Tidal flows have built up a bar at the 600m wide entrance, which makes navigation difficult in large swells.
The entrance is flanked by the rocky Te Rehutae Point, rising to 85m to the west, and Omara Spit to the east.
Commonly caught fish include kahawai, snapper, John Dory, and barracuda.
Common plants found in the Whangapoua harbour include mangroves, the seagrass Zostera muelleri, neptune's necklace seaweed Hormosira banksii, and salt marsh rushes.
More abundant animals include cockles, mud snails, horn shells, whelks, cat's eyes, pacific oysters and cushion stars.