Due to continuing high river levels, drainage and the flood pumps on the Taieri have not been effective in removing water from the area, especially below Allanton.
Taieri farmer Colin Scurr said the floods had brought a lot of sediment and silt to berm land, as well as damage to fences from material swept up in floodwaters.
Continued high river levels and ongoing rain had meant it had been difficult for farmers on some parts of the Taieri to get back on soggy land to begin the clean up.
''The ground has been too wet with the water coming up and down.''
About 70% of James Adam's farm at Otokia was still underwater earlier this week, although it had started to drain away in the past few days.
''It's the slowest we've ever had.
''We flood, but it's usually gone in a week to 10 days.''
The combination of high rainfall and snowmelt had kept rivers up for the past few weeks so gravity drainage on his paddocks had not been working, he said.
On the positive side, it looked like some of the grass that had been underwater was still alive, he said.
''It's a good time of year as the cows are away, but they'll be coming home shortly. We don't need anymore rain or snow.''
Former Federated Farmers Otago chairman Mike Lord said that the area between the flood-free highway and the former highway around Henley relied on gravity drainage, and for that to happen the Taieri River had to go down.
''Those guys have my sympathy.''
While some farmers had expressed concerns about the delay of the new Waipori flood pumps being turned on, reports he had heard suggested they had worked well, he said.
''It was extremely unlucky timing.''
The flood occurred just as the $1.1 million upgrade of the Waipori station, responsible for helping keep more than 7000ha of the Taieri Plain dry, was due to be completed.
Two new German-built flood pumps had only just been installed after the three 80-year-old pumps were removed, the old station shed, built in the 1920s, demolished and a new shed built.
Otago Regional Council Environmental engineering and natural hazards director Gavin Palmer said while there was still some work to complete on the station, the pumps themselves were able to be switched on during the flood.
Given it was their first test in place, the pumps' performance was pleasing, he said.
''We're still working through final testing but their reliability was no concern.''
The new pumps had also worked well given the high river and lake levels, although the gravity outfalls elsewhere were struggling as they were still below the river level.
The time it was taking for water to drain off land was not considered ''abnormal'' given the high rivers, he said.
The concerns of some farmers that drainage was not adequate on parts of the Taieri would be looked at by the council in coming weeks, but any improvement would come at a cost.
The council was also reviewing the performance of modifications to the Riverside spillway, which were also just being completed at the time of flood.
