The lake lies within the boundary of the Malheur National Wildlife Refuge and is the lowest point in the Blitzen Valley drainage.

The depth of Harney Lake is less than 4 feet (1.2 m) during normal water years and has dried up completely during times of drought.

Despite its limited food supply, the lake is part of an important inland marsh ecosystem for migratory birds in the arid southeast Oregon desert.

Malheur and Harney lakes have reduced access by Great Basin redband trout due to irrigation diversions, channelization, draining of marshlands and high alkalinities.

In these closed High Desert basins, redband trout have evolved to survive in environments with vast extremes of both water flow and temperature.