Geoffrey Wharfe, of Tabley Hall Farm in Tabley, was forced to sell his sheep early after floods kept them off the fields.
"I lost a lot of money on them because they were sold before they were ready," he said.
"We kept moving them to fresh land but as the weather got worse they had to go."
The National Farmers Union said that many potato crops had been destroyed or remained unharvested.
"Potato production is important in Cheshire and many farmers have found their crops unharvestable," said Rodney Bacon, policy advisor for NFU Cheshire.
"It's another blow to the agricultural industry which was already suffering from low income before the bad weather struck."
Mr Wharfe said he had been unable to get tractors on to parts of his land for months, leaving manure to go to waste and corn crops left to ruin in the water-logged fields.
"There is a backlog of work to do in the spring now because we haven't been able to plough yet," he said.
"It has caused a lot of inconvenience as well as the expense."
On Monday, a field off Chelford Road, Knutsford, owned by farmer Michael Mitchell, was still looking like a lake after being flooded a few months ago.
Research by the NFU shows that nationally the loss in grain could cost growers up to £300 million and some 822,200 tons of potato crops have been destroyed.
A package of crisis measures to help hard-hit farmers has been introduced after the NFU held emergency talks with the Ministry of Agriculture.
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