The blaze, at Underfall Yard near Cumberland Road, started in the early hours of Saturday, May 6.
It is believed no one was seriously injured by the blaze, but a number of boats and businesses at the historic dockyard were severely damaged.
Robert Boyd-Stevenson, aged 45, of Headford Road, Knowle, has now been charged with arson with intent to endanger life, Avon and Somerset police said.
He has also been charged with a stalking offence.
Stevenson was remanded ahead of appearing before Bristol Magistrates Court yesterday, Monday, May 8.
