Canaletto drew St Magnus and old London Bridge as they appeared in the late 1740s. Between 1756 and 1762, under the London Bridge Improvement Act of 1756 (c. 40), the Corporation of London demolished the buildings on London Bridge to widen the roadway, ease traffic congestion and improve safety for pedestrians. The churchwardens’ accounts of St Magnus list many payments to those injured on the Bridge and record that in 1752 a man was crushed to death between two carts. After the House of Commons had resolved upon the alteration of London Bridge, the Rev Robert Gibson, Rector of St Magnus, applied to the House for relief; stating that £48 6s. 2d. per annum, part of his salary of £170 per annum, was assessed upon houses on London Bridge; which he should utterly lose by their removal unless a clause in the bill about to be passed should provide a remedy. Accordingly, Sections 18 and 19 of 1756 Act provided that the relevant amounts of tithe and poor rate should be a charge on the Bridge House Estates.
A serious fire broke out on 18 April 1760 in an oil shop at the south east corner of the church, which consumed most of the church roof and did considerable damage to the fabric. The fire burnt warehouses to the south of the church and a number of houses on the northern end of London Bridge.
As part of the bridge improvements, overseen by the architect Sir Robert Taylor, a new pedestrian walkway was built along the eastern side of the bridge. With the other buildings gone St Magnus blocked the new walkway. As a consequence it was necessary in 1762 to 1763 to remove the vestry rooms at the West end of the church and open up the side arches of the tower so that people could pass underneath the tower. The tower’s lower storey thus became an external porch. Internally a lobby was created at the West end under the organ gallery and a screen with fine octagonal glazing inserted. A new Vestry was built to the South of the church. The Act also provided that the land taken from the church for the widening was "to be considered ... as part of the cemetery of the said church ... but if the pavement thereof be broken up on account of the burying of any persons, the same shall be ... made good ... by the churchwardens".
Soldiers were stationed in the Vestry House of St Magnus during the Gordon Riots in June 1780.
By 1782 the noise level from the activities of Billingsgate Fish Market had become unbearable and the large windows on the north side of the church were blocked up leaving only circular windows high up in the wall. At some point between the 1760s and 1814 the present clerestory was constructed with its oval windows and fluted and coffered plasterwork. J. M. W. Turner painted the church in the mid-1790s.
The rector of St Magnus between 1792 and 1808, following the death of Robert Gibson on 28 July 1791, was Thomas Rennell FRS. Rennell was President of Sion College in 1806/07. There is a monument to Thomas Leigh (Rector 1808-48 and President of Sion College 1829/30, at St Peter's Church, Goldhanger in Essex. Richard Hazard (1761–1837) was connected with the church as sexton, parish clerk and ward beadle for nearly 50 years and served as Master of the Parish Clerks' Company in 1831/32.
In 1825 the church was "repaired and beautified at a very considerable expense. During the reparation the east window, which had been closed, was restored, and the interior of the fabric conformed to the state in which it was left by its great architect, Sir Christopher Wren. The magnificent organ ... was taken down and rebuilt by Mr Parsons, and re-opened, with the church, on the 12th February, 1826". Unfortunately, as a contemporary writer records, "On the night of the 31st of July, 1827, [the church's] safety was threatened by the great fire which consumed the adjacent warehouses, and it is perhaps owing to the strenuous and praiseworthy exertions of the firemen, that the structure exists at present. ... divine service was suspended and not resumed until the 20th January 1828. In the interval the church received such tasteful and elegant decorations, that it may now compete with any church in the metropolis."