Flooding at the Denby Dale Road junction with the M1 has caused traffic chaos in recent weeks.
Wakefield Council bosses said investigations have located the source of the problem, and one lane of the roundabout on the outbound carriageway from Wakefield City Centre will have to be dug to a depth of over 5m to repair a blockage.
The work will continue over the weekend, and it is hoped it will be completed by early next week, but motorists are being warned that the roadworks will cause delays to traffic, particularly during the evening rush hour.
Drivers are asked to use alternative routes where possible, including junctions 38 and 40.
Denby Dale Road forms part of a diversion route for the closure of Durkar Lane for the installation of a sewer for a new housing development, which was due to start on January 20.
Yorkshire Water has now agreed to delay this road closure for a week until January 27.