As farmers on the Hauraki Plains begin cleaning up after two storms in a fortnight, they are also facing a risk of feed shortages caused by the floods.
One local farmer said they barely had time to recover from the first storm when the next one, Cyclone Cook, hit.
Federated Farmers Waikato provincial president Chris Lewis said it would be "financially devastating" for some farmers, especially after a couple of seasons of low returns.
"They're probably still knee-deep in their overdrafts and now they're going to be knee-deep in floodwaters, and with no income and a lot of bills," he said.
Farmers were waiting for their paddocks to dry out before they could assess the damage to their pastures and get on with remedial work.
But Mr Lewis said farmers should start thinking further ahead and consider what they would need to get through the winter.
That included making sure they had enough supplementary feed.
In the short term, Mr Lewis said he thought there would be enough and there weren't any problems with trucking it in.
But he said that situation could change.
"Come this winter, I have a feeling that the stockpile will run short."
Mr Lewis said farmers should start planning ahead for the next three to four months, and have a stock take of what they have got and what they would need.
There was also potentially pressure from farmers needing supplementary feed in other flood-hit areas, like the Bay of Plenty.
Mr Lewis said the flooding had also meant farmers had to move their livestock to other areas.
However, he said many people had been forthcoming with offers of help, including grazing.
One local farmer, Ian Troughton, said about half his farm - 200 hectares or so - was flooded and his paddocks had been underwater for 10 or 12 days.
He estimated there could be 20 or 25 properties along the river in a similar situation.
For a lot of farmers, Mr Troughton said autumn was looking like it was going to "turn their fortunes around".
They were already under a lot of pressure, but this puts them under even more, he said.
"For many farmers, they haven't been able to harvest their maize silage, so their supplement, in many cases, will be lost. They've already spent a lot of money planting those crops in anticipation that that supplement would be there through the winter and spring.
"They'll have to go back and reassess what they're going to use to replace that."
Mr Troughton said it would take one to three weeks for the floodwaters to recede.
From there, they would be able to assess what damage it had done to their pastures.