The Hillsborough River in Prince Edward Island is a designated Canadian Heritage River flowing through Queens County in the eastern part of the province. The river runs from its headwaters at Head of Hillsborough downstream through the watershed, ultimately emptying into Charlottetown Harbour, bounded by Duchess Point at Victoria Park and Battery Point in Stratford. The watershed lies within the Appalachian-Acadian Physiographic region.

The classic paddling route runs from Mount Stewart downstream to Charlottetown, covering approximately 27 to 28 kilometres. This trip typically takes around six hours total, with roughly five hours and twenty minutes of moving time. Paddlers who have done the route report launching at the bridge in Mount Stewart around 9 AM and taking out near the Armouries area in Charlottetown, where car and trailer access is readily available. There is also a boat launch in Mount Stewart. The route is generally described as a day trip, taking three-quarters to a full day depending on pace and conditions.

The river is tidal along much of its length, and paddlers should account for tidal currents when planning their trip. The most significant practical consideration on this route is wind direction. Due to the land profile and the wider sections of the river, wind can impede progress far more than tidal currents. The area around the old railway bridge at Mount Stewart — locally known as "The Stew" — is a notable feature where tidal flooding and ebbing creates a small wave suitable for surfing kayaks. This spot is considered a rough water practice environment and is used for tidal current skills development. Several side roads off Route 2 are marked as Hillsborough Heritage River access points and lead to the riverbanks.

The river corridor passes through historically and culturally significant territory, with connections to Mi'kmaq heritage and early Scottish settlement. The Hillsborough River Eco-Centre is located along the route and serves as an interpretive facility. The river is also known for striped bass fishing, particularly in the stretch between Mount Stewart and Scotchfort, and no fishing licence is required in this tidal section. Birding is another activity associated with the river corridor. Water quality in the Hillsborough watershed was rated as good in a 2016 provincial assessment.