Initial estimates put the damage bill at more than $100,000, but that could rise once an assessment of the city's roads and other infrastructure was completed and repairs carried out, council managers said.
The Otago Regional Council has also been informed of the possible discharge of contaminated stormwater into Otago Harbour.
Council customer services manager William Robertson said staff fielded about 100 phonecalls from residents worried about flooding, blocked culverts or road closures during the weather event.
Council roading maintenance engineer Peter Standring said Fulton Hogan contractors dealt with at least 50 reports of weather-related problems, from landslips to blocked culverts and mudtanks causing flooding.
Reports were still coming in yesterday, but most issues were caused by the limited capacity of pipes and debris clogging culverts and mudtanks, he said.
That included the basements of homes in Macandrew Bay, flooded when a culvert reached capacity and water backed up, he said.
"We just do the best we can to keep it out of private properties, but inevitably it does get in," he said.
Council staff had spent most of yesterday assessing damage, after slips closed some roads - including Portobello Rd and, for a time, Highcliff Rd, on Otago Peninsula - as 51.4mm fell in the city.
Most of the roading network was checked yesterday and a "reasonable amount" of scouring damage discovered on some unsealed roads, which would need to be regraded and repaired, Mr Standring said.
Some minor rebuilding of sealed road edges would also be required, and the cleanup of slips and other debris was continuing, but no major damage to sealed roads had been discovered, he said.
Repairs would be carried out over the next few weeks, but the repair bill was already estimated to be "around $100,000" and could rise to $150,000 or more, he said. The cost would be met from within budgets.
"It mounts up pretty fast, all these wee things . . . It's quite a concentration of water that we had."
Council water and waste services manager John Mackie said issues facing the council's water network related mainly to the system's ability to cope with the heavy flows.
About 12 council staff worked through the night to keep pumps and other plant equipment operating and cleaning inlet grilles and stormwater grates of debris, he said.
Some treatment plant pumps experienced mechanical failure due to the extra workload created by the "huge flows" of water dealt with, but details were not available yesterday, Mr Mackie said.
The overall cost to the council's water and waste services unit stood in the "early tens of thousands of dollars", but could rise when the pumps' repair bill was confirmed, he said. The bill would be covered by a contingency budget for maintenance and repairs.
The ORC was notified on Sunday of the possibility of "some spills [or] emergency overflows that affect the environment" coming from overflowing council stormwater systems, he said.
Bacteria counts from outfalls into Otago Harbour were not available yesterday, but it was common to have elevated readings during the "first flush" of a storm event, he said.
Despite the difficulties, Mr Mackie remained upbeat, saying the weekend's rain created only "relatively minor" issues and staff had responded well while working "some big hours".
