The temporary closure of the Carlisle site hit supplies of McVitie's ginger nuts, Crawford's custard creams and Carr's water biscuits, among others.
United Biscuits said there had been "substantial flood damage" to electrical equipment and ovens.
Manufacturing director Mark Taylor said customers had written to ask when the biscuits would be back on shelves.
How have we coped without biscuits?
A number of shoppers "rather than buy another pack, they actually hunted down the store manager, harangued him for 10 minutes about why ginger nuts weren't there and left the shop without buying anything", he said.
Storms Desmond and Eva caused widespread damage in Cumbria, Lancashire and Yorkshire.
Nearly 40 million litres of water and 540 tonnes of debris had to be cleared before normal production at the Carlisle site could resume, the company said.
Hundreds of staff, suppliers and contractors worked to get the lines running.
"It was a fantastic team effort to clean the place up, repair it and get it back in great shape," Mr Taylor said.
"We can announce officially the biscuit crisis is over."
The factory employs 640 people and produces 80,000 tonnes of biscuits a year.
Full production has resumed at a factory which flooded in December, leading to a national biscuit shortage.