An architect's plans for a bridge between Kent and Essex would lead to "massive change" in the estuary, the Environment Agency has said.
Sir Terry Farrell set out plans for a road and rail bridge
The proposals by Sir Terry Farrell are for a road and rail bridge linked by man-made islands.
He said the plans would provide flood defences and involve "some kind of barrier".
But Chris Burnham, from the Environment Agency, said it would change the estuary's tidal nature and its ecology.
He said: "What we've found is you would actually have to block off around 85% of the cross-sectional area of the tidal Thames to be able to create that sort of blockage to storm surges.
"If you do that, you would see that actually there would be a massive change to the estuary itself."
And he added: "It would lose a lot of its natural tidal nature, and impact not only the navigation of the river but also the ecology."
Plans for the bridge and islands were unveiled by the architect earlier this year, who also said the proposals could bring regeneration to Essex and Kent, and create employment.
Sir Terry, who designed London's new Home Office building, the MI6 headquarters and Charing Cross station, said the Thames Gateway area should be designated a national park, with the bridge spanning the estuary.
He said he wanted to see an environmentally-friendly scheme in the Thames estuary region, which covers parts of London, Kent and Essex.