Analysts estimate the cost of heavy flooding across northern England could exceed £1.5bn, with small business and insurance firms hit hard.
Initial estimates suggest losses of £900m to £1.3bn so far, according to accountancy firm PwC.
That "could breach £1.5bn" if further rainfall causes more floods, PwC said.
Consultancy group IHS said the flooding caused by Storms Eva and Desmond could wipe up to 0.2% off the UK's economic output this year.
Businesses and homes have been battered by floods in Yorkshire and Lancashire following heavy rain over the Christmas weekend.
The Environment Agency still has nearly 30 severe flood warnings, meaning danger to life, in place for north-east and north-west England, and more than 180 other flood warnings and alerts across England and Wales.
Justin Urquhart Stewart, of Seven Investment Management, said the floods would hurt the economy, as they would dent consumer confidence and wipe out some small businesses.
He told BBC Radio 5 Live: "It's not just a money issue, it's a morale issue and that morale is the crucial element to running an economy."
Small, family-run businesses would be particularly affected, as many might not have insurance, he said.
"Something like this can not only knock them back, it can knock them out altogether," he said.
Christopher Neville, the owner of a small paper business in Radcliffe, Greater Manchester, told the BBC that floods at his factory would "probably put the business under".
"It'll be tens of thousands [of pounds] in terms of the stock we've lost and damage to the machinery," Mr Neville said.
The insurance industry will bear much of the total cost from the flooding - £700m to £1bn of the estimated losses so far, said Mohammad Khan, general insurance leader at PwC.
"The additional damage from Storm Eva and any further damage caused by additional rain will impact relevant insurers' year-end profitability," he said.
Insurers have faced criticism over the affordability of flood insurance, despite the introduction of the Flood Re programme to make it cheaper for businesses to take out cover.
Malcolm Tarling from the Association of British Insurers told the BBC that the "vast majority" of firms should be able to secure flooding insurance.
"Flooding can put many businesses' existence at risk and that's obviously something the insurance industry takes very seriously indeed," he said.
Mr Tarling added that the floods would be "an expensive event", but one that insurers had budgeted for.