The Mangawhero, Turakina and Whangaehu rivers were also rising.
Whanganui District Council emergency managers were watching river levels on Tuesday night, officer Anthony Edwards said.
Temperatures in Whanganui dropped to 12C yesterday, with an expected 6C overnight. Winds were expected to rise during the evening, and turn to the south, and hail was possible on Wednesday morning.
Places farther out in the region fared worse yesterday. Taranaki was hammered by thunder and lightning, rain and wind, with a tornado that damaged eight houses in the coastal town of Rahotu.
Wind toppled trees and powerlines and from South Taranaki across to Whanganui,12,000 people were without electricity.
Powerco network operations manager Phil Marsh was unable to predict when power would be restored. He said working conditions were difficult, and the 13,000 lightning strikes may have damaged equipment.
The central plateau had a tornado in National Park Village and was predicted to get nearly twice as much rain as coastal Whanganui. Rivers and streams were rising fast.
Snow was predicted for the Desert Road, and the New Zealand Transport Agency warned people to expect wintry conditions.
Read more: Whanganui weather forecast