Hezekiah's tunnel shows that almost all fractures and joints cut across the tunnel ceiling and walls.  Therefore the tunnel cannot originally have been a natural karstic-formed geological feature.
There were 4 different kinds of plasters in the tunnel. The oldest plaster was suceeded by Byzantine plaster, next by a Mameluke-period plaster, and finally by a plaster applied in the early 20th century by the infamous Parker Mission.  Natural sedimentary deposits laid down from running water (tufa) and  water seeping through tunnel walls (flowstone, a kind of stalactite attached to tunnel walls) also occur along various attached segments of the tunnel.  Patches of the oldest plaster were preserved beneath flowstone, a critical finding as we shall see.
Numerous drill cores that were collected from along the tunnel floor revealed that tufa and siltistone covered all the plaster layers but were never found beneath the oldest plaster.  This demonstrated that there was no percolating water and thus no incipient channel here that was later widened by Hezekiah's tunnelers.  Had there been a karstic channel guide the tunnelers, sediments deposited from the water (such as covered the Plaster) would have been found beneath the oldest plaster.  The absence of these sedimentary deposits also shows that the ancient plaster was applied soon after the tunnel was dug, before the natural sedimentation process could begin.
According to the Frumkin, Hezekiah's Tunnel is thus "the oldest accurately-dated long tunnel constructed without using intermediate shafts for the excavation work proper.  (one shaft-to-surface chimney does exist near the southern end of Hezekiah's Tunnel, but the researchers have determined from marks on the wall that this shaftwas not used for descending down from the surface and excavating in either direction.
That Hezekiah's engineer depended on acoustic sounding to guide the tunnelers is supported by explicit use of this technique as described in the Siloams Inscription.  The frequently ignored final sentene of this inscription provides further evidence.  "And the height of the rock above the heads of the laborers was 100 cubits."  This indicates that the engineers were well aware of the distande to the surface above the tunnel at various points in its progression.
The now discarded karstic-dissolution-channel theory to explain the route of Hezekiah's tunnel has depreved us of a "rather elegant adaptation of a natural feature."  But it has been replaced by an explanation that Shimron and Frumkin call "a major advance in tunneling technique