This makes Flathead Lake deeper than the average depths of the Yellow Sea or the Persian Gulf.

The lake has an irregularly shaped shoreline and a dozen small islands cover 5.5 square miles (14 km2).

[8] Flathead Lake lies at the southern end of a geological feature called the Rocky Mountain Trench.

The trench, which formed with the Rocky Mountains, extends north into the southern Yukon as a straight, steep valley, which also holds the headwaters of the Columbia River.

As the climate warmed, a portion of the glacier in the Mission Valley receded more slowly than the main body, which kept the lake basin from being filled with sediment.

[9] At one time, probably when the valley was partially filled by a glacier, the level of Flathead Lake was about 500 feet (150 m) higher and drained through the valley west of Elmo, Montana, which is at the end of Big Arm Bay, bottom center in the aerial photo above.

[1] The Seli’š Ksanka Qlispe’ Dam, formerly known as Kerr Dam and built near Polson, controls the top 10-foot of the lake (3.0 m), generates hydroelectric power, and provides water for irrigation to support a federal irrigation project in the area.

[10] Minimum outflow levels from Flathead Lake are designated by the Federal Energy Regulatory Commission (FERC) and are based on flood risk management, power generation requirements, and biological needs to support aquatic life in river systems.

[13] The Columbia River Technical Management Team makes operational recommendations to the agencies that control federal dams.

Made up of representatives from four states, five federal agencies and six tribal nations, it prioritizes fish and wildlife above other system benefits.

[17] Variations to the Flood Risk Management Plan were approved by the U.S. Army Corps of Engineers in 2024 in response to the continuing dry conditions.

[19] The non-native opossum shrimp, (Mysis diluviana), were introduced by Montana Department of Fish, Wildlife and Parks in the Flathead drainage basin to encourage production of larger kokanee salmon; they migrated into Flathead Lake and have altered the ecosystem.

The bottom-dwelling mysids eliminated a recruitment bottleneck for lake trout by providing a deep water source of food where little was available previously.

[25] In addition to these commonly pursued game fish, the lake is also home to other native species that currently[when?]