From 1860, the railway operating companies desired to extend services from London Bridge Station into new stations at Cannon Street and Blackfriars in the City and link to the West End at Charing Cross Station. This required a viaduct, but legally, it was impossible by the 1756 Borough Market Act for the Trustees to alienate their property. The compromise was that only a flying leasehold was given to the railway company for the permanent way, but only for as long as a railway operates on it. The Market continues to trade underneath the arches of the viaduct. Each time there is a railway expansion requiring widening of the viaduct, the Trustees receive a full compensation payment. The last major such expansion was the 1901 extended bridge widening; the 21st-century works programme will also make its contribution. These windfalls have assisted in the finances of the market without any loss of amenity to it.
As part of the Thameslink Programme project, a large number of listed buildings in the Borough Market area have been altered or demolished,[11] potentially destroying the historic fabric of the area. This includes parts of the market itself and much of the area appearing in the aforementioned films. This was immensely unpopular locally and became a contentious issue in the resulting public inquiry, which resulted in delays to the project. Eventually, the inquiry inspector was satisfied with the subsequent plans to restore as much of the market and surrounding area as possible. The overriding need to remove one of the worst bottlenecks in the national rail network and improve transport options considerably over a large portion of London meant that he accepted that some damage to the fabric of the market and surrounding area was unavoidable and justified in order for the scheme to achieve its objectives.
The market building on Bedale Street south-side has had its upper floors removed, as has the Wheatsheaf public house on Stoney Street for the new railway bridge crossing over them. The remaining floors have been re-occupied. The old Market glazed roof on Stoney Street has been re-instated and much improved. The most significant loss was the Smirke Terrace, Nos 16-26 Borough High Street, demolished in 2010. It was a Grade II listed building designed by the notable classical architect Sir Robert Smirke and completed in 1832. The most interesting survivor is The Globe Tavern public house at the junction of Bedale Street and Green Dragon Court, which is passed immediately to its north by the 1900 viaduct and the new bridge immediately to its south-side but with entirely unrestricted access to all sides at pedestrian level.