The proposals, which are subject to parliamentary approval, allow farmers to clear drainage ditches and streams without asking permission.
Farmers had complained that the Environment Agency was micro-managing flood control.
But academics told BBC News that diverting water off farmland could increase floods where people live.
The policy change was announced Environment Minister Liz Truss at the Oxford Farming Conference after what the Department for Environment, Food and Rural Affairs (Defra) said were two successful pilot schemes.
She said: "We will allow farmers across the country to maintain their own ditches up to 1.5km in length from April, so they can clear debris and manage the land."
The decision was welcomed by the National Farmers' Union (NFU).
Its president, Meurig Raymond, said: "The NFU has pressed Defra and the Environment Agency to enable farmers to undertake minor works for many years."
But Professor Alan Jenkins from the Centre for Ecology and Hydrology said he feared the policy could backfire.
"Waterlogged fields are no use to farmers," he said. "They can't maintain their productivity on waterlogged soil so it makes sense for them to manage their fields accordingly.
"There is a potential downside however, in that if we increase drainage in fields during heavy rainfall it's possible there will be increased and faster transmission of water in the river system with a possible increase in flood risk downstream."
Katherine Pygott from the consultancy firm Peter Brett agreed.
"If you are a landowner you may want to maximise productivity on a grouse moor by making it drier - but if you are trying to protect a town you want to keep water back on the uplands.
"It very much depends on local conditions - sometimes it would be unhelpful to speed drainage, sometimes it would not.
"There is a risk of making a free-for-all on drainage. It would be more sensible to make the existing system work."
A government spokesman said over a million acres of prime farmland would be better protected through government investment in flood defences in the 10 years to 2021.

Monarch said it was "trading well" despite a difficult period for the industry because of terrorist incidents, Brexit and the weak pound.
It added that a significant investment would be announced in the coming days.
Over the weekend Monarch denied speculation that the company was going bust.
A spokesperson said they had no idea where the rumours were coming from but that they "were not true".
Speculation about its alleged collapse surfaced from customers on the company's Twitter feed.
The BBC understands the company was in talks with the Civil Aviation Authority last night about its financial situation.
The speculation around Monarch appears to have been sparked by the fact that the airline's CAA licence is due to expire at the end of the week.
So Monarch is in negotiations with the regulator for the licence to be renewed. That requires it to prove that it is financially robust.
Talks between the firm and the CAA, which went on late last night, are likely to be focusing on the "significant investment" that the firm says it expects to announce in the coming days.
It's understood that Monarch has been talking to possible investors including the Chinese conglomerate, HNA Group. If that comes to fruition it could open up new commercial possibilities for the airline.
But on Monday, Monarch released a statement saying it expected to make more than Â£40m in underlying earnings by the end of its financial year in October.
It said: "Our flights are operating as normal, carrying Monarch passengers as scheduled.
"To weather tougher market conditions and to fund its ongoing growth, Monarch expects to announce a significant investment from its stakeholders in the coming days."
The airline is protected by the Air Travel Organisers' Licensing (Atol) scheme - a government scheme that refunds customers if a travel firm collapses, and ensures they are not stranded.
Monarch's website says Atol offers consumer security "where a flight and accommodation have been booked together, some flights booked separately and applies in certain other circumstances".
Earlier this year Low Cost Holidays collapsed, without Atol protection, throwing the holidays of their 27,000 customers abroad into chaos.
Monarch employs around 2,800 staff and is based at Luton airport.
Monarch has been majority-owned by investment firm Greybull Capital since 2014, when it bought a 90% stake in the airline. Greybull also bought a division of Tata Steel this year, as well as 140 M Local convenience stores from Morrisons, which subsequently went into administration.
Experts are warning that plans to allow farmers to clear water courses on their land could make floods worse in towns.
[NEXT_CONCEPT]
Budget airline Monarch says its flights are operating as normal following "negative speculation" about the firm's financial health over the weekend.