Coastal Otago was the hardest hit, and State Highway 1 closed between Dunedin and Palmerston for much of the day, reopening at 4.30pm.
The Dunedin City Council reported 28 road closures across the city, while more than 37 roads were closed in the Waitaki district and more than 30 in Clutha.
Emergency Management Otago group controller Matt Alley said a "significant amount of rain" had fallen in North Otago and the Dunedin area, with 110mm to 150mm of rain recorded in coastal Otago.
However, the weather for the rest of the week is set to improve.
MetService forecaster Aidan Pyselman said the next few days would bring a mix of fine weather and a few showers, but no heavy rain.
Dunedin Mayor Aaron Hawkins said yesterday that with the weather easing, no major issues were anticipated overnight."Our focus now turns to the recovery phase, and staff and contractors will be very busy over the coming days," he said.
North Otago Primary Principals’ Association president and Glenavy School principal Kate Mansfield said her school and numerous others in the region were closed yesterday.
Pearsons managing director Murray Pearson said 27 school bus runs were cancelled due to school and road closures, although schools in town were less affected.
Schools were expecting surface flooding on roads to take more than two days to come down.
Waitaki District Council roading manager Mike Harrison said Corriedale, Waihemo, Omarama and Lake Ohau areas were the worst affected by this week’s weather, but it was too early to know the full extent of the damage.
"There’s certainly some damage to the sealed roads and with the water sitting as a pond it actually softens the road underneath."
Waitaki Mayor Gary Kircher said conditions were particularly difficult for farmers in the district at what was already a busy time of year.
In Karitane, two boats broke free from their moorings and were swept along by the current for about 300m.
Resident Barrie Barber said the boats were "quite sizeable", but had broken away because of debris in the water.
"It’s the debris that comes down and gets around in front of the boats, willow trees and stuff like that. If the moorings aren’t strong enough to take it all, they break away."
Businesses were also impacted by the bad weather.
Barry Dell Plumbing co-owner Liz Carmichael, of Dunedin, said the company had been extremely busy and the company was "at our max".
Commercial customers were caught up but domestic customers were being advised there could be a six to seven-week wait.
Drainage issues were secondary to roofing issues, she said.
"Our roofers, I would have to say, are over-the-top busy," she said.
Dunedin’s Blacks Road Grocer owner Christopher Wilson was forced to close his doors to the public yesterday due to store flooding, the first time that had occurred in the five years he had owned the North East Valley business.
"Out the back there was a big drain and it just started overflowing — it filled up pretty quickly, in about 15 minutes," Mr Wilson said.
Evacuations of those living near the Water of Leith took place on Tuesday night as the river threatened properties.
University of Otago student Georgia Walker (19) and her four flatmates were among those who spent the night elsewhere, waiting for the river to recede.
She watched the river rise before they left, and said it looked as if it was about to break its bank.
"It was crazy how much it changed, we just couldn’t believe it,"
Initially unconcerned, she and her flatmates realised the situation was serious when police arrived.
"We packed up the car — thankfully we have a Dunedin resident flatting with us, so we all evacuated to her house."
She was safely back in her flat by yesterday morning, and no damage had been caused.
