Strong tides had re-shaped and stripped the beaches following the recent severe weather.
Routine annual outer harbour dredging will coincide with the beach replenishment and the sand recovered will be used to restore the beaches.
Coun Robert Gould, Leader of West Dorset District Council, said: “These annual works are crucial to ensuring coast defences are maintained and harbour operations run smoothly.
“We try to limit the inconvenience by doing the works out of season, but we would like to apologise in advance for any disruption caused by the work.”
The dredging will improve access and navigation for boats in and out of both harbours.
Work is dependent on the tides and it may be necessary to carry out the dredging at night, but the district council will endeavour to keep any noise disruption to a minimum.
Work will start in Lyme Regis Harbour on Wednesday, January 29, with Bridport Harbour following suit in early March.
Work is expected to last a week and is dependent on weather conditions. It is taking place out of season to minimise disruption. Harbour users have been informed about the work.