In the 1870s, local interests believed it could become the main port for the north Otago area and a railway line, the Moeraki Branch, was built to the settlement and opened in 1877.

However, the port could not compete with Oamaru and the lack of traffic as well as stability problems caused by difficult terrain led to the closure of the railway in 1879 after only two years' operation.

The south side of the Moeraki Peninsula has an Archaic (moa hunter) Māori site at Waimataitai lagoon, which Atholl Anderson dated as 13th century, placing it in the second wave of New Zealand's early human occupation.

Gavin McLean tentatively linked its occupants to Waitaha, conventionally the third iwi, or tribe, to arrive in southern New Zealand, after Kahui Tipua and Te Rapuwai.

It used to be said Moeraki, like many other places on the east coast, was not a site of permanent occupation in pre-European times, but a major study, published in 1996, shows that is unlikely.

He purchased two boats and all of the equipment needed to catch and process whales from the Americans he recruited others to join him from Weller brothers’ workforce.

[7] During the voyage of the Merrimac and the Martha either on the way to Banks Peninsula or on their return down the coast they must have explored Moeraki for Hughes decided to establish his base there.

Over the next three months the party established a whaling station where they had landed at Onekakara, on the northern side of the peninsula, the site of the present village of Moeraki.

[5] In that same year a large heke (migration party) of Ngāi Tahu Māori from Kaiapoi arrived under Matiaha Tiramorehu.

[8] Despite this increased number of boats the catch decreased slightly and then in 1841 rapidly dropped to nine, then two the following year as the whales moved away to avoid the persecution.

[5] Between 18 and 20 May 1844 Frederick Tuckett (having arrived on the Deborah) inspected Moeraki and the surrounding district as part of his survey to identify a location for the New Zealand Company’s New Edinburgh settlement.

Moeraki remained an isolated community making a living from fishing and small scale farming until increasing demand from the development of Dunedin led to the growing of crops on a commercial basis.

While Moeraki had the best natural harbour in North Otago with its inner roadstead partly protected by a bluff, by 1869 the existing wharf was in poor condition and as it did not extend far enough out to sea there were restrictions on the size of ships that could use it.

[10] To resolve these issues work commenced in 1872 on what was estimated would be a £3,000 project to construct a larger wharf to service the increased trade now passing through the port.

To improve the safety of coastal shipping following several accidents on the dangerous reefs in the surrounding area the Marine Department commenced construction of the Katiki Point Lighthouse on the tip of Moeraki Peninsula in 1876.

Improvements to the port facilities at Oamaru, which saw it taking more trade coupled with the cost of constant maintenance and unreliability of the branch line led to it being closed and the rails removed in October 1879.

Following the closing of the branch railway access to what was the best anchorage in North Otago became dependent on the road, which was prone to slips and thus difficult to maintain in good condition.

Previously, fishers at the port had difficulties disposing of their catch as slow transit times by rail often resulted in the fish being spoilt before it reached the market in Christchurch.

The fishing fleet based at Moeraki in the 1950s and early 1960s predominantly harvested groper, although other species such as blue cod and rock lobster were also caught.

As a number of Māori families had not returned to Moeraki after the war; the focus on the marae diminished; with its use limited to more formal occasions such as tangi and tribal meetings.

At 2.30 am on 24 April 1952 the cargo ship Viggo Hansteen while on a voyage from London, via Panama, to Port Chalmers and Wellington with new British cars and bagged cement ran aground two miles northeast of the Kātiki Point Lighthouse.

[17] Following the tar-sealing of the gravel access road in the early 1960s, there was an influx of newcomers and several boarding houses opened in the village - to accommodate weekend visitors from Dunedin.

In return for exclusive fuelling rights the Shell Oil Company financially assisted with the construction in the inner harbour of a fishing wharf in 1961.

This resulted in a doubling of the number of fishing boats based at Moeraki and prosperous times profits from rock lobster for the community, which lasted into the 1980s.

[14] However the increased number of fishing boats caused stocks of groper, cod, and rock lobster off the coast of North Otago to be seriously decline.

Poor catches of rock lobster in the 1990s impacted on the financial viability of many Moeraki based owner-operators, who sold off their quota to fund their other fishing activities and maintain their boats.

[14] After Wrightson NMA’s parent company Fletcher Challenge consolidated its fish processing activities at Dunedin in the 1980s Skeggs took over their facility.

[20] In response to a heavy rainfall event in May 2010 which resulted in land movement and 28 insurance claims on Haven Street the Earthquake Commission in August of that same year installed 250 metres 250 m (820 ft) of drainage pipe to relieve the build-up of underground water.

However within seven years it was discovered that the ground was too unstable for the building and it was moved again to its present site further west at a former quarry on Haven St.[9][26] The church was granted Heritage New Zealand historic place category 1 status in 2010.

Properties in Moeraki used septic tanks to dispose of their wastewater until a reticulated sewerage system and treatment plant was opened in September 1999.