Central Pier 8 had other lives before the museum moved in. For years it was a Star Ferry terminal, handling the route to Hung Hom; later the eastern side served non-scheduled ferry services. By 2007 it had been taken out of ferry service and designated for restaurants and kiosks. The proposal to convert it into a maritime museum arrived in October 2007 and was accepted by the government. The renovation — a HK$115 million project partly financed by the Hong Kong government — expanded the space to fifteen gallery spaces, more than five times the size of the museum's first home. The final design came from P&T Architects and Engineers, with gallery and interior fit-out by Haley Sharpe Designs and Kingsmen.

The museum did not start at the pier. It opened in 2005 at Murray House in Stanley, one of Hong Kong's colonial landmarks — a 19th-century building that had been dismantled stone by stone and stored in a rural site for over a decade before being reassembled overlooking Stanley Bay. The original collection held more than 500 items and averaged 35,000 visitors a year. The first museum director, Stephen Davies, built the founding collection and negotiated the eventual relocation. By the time the museum reopened at Pier 8 in February 2013, the collection had grown from around 700 items to over 2,000, and the library from 15 books to more than 1,500.

The fifteen galleries span China's maritime heritage, the Canton Trade system, piracy along the South China coast, Hong Kong's harbour, the evolution of modern shipping, naval warfare, navigation, marine art, and the sounds of the sea. One of the oldest objects is a 2,000-year-old ceramic model ship from the Han dynasty. One of the most recently acquired is the windsurfing sailboard used by Hong Kong's Hayley Chan Hei Man at the 2012 Olympic Games. In between: the Gentiloni Paintings, four works painted in Macau in the late 18th century depicting Macau, Whampoa, Guangzhou, and Zhaoqing, which were acquired by the museum in 2010 after sitting in a Brazilian family's possession for two centuries. The 'General' Cannon, captured at Humen during the First Opium War and later kept at the Tower of London and used as a garden ornament, came to the museum in 2010 by donation.

Two objects anchor the museum's identity. The painted scroll Pacifying the South China Sea chronicles Viceroy Bailing's anti-piracy campaign of 1809–1810, including the Battle of Lantau, in which the imperial navy engaged Cheung Po Tsai's forces. The scroll is considered one of the museum's highlights and is displayed prominently in the Sea Bandits Gallery alongside a digitized version visitors can examine in detail. The 'General' Cannon sits nearby — a large naval artillery piece whose journey from a fort at Humen to the Tower of London to a garden and finally to this gallery is a compressed history of empire and its aftermath. Together, the two objects make the same point in different registers: this harbour has been contested, defended, and fought over for a very long time.

Not every exhibit is about war or trade. The Rifleman's Bolt is a copper spike and a granite plaque, unremarkable to look at. The plaque records the surveying activities of HM Rifleman in 1866, when the vessel used the spike to mark a datum point 17 feet and 10 inches above the surrounding terrain while charting Hong Kong harbour. The exhibit was donated by the Surveying and Mapping Office Training School of the Hong Kong Lands Department. The museum also contains the first modern map of the island of Hong Kong — not identified as such until museum staff recognized it in 2007 — and one of the earliest modern marine chronometers. The collection ranges from the monumental to the technical, from piracy to navigation: all of it, one way or another, about the sea that made Hong Kong possible.