Fort Conger is located in Quttinirpaaq National Park on northeastern Ellesmere Island. The nearest community on Ellesmere Island (Grise Fiord) is located more than 800 km to the south, while Canadian Forces Station Alert is approximately 100 km to the northeast. Fort Conger is situated approximately 10 m from the ocean on the east side of Discovery Harbour, with a steep bank (2.5 m high) leading from the site to the ocean. Access is generally only possible by helicopter or by Twin Otter, with a landing strip located about a kilometer from the site. Due to the extreme remoteness of the site, human visitors are rare but cruise ships have been able to penetrate to this location.
Forty-two features, many of which are related to the three historical expeditions described below are located on this tableland. Artifacts are also scattered across the site, although many have become the subjects of unauthorized collection and removal.