BAM Nuttall started construction in July, but has suffered the wettest August and September in the last 30 years, according to the Met Office data.
This has made working conditions for machinery and construction teams on the ground difficult for both the in river works and embankment construction.
Much of the plant and equipment will be moved from the Melbourne Park site from the end of October and will return in 2020.
The Environment Agency said the decision to pause works had not been taken lightly and said it would be of greater benefit, in the long run, to pause rather than attempt to carry on through winter when contractors were likely to make little progress.
Stewart Mounsey, flood manager for Cumbria, said: “I would like to reassure people that pause doesn’t mean stop.
“We will be busy behind the scenes working with our designers and contractor to plan our works for an accelerated start in spring 2020.
“Although we won’t be building embankments in the winter the public may see some activity in the winter months that will be supporting the accelerated return.
He added: “The pause does not affect the completion of our works which were originally planned for spring 2020 to enable the new defences to be built ahead of winter 2020.
“Pausing main construction works in winter 2019 will not affect our 2020 winter readiness or our ongoing preparations for delivery of Phases 2 and 3,” said Mounsey.