One independent wine merchant in Sheffield is counting the cost after flood water caused by June's heavy rainfall swamped his warehouse and shop, causing an estimated £250,000 of damage.
Patrick Jouan, owner of Le Bon Vin, said it could take two months to repair the buildings and re-stock, although he was managing to supply restaurant and internet customers with their orders.
"I have never seen anything like this . I think insurance will cover about 60 per cent of the cost, but this will certainly affect our business , " he said.
The Rhythm & Booze chain, which has branches across north east England, also experienced problems due to the floods, although stores remained dry.
Managing director Martin Swaine said: "It's been a problem with logistics. We had quite a few power cuts and incidents of staff not being able to make it in. We've been running behind with deliveries both into and out of the area . Trade has been surprisingly good, though and sales are on a par with this time last year."
In badly-hit Hull, trade is picking up after a two-week lull. Corrinne Sykes of the Bottle Shop said: "Our stock was OK, but we did have to close for the day and we saw a drop in business for a bit."
English wine producers are also feeling the affects of the bad summer weather.
Julia Trustram-Eve of English Wine Producers said: "Currently it's looking as if it will affect the final volume produced." At Bookers Vineyard in West Sussex, crops have been affected and at Camel Valley in Cornwall, Bob Lindo said yields could be down by 20 per cent.