The council's estimate covers damage caused by intense rain on Thursday night and Good Friday.
Council assets group manager Neil Jorgensen said while the full extent of damage would not be known until the floodwater was gone, costs were not expected to be more than $200,000.
Flooding in June last year caused almost $2 million damage, but that included the loss of a bridge in Danseys Pass.
Mr Jorgensen said ongoing preventive work by the council, including the installation of six wash-over pads around the district, had proved its worth.
''We've been lucky,'' he said.
Another six sites have been identified for wash-over pads, which will cost about $635,000, as part of the Waitaki Resilience Project to provide a strengthened roading network for the community.
Mr Jorgensen asked for the public to be patient as normal grading work around the district's rural roads would be delayed while flood damage was fixed.
Kakanui Valley Rd, which was still closed yesterday, probably sustained the most damage in the Waitaki network, he said.
He did not expect roads to be back to a ''reasonable condition'' for at least another three weeks.
''Really, drive carefully to the conditions and expect some roadworks around the place,'' he said.
