Porirua Harbour was formed by river valleys which were cut four to six million years ago, when the sea level was much lower than it is today. The sea level rose after the glaciations of the Pleistocene Period one to two million years ago, flooding the river valleys and creating the harbour.
Since then earthquakes have raised the headland four to five metres above sea level. The most recent uplift of around a metre was in January 1855. It created the marshland at Te Onepoto Bay and the beach along the western coastline. It also made Porirua Harbour too shallow for large sailing ships.
Te Onepoto Bay provides good habitat for many water birds, the estuary provides a rich feeding ground. Kingfishers visit the bay, eating insects, crabs and small fish and shellfish which are exposed at low tide.
White-faced herons can often be seen around Te Onepoto Bay. They were rarely seen in New Zealand before 1940 but, like the kingfisher, have thrived in the landscape created by the European and are now the most common heron in the country. Little shags, black shags, royal spoonbills and black backed gulls are also seen around the coastline and harbour. The shore plover has also been spotted on the coastal edge of the park.
The two ha coastal kohekohe forest remnant is in an excellent condition. It has two rare Streblus banksii trees (large leaved milk trees) which have been supplemented by planted ones. Underneath the canopy you may find the Doodia australis fern which is not very common in the region.
Since 2006 the wetland behind Onehunga Bay carpark has been planted by the Whitireia Park Restoration Group and is dominated by toetoe and flax. Local pukeko and paradise duck are often seen in the area. The group is working on a "corridor" of planting from the bush block above the gully down to the carpark. This corridor has many wetland plant species and some hardy plants capable of withstanding the salt-laden wind on the dry hills on either side of the gully. These plants provide habitat for wetland birds and improve the water quality in the stream which empties into Onehunga Bay. They also provide a seed source that birds and lizards may help disperse into the rest of the park.
The Restoration Group is also planting the dunes at Onehunga Bay in native species such as spinifex and pingao and threatened plants such as shore spurge, sand tussock, sand daphne and native iris. These are species missing which were once common around the Wellington region's coastline. They provide habitat and a food source for native insects and lizards, maintain the structure of the dunes and help restore the park's original ecosystem.