Farmers in the Waitaki district in North Otago have been moving stock as more rain soaks already saturated pastures and the river levels increase.
Federated Farmers North Otago president Richard Strowger says the heavy rain has caused some problems for dairy farmers with calving underway.
He says the region has gone from very dry a couple of weeks ago to the other extreme and paddocks are becoming very muddy.
Mr Strowger says at this stage most farmers are coping reasonably well and the Otago Regional Council has sent out warnings about moving stock from low-lying areas.
He says if the rain continues it will flood, but people have had plenty of time to deal with it.
The rain is forecast to ease on Thursday.
There's also been extensive surface flooding in South Canterbury after heavy rain there on Wednesday.
But Canterbury Regional Council says river and flood protection systems are coping.
It says the rain has been significantly less than last week but many local roads were closed on Wednesday by flooding from downland streams and run-off, partly due to the ground being already saturated.