The easiest way to prevent future flooding in several key towns would be to demolish buildings in Lewes and widen the river, according to a new report.
However, the Environment Agency warns the move would mean the loss of some of the town's most historic buildings and at least one bridge.
Residents have been warned by the agency there will be no quick and easy solution to prevent flooding in communities along the rivers Ouse and Uck.
The floods wrecked homes and businesses in Lewes and Uckfield last year.
The agency is warning there are no simple engineering solutions and any scheme would have to be built within tight financial constraints.
The report into the flooding last October, which was commissioned by the Environment Agency, has shown the river channel in the area of central Lewes was too small for the extreme flows on October 12, following days of heavy rain.
The flooding was made worse by bridges and buildings along the river.
The agency must now either reduce the amount of flow reaching the channel using barrages, or increase the amount of water which can pass through the Cliffe/Phoenix area.
The agency says another solution would be to build a barrage upstream of Lewes.
But it warned a hastily constructed scheme could result in more flooding in Barcombe and the same could be true of a downstream barrage as far as Newhaven.
The Mayor of Lewes, Councillor John Webber, said: "The first thing to say is that the buildings and the bridge are far too much a central part of Lewes to consider that an option.
"Secondly I would like to feel the residents were being consulted on the solution being considered.
"I would like to know which experts they have spoken to about the possibilities of a second channel which has been done in other areas.
"If they can build a tunnel under the English Channel, surely they can find a second route for the extra water."
As well as trying to come up with engineering answers, the Environment Agency is still trying to secure funding for works.
However, while the agency attempts to resolve the problems, it is also trying to ensure landowners maintain flood defence walls along the River Ouse.
Collapses of the walls could lead to more flooding, even during less severe weather.
Peter Midgley, Sussex area manager for the agency, said: "The flooding in Lewes and the Ouse valley was probably the most severe to affect any community in England and Wales last autumn.
"In Lewes itself the river channel in the Phoenix/Cliffe area was simply too small to cope with the huge torrent of water pouring down the valley from the Uck and Ouse valleys.
"Once flooding began, the bridges and buildings lining the channel simply exacerbated the problem."
He added: "Given the devastation to people's lives, homes and businesses, I can understand the wish to make things happen swiftly but it is important to get this right or we will make the flooding worse or simply pass it on to other homes and businesses."
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