Wauchope veterinarian Michael Ferguson and his team have spent the past few days putting down animals across the region.

Nearby Port Macquarie was among the locations hardest hit, with floodwaters in the Hastings and Camden Haven rivers reaching record levels and inundating parts of the town.

More dead livestock will be found as the waters recede.

"I spoke to a friend of mine and he had 50 cattle or so on the Maria River," Dr Ferguson told AAP.

"He's expecting he might find about five of those left, which is pretty devastating."

The floodwaters came quickly and strongly, he said, and many cattle were literally washed away.

Some miraculously survived, like a calf rescued from a beach near Taree, which copped its worst flooding in almost a century.

Dr Ferguson said he had heard of a cow washing up alive at Little Beach in Bonny Hills, about 20km from the Hastings River mouth.

"That's a heck of a long way for them to be able to stay afloat, swim and survive," he said.

Most don't, drowning or dying of hypothermia and exhaustion.

Even livestock that weren't carried away are at risk.

They're exhausted and uncomfortable, at risk of infection and pneumonia, and there's a shortage of some medications to treat them.

"We try to identify the ones that you can make a difference with," Dr Ferguson said.

"At the same time we have to be very pragmatic ... and decide this one's not going to make it.

"That's not easy."

He says it's incredibly distressing for the farmers too, many still bearing the mental scars from years of drought and the Black Summer bushfire disaster.

"It's from one extreme to the other," he said.

"It's a very cruel situation."

Adding to farmers' distress is the need to dispose of dead livestock and pets quickly, the NSW Department of Primary Industries says.

Members of the community are being encouraged to report dead animals to the DPI and take note of any tags, brands or ear markings on them.

Many owners are unable to bury their own animals due to disease and contamination concerns, so carcasses need to be removed and dealt with elsewhere.

"We have dedicated and highly skilled crews... supporting and assisting landholders with this difficult task, which we understand is also taking a large emotional toll on many producers," incident controller Simon Oliver said.

NSW Farmers chief executive Pete Arkle says it is still early days, but estimates the bill for stock losses will be enormous.

"It will be tens of millions, if not higher in the end," he told AAP.

It's not just stock either - most farms in the area will have lost vital, expensive infrastructure needed to keep them running.

Product has been ruined too.

Avocado farmers are facing the prospect of their water-logged trees dying, the cold and wet conditions are delaying pollination on berry farms, and many oyster producers will now miss out on the Easter boom because of the muddy, polluted waters.

It is a major blow for farmers already at the brink, Mr Arkle says.

NSW Farmers has launched an appeal to raise money for those in the area to rebuild and recover - again.

"What we're now experiencing is that further crisis on top of an already really tough couple of years," he said.

"The human side of this recovery will be as important if not more important than repairing the physical stuff on farms."

Donations can be made through the NSW Farmers website.

Australian Associated Press