Almost cutting the island in two from north to south, the Hillsborough River has always served as a "highway." For centuries, the Mi'kmaq fished and camped along its shores. Europeans settled here in the early 18th century, using the river for transportation and as a major shipbuilding area in the days of sail. There has been some commercial fishing in the river and today shellfish, particularly oysters, are harvested. The capital of Prince Edward Island, CHARLOTTETOWN, where the Fathers of Confederation met in 1864, is located at the mouth of the Hillsborough.
Due to the island's flat topography, for most of its length the Hillsborough is a tidal estuary with very little current. Its extensive salt marshes are rich breeding areas for thousands of marine birds and other land and marine animals. In 1997 the Hillsborough was designated as part of the CANADIAN HERITAGE RIVERS SYSTEM.