The Whangarei Harbour Marine Reserve came into being on 18 October 2006 and comprises two sites - Waikaraka and around Motukaroro/Passage Island at Reotahi. The combined area of both sites is approximately 253.7 hectares or 2.54% of the Whangarei Harbour.

The marine environment in the Whangarei Harbour is of distinctive quality, and the reserve acts as an important nursery for the spectacular marine life. 

The seabed surrounding Motukaroro Island is a feeding ground for an unusually high diversity of fish, and the reserve also includes mangroves, and tidal flats that support a myriad of marine animals and seabirds.