With harvest just around the corner, the National Farmers' Union has said the severe flooding could not have come at a worse time.
Farmers describe the conditions as "extremely difficult"
Thousands of acres are currently under water, with farmers facing a range of problems from weather-damaged fruit to rotting cereals.
There are fears the situation could lead to higher prices for the consumer.
The NFU has highlighted three main problems for the industry after the heavy rains:
- Potential potato blight
- Hay-making written off affecting livestock feed
- Pea harvesting made impossible
In Humberside, farmers say the rain has destroyed a quarter of Britain's national crop of peas.
Food giant Birds Eye said the pea harvest only started last week and it was still assessing how much had been lost.
NFU Vice President Paul Temple, who grows peas on his farm in Yorkshire, said harvesting conditions were "exceptionally difficult".
"We had two months of rainfall here in 13 hours and peas are particularly sensitive to water-logged soils - any longer than 24 hours and it effectively kills the crop," he said.
"We are still bracing ourselves for more heavy rain and it is heartbreaking to work so hard growing a crop that may just rot in the fields."
But he said farmers were a resilient breed and used to fighting battles with the weather.
John Harper is another farmer whose land is under water.
One hundred acres of his 700-acre farm in Holt Heath, Worcestershire, now resembles a rice paddy field.
But underneath the water lies his livelihood - barley, pumpkin, sweetcorn and potatoes.
He said his pumpkin and potato crop were most likely "terminal".
Mr Harper's farm has been in the family for three generations and he described this week's floods as "exceptional".
However, he is not immune to flooding.
The farm backs onto the river Severn and lies in its meadows, so the fields receive a good watering every winter.
But this is the first time the fields have flooded in June, when all the crops are in the ground.
Mr Harper said: "This is a full cropping period, everything is in the ground at the moment and there will be a lot of people affected."
Because of its location, the farm is not insured and so no compensation will be coming Mr Harper's way.
"It's a case of try to do the best you can with what you're left with," he said.