The earliest mention of this church was in 1162 as “St. John upon Walebroc” and the west end of the church stood right on the banks of the river Walbrook. This river which ran right through the centre of the City of London was the main water supply for the Romans. The Temple of Mithras (now under the Bloomberg building) was on its banks too. Sometime around 1440 the river was covered over and culverted although the bridges still remained. The path of the river is now the street known as Walbrook which runs past Mansion House and the church of St Stephen Walbrook and on past Canon Street Station down Dowgate Hill and Cousin Lane to the Thames. If you venture onto the foreshore of the Thames at low tide you can find the outflow of this hidden river behind a large iron sluice gate. The river is also commemorated in a sculpture called “Forgotten Streams” by Christina Iglesias outside the Bloomberg building.
Back to the church of St John the Baptist. In 1412 the church was enlarged when some land to the north of the church was swapped with some land to the east of the church. This exchange meant the road down Dowgate Hill could be widened and the church extended north towards Cannon Street. The Agas Map from 1560 clearly shows the enlarged church. John Stow in his Survey of London published in 1598 had this to say :
“This parish church is called St. John upon Walbrooke, because the west end thereof is on the very bank of Walbrooke, by Horseshew bridge, in Horseshew bridge street. This church was also lately new built; for about the year 1412, license was granted by the mayor and commonalty to the parson and parish, for enlarging thereof, with a piece of ground on the north part of the choir, twenty-one feet in length, seventeen feet and three inches in breadth, and on the south side of the choir one foot of the common soil. There be no monuments in this church of any account, only I have learned, William Cobarton, skinner, who gave lands to that church, was there buried 1410, and John Stone, tailor, one of the sheriffs 1464, was likewise buried there.”
The church was repaired and redecorated in 1621 but sadly then destroyed in the Great Fire of 1666. It was decided not to rebuild the church and the parish was united with St Antholin Budge Row. Then in 1821 St Antholin itself was demolished to make room for Queen Victoria Street and the two parishes combined with St Mary Aldermary.
If you are looking for physical remains of St John the Baptist you are in luck. There is a fine memorial in Cloak Lane near Cannon Street station. If you look on the pillar next to Birley Sandwiches in the Walbrook Building you will see a parish boundary marker. There is another one further down the hill in College Street near the church of St Michael Paternoster Royal. In the church of St Mary Aldermary near the toilets for the coffee shop you will see a wall plaque mentioning St John the Baptist. Also remains from then churchyard of St John the Baptist have been reinterred in both Brookwood Cemetery an the City of London Cemetery (CLC) along with those from St Antholin.
the wikipedia page is here