The first five years after the signing of the Treaty were a disaster, first under governor Hobson then under the ineffectual FitzRoy. Relations between Maori and pakeha began to deteriorate immediately, as the capital was moved from Kororareka to Auckland and duties were imposed in the Bay of Islands. The consequent loss of trade from passing ships precipitated the first tangible expression of dissent, a famous series of incidents involving the Ngapuhi leader Hone Heke , who repeatedly felled the most fundamental symbol of British authority, the flagstaff at Russell . The situation was normalized to some degree by the appointment of George Grey , the most able of New Zealand's governors and a man who did more than anyone else to shape the country's early years. He was economical with the truth and despotic, but possessed the intelligence to use his deceit in a most effective (and often benign) way. As Maori began to adapt their culture to accommodate pakeha in a way that few other native peoples have - selling their crops, operating flour mills and running coastal shipping - Grey encouraged the process by establishing mission schools, erecting hospitals where Maori could get free treatment, and providing employment on public works. In short, he did what he could to uphold the spirit of the Treaty, thereby gaining enormous respect among Maori. Sadly, he failed to set up any mechanism to perpetuate his policies after he left for the governorship of Cape Town in 1853. Under New Zealand's constitution, enacted in 1852, Maori were excluded from political decision-making and prevented from setting up their own form of government; although British subjects in name, they had few of the practical benefits and yet were increasingly expected to comply with British law.

By now it was clear that Maori had been duped by the Treaty of Waitangi: one chief explained that they thought they were transferring the "shadow of the land" while "the substance of the land remains with us", and yet he now conceded "the substance of the land goes to the Europeans, the shadow only will be our portion". Growing resistance to land sales came at a time when settler communities were expanding and demanding to buy huge tracts of pastoral land. With improved communications pakeha became more self-reliant and dismissive of Maori, who progressively began to lose faith in the government and fell back on traditional methods of handling their affairs. Self-government had given landowners the vote, but since Maori didn't hold individual titles to their land they were denied suffrage. Maori and pakeha aspirations seemed completely at odds and there was a growing sense of betrayal, which helped to replace tribal animosities with a tenuous unity. In 1854, a month before New Zealand's first parliament, Maori held inter-tribal meetings to discuss a response to the degradation of their culture and the rapid loss of their land. The eventual upshot was the 1858 election of the ageing Te Wherowhero , head chief of the Waikatos, as the Maori "King", the leader of the King Movement behind which Maori could rally to hold back the flood of pakeha settlement. Initially just the Waikato and central North Island iwi supported the King, but soon Taranaki and some Hawke's Bay iwi joined in a loose federation united in vowing not to sell any more land. This brave attempt to challenge the changes forced upon them gave Maori a sense of purpose and brought with it a resurgence of ancient customs such as tattooing. While some radical Maori wanted to completely rid the country of the white menace, most were moderates and made peaceful overtures that pakeha chose to regard as rebellious.

By now, most settlers felt that the Treaty of Waitangi had no validity whatsoever and sided with the land sellers to drive the government to repress the Maori landholders. There had been minor skirmishes over land throughout the country, but matters came to a head in 1860, when the government used troops to enforce a bogus purchase of land at Waitara, near New Plymouth. The fighting was temporarily confined to Taranaki but soon spread to consume the whole of the North Island in the New Zealand Wars , once known by pakeha as the Maori Wars and by Maori as te riri pakeha (white man's anger). Maori were divided: most of the supporters of the King movement, particularly the Waikatos, traced their whakapapa (genealogy) back to the Tainui canoe and some others chose this opportunity to settle old grievances by siding with the government against their traditional enemies. Through the early 1860s the number of pakeha troops was tripled to around 3000, providing an effective force against Maori who failed to adopt a co-ordinated strategy. The warrior ethic meant there was no place for more effective guerrilla tactics, except in the east of the North Island, where Te Kooti kept the government troops on the run. Elsewhere Maori frequently faced off against ranked artillery and, though there were notable successes, the final result was inevitable. Fighting had abated by the end of the 1860s but peace wasn't finally declared until 1881, when the Maori fastness of the "King Country" (an area south of Hamilton which still goes by that title) was finally opened up to pakeha once again.

British soldiers had been lured into service with offers of land and free passage and, as a further affront to defeated Maori, many of them were settled in the solidly Maori Waikato. Much of the most fertile land was confiscated - in the Waikato, the Bay of Plenty and Taranaki - with little regard to the owners' allegiances during the conflict. By 1862 the Crown had relinquished its right of pre-emption and individuals could buy land directly from Maori, who were forced to limit the stated ownership first to ten individuals and later to just one owner. With their collective power smashed, there was little resistance to voracious land agents luring Maori into debt then offering to buy their land to save them.

Throughout this period, Maori tradition was ignored by settlers and an Anglo-Saxon world view came to dominate all aspects of New Zealand life; by 1871 the Maori language was no longer used for teaching in schools. A defeated people were widely thought to be close to extinction: Anthony Trollope in 1872 wrote "There is scope for poetry in their past history. There is room for philanthropy as to their present condition. But in regard to their future - there is hardly a place for hope."

Meanwhile, as the New Zealand Wars raged in the North Island, gold fever had struck the South. Flakes had been found near Queenstown in 1861 and the initial rushes soon spread to later finds along the West Coast. For the best part of a decade, gold was New Zealand's major export, but the gold provinces never had a major influence on the rest of the country, nor does the gold era retain the legendary status it does in California and Victoria. The major effect was on population distribution: by 1858 the shrinking Maori population had been outstripped by the rapidly swelling horde of pakeha settlers, a number which doubled during the first three years of the gold rush, most settling in the South Island where relations with Maori played a much smaller part. The South Island prospered, with both Christchurch and Dunedin consolidating their roles, serving the surrounding farms and more distant sheep stations. Dunedin became the largest town in the country, the influx of the "New Iniquity" radically changing the city's staunch front of the "Old Identity".