A metropolitan bishop of London attended the Council of Arles in 314, which indicates that there must have been a Christian community in Londinium by this date, and it has been suggested that a large aisled building excavated in 1993 near Tower Hill can be compared with the 4th-century Cathedral of St Tecla in Milan. However, there is no archaeological evidence to suggest that any of the mediaeval churches in the City of London had a Roman foundation. A grant from William I in 1067 to Westminster Abbey, which refers to the stone church of St Magnus near the bridge ("lapidee eccle sci magni prope pontem"), is generally accepted to be 12th century forgery, and it is possible that a charter of confirmation in 1108-16 might also be a later fabrication. Nonetheless, these manuscripts may preserve valid evidence of a date of foundation in the 11th century.
Archaeological evidence suggests that the area of the bridgehead was not occupied from the early 5th century until the early 10th century. Environmental evidence indicates that the area was waste ground during this period, colonised by elder and nettles. Following Alfred's decision to reoccupy the walled area of London in 886, new harbours were established at Queenhithe and Billingsgate. A bridge was in place by the early 11th century, a factor which would have encouraged the occupation of the bridgehead by craftsmen and traders. A lane connecting Botolph's Wharf and Billingsgate to the rebuilt bridge may have developed by the mid-11th century. The waterfront at this time was a hive of activity, with the construction of embankments sloping down from the riverside wall to the river. Thames Street appeared in the second half of the 11th century immediately behind (north of) the old Roman riverside wall and in 1931 a piling from this was discovered during the excavation of the foundations of a nearby building. It now stands at the base of the church tower. St Magnus was built to the south of Thames Street to serve the growing population of the bridgehead area and was certainly in existence by 1128-33.
The small ancient parish extended about 110 yards along the waterfront either side of the old bridge, from 'Stepheneslane' (later Churchehawlane or Church Yard Alley) and 'Oystergate' (later called Water Lane or Gully Hole) on the West side to 'Retheresgate' (a southern extension of Pudding Lane) on the East side, and was centred on the crossroads formed by Fish Street Hill (originally Bridge Street, then New Fish Street) and Thames Street. The mediaeval parish also included Drinkwater's Wharf (named after the owner, Thomas Drinkwater), which was located immediately West of the bridge, and Fish Wharf, which was to the South of the church. The latter was of considerable importance as the fishmongers had their shops on the wharf. The tenement was devised by Andrew Hunte to the Rector and Churchwardens in 1446. The ancient parish was situated in the South East part of Bridge Ward, which had evolved in the 11th century between the embankments to either side of the bridge.
In 1182 the Abbot of Westminster and the Prior of Bermondsey agreed that the advowson of St Magnus should be divided equally between them. Later in the 1180s, on their presentation, the Archdeacon of London inducted his nephew as parson.