In 1823 royal assent was given to ‘An Act for the Rebuilding of London Bridge’ and in 1825 John Garratt, Lord Mayor and Alderman of the Ward of Bridge Within, laid the first stone of the new London Bridge. In 1831 Sir John Rennie’s new bridge was opened further upstream and the old bridge demolished. St Magnus ceased to be the gateway to London as it had been for over 600 years. Peter de Colechurch had been buried in the crypt of the chapel on the bridge and his bones were unceremoniously dumped in the River Thames. In 1921 two stones from Old London Bridge were discovered across the road from the church. They now stand in the churchyard.
Wren's church of St Michael Crooked Lane was demolished, the final service on Sunday 20 March 1831 having to be abandoned due to the effects of the building work. The Rector of St Michael preached a sermon the following Sunday at St Magnus lamenting the demolition of his church with its monuments and "the disturbance of the worship of his parishioners on the preceeding Sabbath". The parish of St Michael Crooked Lane was united to that of St Magnus, which itself lost a burial ground in Church Yard Alley to the approach road for the new bridge. However, in substitution it had restored to it the land taken for the widening of the old bridge in 1762 and was also given part of the approach lands to the east of the old bridge. In 1838 the Committee for the London Bridge Approaches reported to Common Council that new burial grounds had been provided for the parishes of St Michael, Crooked Lane and St Magnus, London Bridge.
Depictions of St Magnus after the building of the new bridge, seen behind Fresh Wharf and the new London Bridge Wharf, include paintings by W. Fenoulhet in 1841 and by Charles Ginner in 1913. This prospect was affected in 1924 by the building of Adelaide House to a design by John James Burnet, The Times commenting that "the new ‘architectural Matterhorn’ ... conceals all but the tip of the church spire". There was, however, an excellent view of the church for a few years between the demolition of Adelaide Buildings and the erection of its replacement. Adelaide House is now listed. Regis House, on the site of the abandoned King William Street terminus of the City & South London Railway (subsequently the Northern Line), and the Steam Packet Inn, on the corner of Lower Thames Street and Fish Street Hill, were developed in 1931.
By the early 1960s traffic congestion had become a problem and Lower Thames Street was widened over the next decade to form part of a significant new east-west transport artery (the A3211). The setting of the church was further affected by the construction of a new London Bridge between 1967 and 1973. The New Fresh Wharf warehouse to the east of the church, built in 1939, was demolished in 1973-4 following the collapse of commercial traffic in the Pool of London and, after an archaeological excavation, St Magnus House was constructed on the site in 1978 to a design by R. Seifert & Partners. This development now allows a clear view of the church from the east side. The site to the south east of The Monument (between Fish Street Hill and Pudding Lane), formerly predominantly occupied by fish merchants, was redeveloped as Centurion House and Gartmore (now Providian) House at the time of the closure of old Billingsgate Market in January 1982. A comprehensive redevelopment of Centurion House began in October 2011 with completion planned in 2013. Regis House, to the south west of The Monument, was redeveloped by Land Securities PLC in 1998.
The vista from The Monument south to the River Thames, over the roof of St Magnus, is protected under the City of London Unitary Development Plan, although the South bank of the river is now dominated by The Shard. Since 2004 the City of London Corporation has been exploring ways of enhancing the Riverside Walk to the south of St Magnus. Work on a new staircase to connect London Bridge to the Riverside Walk is due to commence in March 2013. The story of St Magnus's relationship with London Bridge and an interview with the rector featured in the television programme The Bridges That Built London with Dan Cruickshank, first broadcast on BBC Four on 14 June 2012. The City Corporation's 'Fenchurch and Monument Area Enhancement Strategy' of August 2012 recommended ways of reconnecting St Magnus and the riverside to the area north of Lower Thames Street.