However, most observers did not think the flooding would be serious.
The ORC warned rain forecast for the Main Divide could spill over into Otago lakes and rivers.
A flood warning was issued for Lake Wakatipu yesterday, as it was already marginally over its first flood alert warning level of 310.8m above sea level.
Up to 100mm of rain was expected at the divide and 25mm to 50mm of rain over the rest of the catchment today.
Lake Wanaka was just 20cm below its first flood alert level of 279.4m yesterday.
ORC flood manager Phillip Purves said further rain was predicted for the Clutha catchment and that lakes Wanaka and Wakatipu were expected to peak tomorrow morning, at higher than present levels, but they would cause only minor flooding of low-lying areas.
High flows were expected in the Kawarau and upper Clutha Rivers, and in the lower Clutha River downstream of Roxburgh to Balclutha into the weekend, as a low-pressure system passes across the South Island today and tomorrow.
However, MetService weather ambassador Bob McDavitt said the low would weaken as it approached.
"There may still be sufficient amounts of rain reaching the Clutha catchment during Thursday, so that people near the already-high Southern Lakes and rivers should keep a close watch for further rises in water levels," he said.
As the low moved away tomorrow, a cool southerly wind change was expected to spread across the eastern South Island, Mr McDavitt said.
Drizzle returned to Wanaka yesterday and more rain is forecast before tomorrow, which could push Lake Wanaka up to 280.2m and into Ardmore St for the first time since 1999.
However Wanaka Chamber of Commerce president Leigh Stock said heavy rainfall warnings in the past couple of weeks had fallen short and he expected this one would, too.
The Clutha River is still in flood at the outlet and was flowing at 676cumecs at noon yesterday, while the Makarora rain station recorded 4mm and the Matukituki rain station 0.5mm.
The Department of Conservation Outlet Track along the Clutha River remains flooded in places and the Roys Bay jetty is still under water.
The marina jetty and Ruby Island picnic and barbecue area are also under water.
Rising lake levels in Queenstown and Wanaka were "not enough to cause panic", Queenstown Lakes Mayor Vanessa van Uden said yesterday.
"It is business as usual. We have got a lot of people monitoring it and the processes are in place, but there is no reason for concern," she said.
Since the start of December, Lake Wakatipu has risen almost 1m (from 309.9m above sea level to 310.8m yesterday morning), and Lake Wanaka more than 2m (from 277.2m, to 279.3m yesterday morning).
Ecan figures showed the Waitaki River's flow at Kurow eased yesterday, from 1240 cumecs on Monday to 1202 cumecs at noon yesterday.
