Two years ago, a 100,000cu m ''slug'' of gravel, silt, weeds and rubbish washed down the river and accumulated in the main channel, putting the nearby Te Anau sewage ponds at risk of flooding.
That flood, and one six months earlier, caused gravel to block the river mouth at Lake Te Anau, which meant the river backed up and flooded about 12ha of farmer Max Slee's land.
The council's catchment manager, Noel Hinton, said a working party had spent the months since trying to find a solution.
Asked why it had taken so long, he said everyone wanted to make sure the solution was the right one.
''This is a very complex, dynamic piece of river. It is located on a steep gravel fan and there is always going to be a [flooding] threat.''
The aim of the repairs was to try to keep the river within its defined riverbed or channels when the river rose, and that would be expensive.
The budget was $400,000 but could be higher, he said. So far, 40,000 had already been spent under the emergency provisions of the Resource Management Act to clear the channel immediately after the second 2013 event.
''The solution is about what's best for the long term. We can't afford to be spending $400,000 every couple of years.''
The work would be funded by the council and other parties, including Te Anau ratepayers and the NZ Transport Agency, which administers the Milford road highway near the river.
Mr Hinton said general agreement had been reached on 75% of the repair work and agreement on the rest was imminent.
The point of difference lay in what work was best for the 900m stretch of river below the Milford road bridge.
Members of the Upukeroa River liaison group wanted an ''intervention'' to straighten the main river channel, but Environment Southland favoured using rocks to protect the edges of the entire riverbed and letting the floodwaters flow within them, he said.
An assessment of the alternatives was being carried out now and a decision was due soon.
Once all parties had decided on the preferred option and its cost, the work would be ''all a goer'', Mr Hinton said.
