Grape growers in Marlborough may lose a large part of their crops due to the storm.
MetService said Marlborough had more than 200mm of rain over 36 hours.
The Marlborough Rural Support Trust said larger grape growers had already brought in their harvest.
But co-ordinator Ian Blair said some smaller growers were out at the height of the storm trying to bring in as much of the crop as they could.
He said the remainder of the grapes could be lost as they swell and burst their skins, then become diseased.
Weeks of rain in Canterbury have left grain crops too drenched to be harvested.
Federated Farmers says members across the South Island are also struggling with damaged buildings, destroyed fencing and slips.
However, it does not think assistance from central Government is needed.