East Riding Council is working with the Environment Agency and the South Holderness Internal Drainage Board on the scheme, due to start on April 6, close to Sand-le-Mere caravan site at Tunstall.
Coastal erosion has seen chunks of cliff lost from an embankment built in the 1950s, leading to fears that in a storm seawater could surge into Tunstall Drain, flooding fields and villages and even cutting off a large chunk of southern Holderness.
Ralph Ward, clerk of the South Holderness Internal Drainage Board, said: "It would have to be an extremely severe event for anything like that to happen.
"This (scheme) should prevent a tidal surge causing any issues, we hope."
He said the board would have preferred to put an embankment 200m inland to replace the existing one.
But they've been unable to do so as a result of a "do nothing" policy, agreed by successive Governments.
Coastal defences are judged "not economically, socially or environmentally sustainable" for much of sparsely inhabited Holderness, which has one of the fastest eroding coastlines in North West Europe.
Mr Ward said: "We've been waiting for the works to be done for over 10 years.
"It is not maybe the ideal situation, but it is what we are allowed to do under present UK and East Riding coastal policy - you aren't allowed to defend the coast."
However he said the new water flow control structure at Thirtle Bridge should prevent farmland from being contaminated with saltwater and protect species like water voles living in the freshwater drain.
The council’s contractors, Breheny Civil Engineering Limited, are programmed to take 12 weeks to complete the works, with completion scheduled for June 28.
During the works, the B1242 at Thirtle Bridge will have to be closed, and a signed diversion route will be in operation.
Local residents, farmers and Sand Le Mere caravan park have been informed.
Councillor Chris Matthews, portfolio holder for strategic property and infrastructure, said: “This is a very important scheme for the people of the area around Sand Le Mere and Tunstall.
"We will be building a new water flow control structure at Thirtle Bridge.
"This will allow for the control of water flowing from the east, meaning that flooding of land to the west of the B1242 will be much less likely.
“We apologise to road users for the essential road closure during these works, but assure local residents that this scheme will bring significant benefits.”