In places, the bedrock floor of the valley occupied by Lake Chelan, which is buried by Pleistocene glacial and lacustrine sediments, lies at least 1,529 ft (466 m) below sea level.

[12] The fjord-like topography of the Lake Chelan valley results from repeated glacial erosion and deposition (maybe nine or ten times) during the Pleistocene Period.

The deposits of the northwestward advancing Okanagan lobe are characterized by large, basalt glacial erratics.

[14] The depth of the Lucerne Basin and the elevation of glacial till and moraines and glacier-scoured bedrock on the walls of the overdeepened Lake Chelan valley indicates that the thickness of the Skagit Lobe was over 1 mi (1.6 km).

The two basins are separated by a sill rising to within 122 ft (37 m) of the surface, at a point known as the narrows, at which the lake is only 0.35 miles (0.56 km) wide.

[8][9][15] The upper basin of Lake Chelan is surrounded by more mountainous terrain, resulting in few beaches along the shoreline.

[citation needed] The name Chelan is a Salish Indigenous word, "Tsi - Laan," meaning 'Deep Water'.

[20] Due to the isolated nature of Lake Chelan, especially at its northern reaches, there is not a large population that resides along the shore.

At the mouth of the Railroad Creek sits Lucerne, a small community of private cabins served by commercial boats.

[23] Lucerne is also the primary gateway to the community of Holden Village, a Lutheran retreat center located 11 mi (18 km) inland from the lake.

With approximately 50 long-term residents, Holden includes one of the few remaining public K-12 two-room schools in the contiguous United States.

[31] In addition to the protected land located directly on the shores of Lake Chelan, Stehekin serves not only as a gateway to the Lake Chelan NRA, but also to the rest of the North Cascades National Park Complex, Stephen Mather Wilderness, and adjacent National Forest Wilderness Areas.

[32] Approximately 87% of the Lake Chelan watershed is owned by either federal, state, or local entities, with the rest in private ownership.