Septic tanks were known to have overflowed in some coastal areas and the best thing people could do to avoid health problems was to stay out of any flood-affected waterways, Dr Mills said.
Shellfish should be avoided for up to 28 days because they could store viruses.
"Viruses hang around in shellfish for a long while. With things like norovirus and other gastro bugs, shellfish are very good as sucking them up and storing them so we don't want people to risk it."
The public health risk was deemed medium high and swimmers, kayakers and anybody involved in activities which could lead to head immersion should stay out of the water for five days.
Whangarei District Council infrastructure and services group manager Simon Weston said contaminants would be in all flood water, streams, rivers and the harbour after the prolonged rainfall.
"However, particularly in rural areas, private septic tank and effluent holding systems may be vulnerable and, in Whangarei urban areas, some manholes may have surcharged," Mr Weston said.
"The advice is to keep out of the water until it is clear and not to consume shellfish or wetfish caught in the storm area."