The county seat, Huntingdon, located at 45°5′ N and 74°10′ W, straddles the border between Hinchinbrooke and Godmanchester.
A notable feature of Huntingdon County is the presence of the Saint Regis Akwesasne Mohawk Reserve at the westernmost point of the county in the Township of Dundee.
That area of the Saint Lawrence, like many along its length, contains many small islands.
The American side of the Reserve is Franklin County, New York.
Most of the County became part of the MRC de Le Haut-Saint-Laurent except for a small section in the far east (The Township of Hemmingford and the Village of Hemmingford) which became part of MRC de Les Jardins-de-Napierville.