Preliminary shafts were dug, the work beginning in 1837, to ascertain the geological conditions, on the same straight alignment on which the tunnel was eventually built.

[5] The plans were therefore revised to situate the tunnel in more stable strata at a shallower depth, at the expense of steeper gradients on the approaches.

This also reduced the length of the tunnel from 2,830 yd (2,590 m), on a 1 in 352 gradient in the 1836 plan, or 2,730 yd (2,500 m) on 1 in 330 in the 1838 plan (1 in 90 in the main tunnel, as built, and 1 in 57 on the approach to it), and so reduced construction costs; a 1950 article, based on the original contract and specification, quoted the directors as saying it would, "considerably diminish its length and expense" and asserted that this was the actual reason for the change to the shallower depth, rather than simply an effect of it.

Brunel was quoted as reporting in October 1841 that, "the drainage of the water is obtained into the lower oolite, without pumping, at one of the intermediate shafts"[7] Therefore, although it included the geological cross-section (drawn by GWR engineer, Mr. R. P. Brereton),[8] it made no mention of fuller's earth problems.

[4] Later articles say the section shows that the header, on the originally-proposed deeper level, passes through a much greater length of fuller's earth than the tunnel as built, and that it also makes it clear that information gained from digging the shafts would have made it apparent that this would be the case.

[14] The original timbers were removed and the pits spanned with prefabricated concrete beams reinforced with bullhead rail and shear links.

The operation was carried out under a complete possession over a period of seven days by over 100 people working 12-hour shifts, many of whom were accommodated in temporary buildings at the site.

[citation needed] Not until the old beams were removed did it become known that the pits had indeed been backfilled in the course of earlier work and the fears of falling into a six-metre hole were unfounded.

[22] On 9 December 2009 a door on an HST came open in the vicinity of the tunnel and a passenger attempted to close it, without success but at some personal risk.

A local newspaper attempted to sensationalise the incident by stating that the passenger concerned was "almost thrown from the train" as the door "flew" open.

[23] Local councillor Andrew Gravells is quoted as saying that trains should be fitted with devices to prevent departure from stations if doors are open.

Disruption to train services was caused on 17 January 2011 when a huntsman and twenty fox-hounds trespassed on the line near the east end of the tunnel.