By February 1839, the Weller brothers of Otago (modern Otakou) had set up a saw pit on the opposite side of the harbour, which appears to have been at Sawyers Bay.

In 1840, Port Chalmers and the whole western shore of Otago Harbour (from about Burkes to Otafelo Point) was included in Te Matenga Taiaroa's sale of land to the French whalers Pierre Darmandarits and Edouard DuBern, brothers-in-law and business partners.

That year Kohi fell ill, and thinking himself at the point of death, feared that his young son Timoko, would never have any benefit from a sealing boat in which he had a share.

To appease the other partners in the boat who were outraged upon hearing what he had done Kohi after consulting his wife Piro, consented at Otaheiti to be strangled as punishment.

In 1844 the schooner Deborah under the command of Captain Thomas Wing was chartered by Frederick Tuckett of the New Zealand Company to assist him in choosing a site for the projected New Edinburgh settlement.

The Deborah departed on 23 June leaving behind Tuckett, who was living in a small three-bedroom cottage made of loose bricks that he had built on the beach.

On 15 July 1844 William Wakefield of the New Zealand Company visited accompanied by John Jermyn Symonds (representing the government) and George Clark.

In December 1844 Tuckett left and returned to England, with William Davidson taking over his cottage and position as the New Zealand Company's local representative.

[7] At first the European settlers intended to christen the settlement ‘New Leith’ or ‘New Musselburgh’, as they disliked the Māori name of Koputai; but the Lay Association of the Free Church of Scotland (later known as the Otago Association), desired that the port might be named after Thomas Chalmers, the leader of the Free Church movement in Scotland and this suggestion was adopted.

The second ship, the Philip Laing arrived on 15 April 1848 to find a settlement surrounded by dense bush to the water's edge except for a small clearing behind the centre of the beach and consisting of the New Zealand Company's store, Tuckett's former cottage and three whare (Māori huts).

[7] The arrival of organised European settlement eventually led to the town superseding the earlier Otakou as the harbour's international port.

On 31 May 1855 the customhouse was robbed, and a chest, containing about £1,400, was carried away, but was afterwards recovered from the harbour, where the thieves had thrown it on some rocks upon finding that they were unable to open it before daylight exposed them to potential capture.

[12] with a population of at least a 1,000, with five hotels, three restaurants, six general stores, two chemists, two bakeries, two barbers, two blacksmiths, two churches, two schools, and a Masonic Hall (which functioned during the week as a courthouse).

As the region's rapidly increased due to the Gold Rush scheduled ferry services began between Port Chalmers and Portobello and ran from 1876 to 1954.

The development of the town reflected the growth of Dunedin and Otago with rivalry between the city and Port Chalmers over which would handle the bulk of shipping.

While docked in Port Chalmers for repairs and restocking, several of her crew refused to continue with the voyage, and four New Zealanders were recruited several days later at Stewart Island.

This dangled carrot drew Robert Falcon Scott, who visited with both the Discovery in December 1901 and his final doomed Terra Nova expedition to Antarctica in November 1910.

[18] In June 2019 a $2.9 million project was begun by Port Otago to stabilize the east and north-east sides of Flagstaff Hill and return Beach Street to its original position.

[10] Campbell Buchanan Lane commemorates a young Port Chalmers sailor who died in action in the Solomon Islands in January 1943.

[21] From the 1990s onwards cruise ships began calling at Otago Harbour, a trend that continues to expand with 153,000 disembarking of the 229,000 passengers bought on 115 vessels (104 into Port Chalmers) during the 2018–2019 season.

Following its taking over operation of the wharves from the Railway Department the Otago Harbour Board moved its headquarters to Port Chalmers in 1929.

[7] Morgan & Cable later changed its name first to the Maori Iron Works and later in 1906 to Stevenson & Cook which during the Second World War built seven Castle class minesweepers at Boiler Point for service with Royal New Zealand Navy.

The company purchased the hulk of the barque ‘’Don Juan’’ in 1878 and moored it between the Bowen and George Street piers where it was used as a carpenters’ workshop and sailmakers loft.

Between 1920 and 1930 a large number of the Norwegian whaling vessels based at Stewart Island were refurbished by the workshops of the Union Stream Ship Company.

When the port's facilities were expanded, part of the bluff was removed, including the area of Hotere's studio, despite strenuous objection from many of the town's residents.

Part of the bluff close to the removed portion is now a sculpture garden, organised in 2005 by Hotere and featuring works by both him and by other New Zealand modern sculptors.

[7] From the time of the first settlement there were a number of small private schools in Port Chalmers with some remaining in existence in one form or another until the end of the 19th century.

[40] In 1898 Mother Mary MacKillop, and two Josephite Sisters, arrived into Dunedin on the request of the parish priest of Port Chalmers to assist with teaching.

[42] Parts of 2016 drama The Light Between Oceans starring Michael Fassbender, Alicia Vikander and Rachel Weisz was filmed here in 2014, notably the bookshop and haberdashery scenes.

During shooting the main street was covered in gravel and thousands of people turned up each day hoping to catch a glimpse of the actors.