Canalside residents say they might as well be living "in the middle of Tesco" because towpaths remain open making social-distancing impossible.
Waterway homeowners say large numbers of people are still passing within a metre of their properties or boats on narrow towpaths.
But it is not "practical nor desirable" to shut paths, canal bosses say.
The Canal and Rivers Trust (CRT) manages 2,000 miles of England and Wales waterways.
Nina Marie, who lives next to the canal in Bathampton, Somerset, posted on Facebook that she had counted more than 3,700 people pass her cottage on Thursday.
"The paths are far less than 2m wide. It is literally impossible to keep distance," she said.
"The paths should be open only to those who live there."
'Want some protection'
Leb Landymore, who is moored near Bradford-on-Avon in Wiltshire, said boaters "want some protection".
"We're literally a metre away from the actual path so we're that close to the public, coming out and exercising," he said.
On the CRT twitter account, Tina Butcher described towpaths as a "hotbed of virus transmission".
"I might as well go live in the middle of Tesco," she tweeted.
In a statement, the CRT said it was "following government guidance" and had advised people using towpaths "not to congregate, keep moving and strictly observe social distancing".
"Whilst we are discouraging use of the towpath where boats are moored, if people do approach a boat, there should be no risk to those on board provided they stay on their boat while they pass," it said.
It said towpaths "have to stay open for those living along the waterways" and for trust staff and it was "neither practical nor desirable to close stretches of them".