Augé said samples of marine pests - and any other suspect animals or plants - will be collected for identification by taxonomists where their identity is unknown.
The results of the survey will be shared publicly once all collected samples have been identified.
"At this stage, we hope to be able to do this before the end of the year."
Cr Smart said the results will be used as part of a collaborative approach to manage marine pest risks in the Kaipara Harbour by NRC and Auckland Council.
The survey comes as the country's four northernmost regional councils - Northland, Auckland, Waikato and Bay of Plenty Toi Moana - seek public feedback as they collectively consider creating a consistent regulatory approach to marine pests.
For several years the council have been working alongside Biosecurity New Zealand and boaties from all over to stop the spread of unwanted marine pests.
NRC said while Biosecurity New Zealand manages national rules to minimise the risks of new pest species arriving on vessels from overseas, the regulations for vessels moving around within coastal waters vary from region to region.
A number of potential options are being considered.
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