Mokoia Island's fertile soils saw it used by the Te Arawa people for growing food crops, especially kumara (sweet potatoe). This resulted in most of the bush being burned and cleared and the steep slopes being cut into terraces. However, many native trees were also planted such as Karaka, Totara, Whau and Puriri. In the early 1800s, visiting missionaries planted a wide variety of crops and trees but today the only remnants of these are a few fruit trees and some poplars.
Perhaps the most important impact on the Mokoia environment by European settlers was the accidental introduction of the Norway rats which were already well established by the year the Treaty of Waitangi was signed. Mice also hitched a ride to the island about the time that people introduced cattle, sheep, horses, pigs and, perhaps worse of all, cats. Amazingly, neither possums nor stoats ever made it to the island.
Over centuries Mokoia has been the subject of many episodes of ownership dispute and invasion. Although this century has been no exception there has been less bloodshed as the conflict moved to the courts in 1916. Eventually, the Maori land court awarded the island to four tribes which now administer the wildlife refuge as a trust board.
During the 1950s, Mokoia was used by the Department of Internal Affairs as a nursery for young pheasants which were released around the country as game for hunters. The grain used to feed these birds led to a population explosion of rats on the island. About the same time a surplus population of Weka were transferred from areas between Gisborne and the Coromandel and were deposited on Mokoia Island. Some native reforestation plantings were attempted in the 1960s but the rats were so profuse that nothing survived for long.
Goats were introduced into a fenced off area to control blackberry which had colonised the cleared land on the island. Unfortunately but not surprisingly, the goats turned their noses up at the blackberry and escaped into the bush instead. Consequently there was little regeneration occurring on the island until the goats, rats and a few remaining sheep were eradicated in 1989 and 1990.
Although the mice remained, the years following the eradication programme saw the immediate plant regeneration under way and the corresponding return of native birds such as Tui, Fantails and Grey Warblers and of insects, which the birds feed on, as well as Weta.
Tieke, Northern Saddleback, from the population on Tiritiri Matangi, Hihi, Stitchbird, from Hauturu (Little Barrier) and Toutouwhai (North Island Robin) from the nearby Mamuku ranges have since been released on the island. In 2003, three young Kiwi were released onto the island as part of the Kiwi Recovery Programme.
— Alex Eagles, 2003