This deep water port has strong historical ties to the European settlement of the Otago area. Founded in 1844, the early wooden buildings were soon replaced with brick and stone as the wealth of the Otago gold rush began to flow. Many of these early sturdy homes remain, forming part of the bohemian charm of this seaside town.

In 1882, the first frozen meat exports from New Zealand left through Port Chalmers. This trade continues today through the adjacent modern container terminal. Several early Antarctic expeditions left from Port Chalmers, and there remains a memorial to Captain Scott, whose 1901 and 1910 expeditions departed from here.