Teams of contractors will be using heavy machinery and pontoons to undertake the work, which will protect and repair the land side and moat walls.
Nelson's Tunnel will be closed for the duration of the work with a diversion in place.
Lord Nelson crossed the moat during his last departure from England in 1805.
Councillor Dave Ashmore, cabinet member for environment and climate change at Portsmouth City Council, said: ‘Long Curtain Moat and the surrounding areas are so important to Portsmouth and very highly regarded nationally in terms of their historic importance as a Scheduled Ancient Monument.’
The work will take place on weekdays from 7am to 7pm, with it due to be completed by the end of October.
It forms part of the Southsea Coastal Scheme, which will see the building of new flood defences.