From its source, the upper reach of the river extends approximately 16 miles (26 km) to the point where it enters Chilkoot Lake.

At the head of the lower reach of the river, on the shore of the lake, lies a prehistoric village which was a Chilkoot Indian settlement.

The river, in its first one eighth mile (below the lake) has formed a pool, and then flows through a number of rapids strewn with boulders covered with moss in some stretches and the remaining part is flat but with rocky bed.

It was an important location for the southeast Alaskan Tlingits who reportedly settled here during pre-historic days when they became occupied in salmon and hooligan fishing.

However, in the mid 20th century boats were used to transport construction materials and to the homestead built by Cox in the upper reach of the river.

These studies also indicated that anadromous fish, coho, Dolly Varden, and an occasional chum salmon were found above the Chilkoot Lake in the spawning and rearing grounds.

[21] The aqua fauna found in the Chilkoot River are caught by the Tlingit Alaskan tribes by using long-handled scoop nets known as go qtc (gukwC), which is 18 inches (46 cm) wide at the mouth and 10 feet (3.0 m) deep.

Semi conical baskets made of spruce rods are used in the fishing weirs built across the river to capture eulachon.

A single man would then stand on the platform and using a gaft[22] hook capture the salmon fish that traveled up the artificial channel.

The fish species that are found in the Chilkoot River below the lake outlet are generally the sockeye salmon and Oncorhynchus nerka.

The prehistoric Chilkoot village has been converted into a camping area developed by the State Parks and Outdoor Recreation Division of the Alaska Department of Natural Resources.

[23][24][25] Conflicts have arisen in the Chilkoot River Corridor (CRC) between humans and Alaskan brown bears, which frequent this region in large numbers during the months of August–September in search of spawning salmon.

Consequently, a large number of visitors travel to the area to watch bears and bald eagles harvesting salmon along the river.

The basic objective of this project was to develop and enact a plan for the longterm sustainable management of the existing natural, cultural, historical, and socio-economic resources of the Chilkoot River Corridor.

After several meetings, the CRC has identified for action the following, as a guide to the Alaska Chilkoot Bear Foundation to act upon:[1] These issue relate to enhancing capability of the State Agency to Manage Recreational Use, create a self-help program for the visitors to avoid interference; minimize use of overnight camping along the CRC, create more spacious parking space and avoid incidence of damage to the lake from use of motorized transport; minimize, respect and preserve Chilkoot Historical Resources; launch 'Public Awareness Programs' of the cultural significance of the area and help existence of the Chilkoot Culture Camp.

[1] Wildlife issues of concern are: avoidance of ‘Human-Wildlife Conflicts’ by monitoring and improving visitor activity with adequate interaction; to enhance habitat and scenic values, and to ensure that exclusive corridors are maintained for the Brown Bears to access/egress their feeding areas in the Chilkoot River, totally unhampered.

[1] This essential planning is a continuing process to identify and interpret 'Brown Bear Habitat and Use Patterns' so that the Agency could take appropriate further development decisions.

These guidelines have been published in the form of 'Statutes and Regulations' made applicable throughout the state of Alaska including the Chilkoot River Corridor.

A plaque has been displayed at the visitor center on the right bank of the Chilkoot River near the heritage monument of the Tlingits, the “Deer Rock.” A summary of the statute regulations is recorded as:Your actions should not create a situation where bears are attracted to your activities and they should not obtain fish or food from you.