In 1867, Warren was recruited by the Palestine Exploration Fund to conduct Biblical archaeology reconnaissance with a view of further research and excavation to be undertaken later in Ottoman Syria, but more specifically the Holy Land or Biblical Palestine. During the PEF Survey of Palestine he conducted one of the first major Excavations at the Temple Mount in Jerusalem, thereby ushering in a new age of Biblical archaeology. His most significant discovery was a water shaft, now known as Warren's Shaft, and a series of tunnels underneath the Temple Mount.