Gardeners face forking out a fortune to replace plants that have rotted during the wet winter.
Experts warned that trees, shrubs and herbaceous plants may fail to spring into life, as roots have turned to mush.
Gardeners on heavy clay soil are likely to be worst affected but plants on lighter sandy soils may also struggle – as nutrients have been washed away.
“We’re going to have to deal with a reasonable level of plant losses due to waterlogging,” said Jon Webster, curator of RHS Garden Rosemoor in Devon.
“Some areas of the UK did not dry out all summer or during winter. The water table is high and ground is sodden. A lack of air in the soil can lead to rotting.
“It’s hard to believe that this time last year, parts of the UK were declared drought zones!”
Paul Hansord, managing director of Thompson & Morgan, echoed Jon’s concerns.
“The land has been sitting wet for months now,” Paul told AG. “And in gardens that do not have good drainage, there is a bigger chance of plant losses.
“Foxgloves, for example, like their feet dry and echinacheas could also struggle,” he warned.
Paul said seed potatoes, which should have been lifted in October, are still in the ground because waterlogging has made harvesting impossible. This could affect supplies and prices for the 2014 season.
RHS principal horticultural advisor Leigh Hunt said waterlogged soil was a perfect breeding ground for pathogens, particularly phytophthora.
Leigh said: “Roots are not meant to be submerged under water for long periods unless they’re bog or water plants.
“Without roots, plants can’t grow. Damage has been done and many gardeners may not notice until spring.
“Where roots are damaged but not dead, leaves may start to unfurl, but plants will not do well as roots can’t supply what’s needed.”
Horticultural Trades Association director of business development, Tim Briercliffe, said garden centres had high levels of stock and were geared up for gardeners looking to replace lost plants.
“But I don’t expect losses to be as high as after the last two winters when we had very low temperatures,” Tim concluded.