The Hillsborough River arises from groundwater springs in the center of Prince Edward Island and flows southwest for 45 kilometers (km) to its mouth at the Northumberland Strait in the Atlantic Ocean. The river system is the largest on the island – its 350 sq. km drainage area is equal to one-fifteenth of the total island land mass. The landscape around the Hillsborough is flat or gently rolling, with the highest point in the watershed at only 75 meters (m).
In many ways the Hillsborough River, deemed PEI's passageway to the sea, is symbolic of the island itself. Its character derives from the island's rich agricultural heritage and the inescapable presence of the sea. Over half of the river's length is ocean estuary where freshwater and saltwater mix to create a rich marshland habitat for a variety of fish and waterfowl species. For three-quarters of its length, the level of the Hillsborough rises and falls under the influence of the ocean tides. The river does not empty directly into the sea but rather gives way gradually to the saltwater of Charlottetown Harbor.
The natural harbor at the mouth of the river was very important in the island's logging history. It served as a logging basin when the early British settlers cleared the island's densely wooded forests to feed its thriving timber and shipbuilding industry. The Hillsborough was vital to this industry since it is the only waterway in PEI big enough for large ships. The sudden technological change from sail to steam in the latter half of the 19th century killed the shipbuilding industry. By the start of the 20th century the great island forests were gone and much of the land had been converted to agriculture. The only remaining vestige of the island's original forests is along the Hillsborough at Royalty Oaks on the outskirts of Charlottetown.
The river was named after the British Earl of Hillsborough. Its original Native Mi'kmaq name was Elsetkook, meaning "running close by high rocks." The rich cultural heritage and scenic beauty of the Hillsborough make it an important part of Prince Edward Island's booming tourism industry. In recognition of its importance it has been nominated as a Canadian Heritage River.