I've just done some research on the churches of "Oranges and Lemons" for my monthly newsletter. I was looking for a link to a photo of "Old Bailey" (St Sepulchre-without-Newgate, or the Church of the Holy Sepulchre, Newgate, otherwise known as Old Bailey)and found this question. Oranges and lemons were apparently paid to the churchwardens as a toll for the priveledge of carrying fruit unloaded from ships anchored in the Thames through the churchyard of St Clements Eastcheap. In mediaeval times, St Clements Eastcheap had a large churchyard, which may have extended as far as the river, or pehaps a footpath took a shortcut through the churchyard. In any case, St Clements Eastcheap is not too far from the present site of Billngsgate Fruit Market....
St Martin Orgar, Cannon Street is probably the St Martins in the song - another City Church - it was burned and partly destroyed in the Great Fire of 1666, and is now listed as a "ruined church", though the tower survives. I have links to photographs of all 6 "Oranges and Lemons" churches, and other interesting info, including "The True Story of Dick Whittington" four times (Lord) Mayor of London, in my newsletter (on aspects of Folk Music), available from my website.
Best wishes,
Lesley Halamek

http://halamuspublishing.com.au
E-mail: halamus@halamuspublishing.com.au