The Otago Regional Council was closely monitoring both lakes yesterday.
They were on first flood alerts and expected to peak last night without causing significant flooding.
The ORC was predicting Lake Wakatipu to reach about 311.035m, over the first flood warning level of 310.800m but below the possible flood level of 311.3m, which would bring some water into low-lying reserve areas of Queenstown Bay.
Council duty flood manager Phillip Perves said the rain had stopped in the headwaters of both lakes yesterday and the council was now monitoring the inflow and impact on the lakes.
It was thought the rainfall was comparable to last week's event, although due to that event lake levels were higher to start with, he said.
Lake Wakatipu was sitting at 310.899m at 4pm yesterday and was still rising.
The rain that fell in the hills above Lake Wanaka was more significant than last week.
The Clutha River at the Cardrona confluence was on flood alert at 702.454cumecs at 4pm while the lake gauge was at 279.342m at 4pm.
Wanaka chamber of commerce president Leigh Stock was maintaining a close watch on the water levels.
Yesterday morning's rain had cleared by noon and with mostly fine weather forecast from today until Sunday, those people spoken to by the Otago Daily Times felt confident the lake would not reach the 280m potential flood level.
Mr Stock said a flood alert issued on Sunday night was lifted early yesterday morning after it became apparent there had been less rain overnight at Makarora than the 150mm forecast - 72mm fell in the 24 hours to noon yesterday.
Mr Stock said the regional council flood models suggested the lake should peak at about 279.6m about 9pm, which was above the flood alert level of 279.4m but below the possible flood level of 280m.
"The Queenstown Lakes District Council and civil defence will take action if needed.
But I don't expect it to happen," Mr Stock said.
The Wanaka Marina Committee warned boat owners on Sunday to move their moored craft to prevent damage from waves, wind and driftwood.
"I don't think there is any chance of it flooding," committee chairman Duncan McFarlane said.
A major earth and tree spill closed State Highway 6 at Chelsea Creek, between Makarora and Haast, about 5.45pm yesterday.
The road reopened fully about three hours later.
Persistent rain in the Clutha and Kawarau catchments meant water continued to be spilled through the Clyde dam, as the high flow was too much for the dam's generators to cope with.
Although the Clutha River was high, there were no concerns about the level of the Manuherikia River, unlike last week, when several campers in the Alexandra Holiday Park had to be shifted from sites near the river.
Further north, 74.5mm of rain had fallen by 4pm yesterday at Aoraki/Mount Cook, bringing the total for the past seven days to 567mm.
The Waitaki River at Kurow had dropped to 1408cumecs at 2pm.
Yesterday morning, Environment Canterbury said the high discharge flows from the Benmore dam over the past four days had created a buffer in the Waitaki lakes system in the meantime and the flow into the lower Waitaki River would be reduced to between 1300 and 1400cumecs over the next 24 hours.
The overcall catchment system would continue to be monitored closely.
A temporary barrier preventing the Waitaki Bridge village being flooded, was erected on Sunday after properties in the Waitaki Bridge camp started flooding, and would remain in place until the water level dropped in the Waitaki River.
Waitaki District Council emergency services manager Chris Raine said a groyne had broken and water was pouring into the paddock area on the northern side of the camp.
Water was where it would not normally be and it had to be pumped from around properties after civil defence was called at 4.30pm.
While the water level was going down yesterday, more rain was forecast on Thursday.
The 1.25m high steel barriers were bolted together with a tarpaulin going over the top and took 10 people two and a-half hours to put up.
