A warning against in Whangarei's harbour, put in place on Saturday because of a sewage overflow, is expected to remain in place for about a week.
About 100mm of rain fell on Whangarei in a storm that created floods and damaged property from Northland to Waikato before moving south.
The heavy rain caused a sewage overflow and Northland District Health Board on Saturday warned people not to swim or gather shellfish.
The warning against swimming is likely to remain for a week and people are advised not to gather shellfish for another four weeks.
Whangarei District council drainage manager Gary Oldcord said the deluge hit between 3am and 6am on Saturday.