State Highway 53 in Wairarapa and State Highway 56 in Manuwatu could be closed until Sunday morning.
Detour routes in and out of Martinborough are now open after flooding closed them briefly on Saturday morning.
SH56 is closed at Opiki, north of Shannon, because of flood levels in the Manuwatu river.
The Transport Agency also advised drivers to be cautious on the Desert Road, which may be closed on Saturday night.
School holiday motorists are advised to allow extra time for their journeys. A heavy rain warning is in place for the lower North Island, south to Marlborough and Kaikoura, and north to Gisborne and Hawke's Bay.
Snow is expected down to 200 - 300 metres on the Rimutaka Hill Road and the Desert Road, though both are still open.
Snowfall warnings are in place for Lewis and Arthur's Passes and the Milford Highway.
MetService is warning Gisborne residents to expect heavy rain.
A severe weather warning hs been issued for the region, another 70mm - 90mm of rain is expected to fall before Sunday night.
A strong wind warning was also issued for Marlborough and Wellington, with gusts of up to 130km per hour in some places.