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A council report, released yesterday, confirmed a partly blocked screen at the Portobello Rd pumping station prevented the facility operating at full capacity to drain floodwater from South Dunedin streets.
The station had operated at only two-thirds capacity for much of the downpour, meaning floodwater was nearly twice as deep on average and took longer to drain away.
But council infrastructure and networks general manager Ruth Stokes said any blame for flooding damage lay with ''the sheer volume of [rain] water'' - not the council's infrastructure.
''With that amount of water, there were always going to be challenges.''
She could not say - or rule out - whether the pumping problems had contributed to damage caused to homes, as ''street by street, property for property, we can't extrapolate that''.
''It [pump problems] wasn't the straw that broke the camel's back, by any stretch of the imagination.''
Instead, the council was facing a bill of up to $500,000 to improve the pumping station's screen, located upstream and designed to protect it.
Council water and waste group manager Laura McElhone, in her report, said the pumping rate was determined by water flows between the screen and pumps, but the screen had to be manually cleared of debris.
That was done each week, including on May 29, just days before the June 3 flood, she said.
However, during the flood, workers could only partly clear the screen due to the high flows, meaning water flow was restricted, slowing the pumping rate.
Council wastewater treatment manager Chris Henderson said the floodwater was deeper and took longer to drain as a result.
Modelling showed the flooding was about 490mm deep, on average, across affected areas of South Dunedin, which could have been reduced to about 295mm if the pumps had worked perfectly, he said.
''There was nothing we could have done to avoid it, but it [the flood] could have been for a reduced duration.''
Dunedin South Labour MP Clare Curran, in a statement yesterday, reiterated her criticism of the flooding response and said the council's report ''raises more questions than answers''.
That included whether ''flawed maintenance'' of the stormwater network and mud tanks were a contributing factor, and whether that was to blame for flooding affecting homes in other parts of the city.
''I expect the council to fully investigate all of those,'' Ms Curran said.
Dr McElhone's report said the rainfall had ''significantly exceeded'' predictions and the stormwater system's capacity to cope.
The council's rules now required new developments to accommodate a 1-in-10-year rainfall event within pipes, while beyond that ''secondary flow paths'', such as roads, were expected to keep flooding from reaching the habitable floors of homes.
However, the rules only applied to new developments, and parts of the existing network did not meet that standard - something the council was already working to fix, she said.
While it appeared ''superficially'' the network should have been able to cope, based on designs when construction began in the 1950s, ''several of the significant design assumptions did not hold true''.
That included an assumption only 45.7% of rainfall would land on hard surfaces and be carried into the stormwater network, while the rest soaked into softer ground, Dr McElhone's report said.
The spread of sealed surfaces with development since then meant about 60% of rainfall was now carried into the stormwater network, reducing the network's ability to cope, she said.
Groundwater levels were also elevated at the time of the flood, rising to the surface in some locations, meaning ''that across much of South Dunedin, little, if any, water was able to soak into the ground''.
The council had identified ''opportunities to improve'', including at the Portobello Rd pumping station, but a separate report expected earlier next year would discuss the performance of the city's mud tanks, she said.