of Constantinople in 1453. In the mid-16th century, Gilles records how he rediscovered the Basilica cistern. He highlights the supposed ignorance of the locals (that nonetheless knew they could collect water if they lowered buckets into the cistern) about the cistern's existence, priding himself with the achievement of (re)discovery.

Gilles' records in De Topographia Constantinopoleos 2.20 that he explored the cistern by boat, and that it was filled with fish. He describes the measurements as '360 feet long, 182 feet broad, and 224 Roman paces in circumference'. He also gives a description of the brickwork being in good condition and gives a survey of the pillars and their capitals. In Gilles time (16th century) pipes still supplied water to the Basilica Cistern.