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.