Wanaka and Queenstown received the worst of the rain as it passed over Otago, with more than 100mm falling at Makarora and also Glenorchy between Monday afternoon and yesterday afternoon.
Queenstown was also battered by strong winds and at 7pm yesterday Lake Wakatipu was marginally above the first flood alert level of 310.8m above sea level.
Areas of Queenstown remained in darkness after a power failure.
Parts of the resort lost power about 1.20pm "but we've only just been made aware of it", Delta systems control manager Graeme Johnson, of Cromwell, said at 8pm.
The levels of Lakes Wanaka and Wakatipu climbed steadily yesterday, and campers near the rivers flowing from Upper Waitaki hydro lakes were moved as excess water was spilled.
The rain caused slips and minor flooding and temporarily closed several roads across the region.
It also disrupted flights from Queenstown and resulted in the cancellation or postponement of several events, including the first day of the national bowls championships in Dunedin, the Omarama Rodeo and the Hawea picnic races.
Lake Wanaka reached 279.2m, just under its first flood warning level, yesterday afternoon and Lake Wakatipu passed its first flood alert to rise to 311m before levelling off.
The high lake levels did not affect daily activity in the two resorts, where it was business as usual.
Queenstown Lakes District Council harbourmaster Marty Black urged people to stay off "dangerous" rivers for the next few days.
Strong winds caused flights to be diverted, and one lucky motorist escaped uninjured as a branch smashed through his vehicle's front windscreen.
Rivers were still rising last night, but by 6pm, the Clutha River at the Cardrona confluence, the Pomahaka River south of Moa Flat and Deep Stream at the SH87 bridge were the only three Otago rivers to reach their first flood warning levels.
The Otago Regional Council warned high flows could be expected in the lower reaches of the Clutha River as floodwaters drained from the lakes.
Low-lying areas near the river could be affected, and farmers should move stock to safer ground.
There were no problems with river flooding in eastern and central Otago.
In the Upper Waitaki, about 400mm of rain at Mt Cook in just 36 hours, combined with heavy rain elsewhere in the catchment, forced Meridian to spill water from Lakes Tekapo, Pukaki and Ohau.
Campers were warned to beware of rapidly rising water levels along rivers, and up to 100 people camped beside the Ahuriri River near Omarama were advised to move about 5am yesterday.
Environment Canterbury also warned water was being spilled from the Benmore, Aviemore and Waitaki dams, which would boost flows in the lower Waitaki for the next few days.
It issued warnings to farmers, landowners, holiday- makers and campers beside the lakes and also the lower Waitaki to take extra care.
In Dunedin there was little wind, and rain caused limited surface flooding and some minor slips.
The first day of the New Zealand bowls championships was abandoned because of flooded greens.
Elsewhere in Otago, the rain provided some welcome relief. North Otago pastures got 40mm-50mm, with the rain swelling the low Kakanui, Shag and Waianakarua Rivers, while low flows in some Central and South Otago rivers were relieved by about 50mm-60mm of rain.
Central Otago principal rural fire officer Owen Burgess said Alexandra's 36.7mm of rain in 24 hours "dampened things down nicely".
In Queenstown late last night, Delta was still working to restore power to the Lower Shotover, Tuckers Beach Rd, Domain Rd and the Skyline Queenstown gondola resort.
All weather warnings for the South Island were lifted at 3pm yesterday.
The Waikouaiti Volunteer Fire Brigade attended two flooding incidents yesterday.
At 5.30am, a unit was called to 112 Beach St, where a garage had been flooded by heavy rain.
At 4pm, a fire crew was called to the Waikouaiti Camping Ground, where it pumped out 60cm of water from a low-lying camping area, volunteer Ian Harkness said.
