The NZ Transport Agency said there was surface flooding on State Highway 6, Arrow Junction to Queenstown and SH6A from Frankton to Queenstown.
Queenstown Lakes District Council said motorists may expect delays due to the flooding.
"Rock falls have been reported on the Glenorchy-Queenstown Road, between Wye Creek and Staircase Creek, and on the Crown Range. Be extra vigilant if you're going to be in any of those areas."
Flooding was also affecting the road in places from Haast to Hāwea, it said.
The road from Dunedin to Plamerston (SH1) had some ice on it, while black ice was in places on SH85 from Kyeburn to Palmerston and SH87 from Outram to Kyeburn.
However the NZTA said those roads had improved by 8.45am.
The Crown Range Road is expected to get a few snow showers this morning and 1 to 2cm of snow could accumulate.
"This is currently being ploughed, but be prepared to take it easy if you're headed that way. Don't forget to stick those chains in the boot," the QLDC said.
Yesterday MetService put a heavy rain warning was in place for the Otago headwaters.
"Heavy rain may cause streams and rivers to rise rapidly. Surface flooding and slips are also possible and driving conditions may be hazardous."
