The raging Whanganui River peaked at 14.60m at Pipiriki at 4pm on Tuesday and dropped dramatically between midnight and 1am Wednesday morning.
Pipiriki tour operator Josephine Haworth said the flooded river left mud in its wake and there was still debris floating down river.
The rain stopped falling in Pipiriki about 2.30pm on Tuesday and only a couple of showers fell over the upriver area that night.
In the Waimarino, residents living around the Makotuku Stream and Mangawhero River are being advised to stay away from waterways until further notice following the Raetihi and Ohakune wastewater treatment plants being flooded in Tuesday's weather bomb.
Ruapehu District Council chief executive and Civil Defence controller Peter Till said signs had been posted advising people to not drink, swim, bath or collect food from the waterways.
"The rain fall yesterday was an extreme event that saw the level of the rivers rise by several metres and flood both wastewater treatment plants."
Raetihi and Ohakune residents are being asked to conserve water as the drinking water treatment plants stopped production during flood events.
"Even though getting this volume of rain in such a short space of time is a rare event, council will look into whether the stopbanks protecting the wastewater treatment plants are high enough," Mr Till said.
Meanwhile, roading crews were out clearing roads and assessing damage.
The council kept its emergency operating centre open and call-centre staff worked after-hours on Tuesday night.
There were 26 separate incidents affecting roads listed on the council's website www.ruapehudc.govt.nz, covering everything from flooding, drop-outs, trees down and big slips which would take some time to clear.
The council is asking residents to phone 0800 123 123 732 to advise any flooding, slips or other storm related issues affecting roads. "Information from local residents on the ground is invaluable at a time like this in assisting to ensure that we have the latest information listed for people to utilise."