While there were no major issues, the Dunedin City Council and Otago Regional Council staff and contractors would continue to monitor the situation and respond as needed.
Much of New Zealand was expected to stay wet for most of this week.
Figures from the Otago Regional Council showed that from 1am until 2pm on Monday, 46mm of rain had fallen at Mosgiel, 76.5mm at Swampy Summit and 57mm at Sullivans Dam.
The MetService was forecasting another 15mm to 20mm of rain until 8pm, but conditions were expected to ease.
The DCC said there had been localised flooding in some areas of Mosgiel and East Taieri and several roads have been closed, including around the Silver Stream. Motorists were asked to drive carefully.
Small waterways such as the Owhiro Stream and Quarry Creek have been high at times and East Taieri School was closed on Monday due to the risk of flooding from a rapidly rising creek.
Water was also ponding on some farmland and the DCC said there had been reports of minor surface flooding on some Dunedin sportsfields and reserves.
Dunedin City Council chief executive officer Sue Bidrose said staff from the DCC and ORC had been out during the day to make sure issues were responded to "as quickly as possible".
"Most of the issues relate to localised flooding. Key stormwater screens around Dunedin and Mosgiel are being proactively checked," she said.
"Overall, infrastructure is coping well, apart from a small number of localised issues where capacity has been reached.”
Dr Bidrose said staff would continue to monitor the situation. To report issues with mud tanks or other DCC infrastructure, please call (03) 477-4000.
For Mosgiel residents wanting to divert running water, sandbags and sand were available from about 4pm from the Memorial Park car park beside the stadium/Mosgiel Memorial Gymnasium.
Fulton Hogan Central Otago District Council engineer Conor Muir warned river levels in the Maniototo were getting high. They were "not a problem at this stage", but the situation was being monitored.
Oamaru flooding
Firefighters from the Oamaru Volunteer Fire Brigade were called to assist an Oamaru businesswoman with flooding issues this afternoon.
A carpark behind the woman's business was flooding about 1.15pm, a Fire and Emergency New Zealand spokesman said, and the woman was "distraught" about the situation.
Firefighters found the flooding was due to a blocked drain. They cleared as much water as they could and advised her to contact the Waitaki District Council to clear the drain and to use sandbags until the water cleared.
ORC watching river levels
Many Otago rivers were starting to drop even though heavy rain was continuing in parts of the region on Monday night.
The Otago Regional Council said the day's rainfall had caused surface flooding in several parts of the Taieri and its flood management team was monitoring river levels closely.
Based on current rainfall and MetService’s latest forecast, ORC said there was no concern that the Taieri River or the Silver Stream would overtop their banks.
Drains were running full and it was expected surface flooding would affect roads, including Dukes Rd.
The Taieri was high and rising at Outram, while the Kakanui was high at Clifton Falls and dropping, the regional council said.
ORC operations staff were continuing to check drains on the Taieri and for the most part no significant or extended overtopping has been seen.
On the Lower Clutha scheme drains and pumps had been checked and there were no problems.
The ORC has a 24-hour duty flood manager monitoring river and lake levels. Information on river and lake levels was also available on its Waterinfo website, through the Flow phone on 0800 426463, or via Twitter alerts.
