The port of Saint John has three container lines servicing it those being MSC, CMA CGM and Hapag-Lloyd.

Though the fort was sacked in 1645, the river remained an important trade route for French, English and First Nations traders throughout the 17th and 18th centuries.

The Great Famine of Ireland of 1845–1849 saw a large immigrant influx, and to handle the new arrivals, the government constructed a quarantine station and hospital on Partridge Island at the mouth of the harbour.

In 1859, Partridge Island also became known as the site of the first successful demonstration of an automated steam-powered foghorn, invented by the Scotsman Robert Foulis who had settled in the city.

In 1889 the Canadian Pacific Railway opened a line across the state of Maine from Montreal to Saint John and transferred the majority of its trans-Atlantic passenger and cargo shipping to the port during the winter months.

In 1994 CPR left Saint John when it sold the line to shortline operator New Brunswick Southern Railway.