Major sections of South Island highways remain closed following wild weather over the weekend

Flooding caused 18 highways to be partially shut and two days later a handful of sections remain closed.

Waka Kotahi will re-open State Highway 65 at 10am to restore the link from Murchison to Nelson.

But there will be delays, with a five kilometre stretch down to one lane as crews clear many slips.

The worst area is the Marlborough region and the transport agency hopes to open highway 63 from St Arnaud to Renwick by the end of the day.

But some Marlborough Sounds roads will take weeks - if not months - to fix, with some communities still isolated.