David Hay, who has just returned from coaching the GB Olympic ladies curling team in Sochi, says 140 acres of his land is being ruined by the River Tay bursting its banks.
The flooding on his farm at Easter Rhynd, near Perth, waterlogs two fields at a time and has already ruined his wheat crops.
He is concerned the damage is also going to ruin this year's potato harvest and is looking at a deficit of £250,000 by the end of the year.
Mr Hay, who farms with his wife Erika and son Finlay, said: "The wheat is almost certainly ruined now and I don't know if we will be able to plant potatoes.
"We think we will need 7200 cubic metres of material to restore the bank but we won't be able to start work until the river is much lower in May or June. The banking has been under enormous pressure this winter.
"On January 15 we had one of the highest tides on record. There had been a lot of rainfall to the west, the atmospheric pressure was very low. This combined with strong winds from the west driving the water down the Earn and the Tay resulted in a massive tidal surge and that really opened up the breach."
The area affected includes two fields, one of 75 acres sown in wheat. The other is 65 acres and is where potatoes were due to grow this year.
The breach of water on the bank was first found in December last year and is now around 164 feet wide and about 39 feet deep.
The costs of repairing the breach and the loss of crops are uninsured and will have to be met by the farm.
There is government support available for compensation in England, but not in Scotland.
Work was done to repair the bank, which dates back to the 1850s, in 1980 by Mr Hay and his father. The work was stopped by Sepa over concerns about the material used for the repairs.
The current breach has occurred just beyond the point where the repair work was stopped. It remains unclear how much topsoil has been lost in the affected fields.
NFU Scotland president Nigel Miller said: "Farmland sits low down on the list of priorities when it comes to discussing flood defences but, given the risk that flooding now poses for some of our prime agricultural land, its importance must increase if we are to be serious about production and natural resources.
"We hope to meet Environment Minister Paul Wheelhouse and will present him with the case studies from many acres where flooding is having an impact on farmland and where resilience measures are needed with urgency.
"NFUS is also funding an independent expert in flood prevention to assess what defences and engineering may provide solutions."
l Cycle charity Sustrans has appealed for users of the National Cycle Network to let them know which parts of it have been damaged by the recent bad weather.
The route has suffered from the flooding, with route signs blown over, fence posts washed away and paths destroyed by landslides along the path from Shetland to the mainland and throughout England, Wales and Northern Ireland down to Cornwall.