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A Metservice heavy rain watch is in place for the Otago headwaters, with another period of heavy rain expected to begin this evening.
Heavy rain is forecast from about 5pm, and thunderstorms are possible tomorrow morning.
Around the Southern Alps between 100mm and 150mm of rain is forecast to fall, and about 80mm to 110mm of rain is forecast to fall within the area about 20km further east.
"The largest accumulations are likely in the north of the catchment," MetService said.
"Peak rates of 15 to 25mm per hour [are expected] about the Main Divide Monday night and Tuesday morning."
MetService said further periods of heavy rain were expected this week, and additional warnings were likely to be issued closer to each event.
The Otago Regional Council’s duty flood officers announced yesterday they would be monitoring the impact of rainfall on river and lake levels.
Since high flows were expected in the Clutha River, Contact Energy had said it would lower the water levels in Lake Roxburgh for flushing sediment within the lake.
A statement from the ORC said the step would result in an increased flow from Roxburgh Dam.
ORC natural hazards manager Jean-Luc Payan said given the consent conditions, and the operating procedures Contact Energy had in place, the council was "not expecting any safety issues".
The outflow from Roxburgh had been increased by about 100 cumecs, or 10% of the total flow, Mr Payan said.
"People can expect to see a slight increase in flows and water levels in the river downstream of the dam but this is likely to be nearly imperceptible," he said.
The increased outflow from Roxburgh Dam was not expected to cause any flooding along the Clutha River, and in the longer term the flood hazard for Alexandra was expected to be reduced.
Mr Payan said that would be achieved by moving the sediment from the delta near the upstream of the reservoir further into the reservoir.
"This will, in the long term, ensure improved flow capacity in the vicinity of Alexandra."