Historically, the majority of spawning occurred in Pine Creek, a tributary on the western shore of the lake. Due to extremely low lake levels and accompanying population decline observed in the 1930s and 1940s, resource managers feared the species may go extinct. As a result, a weir was installed on Pine Creek in the late 1950s to capture Eagle Lake rainbow trout during their spawning migration. Eggs and milt are collected, fertilized, and transported to state fish hatcheries where they are reared for nearly a year and a half until they are large enough to be replanted into Eagle Lake or other waters across the state. This artificial rearing process and back-stocking into Eagle Lake allows for continued survival of this species until natural spawning in Pine Creek can be reestablished.
The need for a fish weir currently prevents natural reproduction at self-sustaining levels. Since Eagle Lake rainbow trout have undergone more than 60 years of artificial selection in a hatchery setting, this may have long-term negative effects on their genetic integrity.
Additionally, Pine Creek flows intermittently into Eagle Lake and is dominated by non-native brook trout that were introduced in the 1940s. A top restoration goal is to remove non-native brook trout and reestablish natural spawning of Eagle Lake rainbow trout in Pine Creek. To help with this, the fish weir was modified in 2012 to allow spawning Eagle Lake rainbow trout some access to Pine Creek.
Eagle Lake rainbow trout face other threats, including habitat degradation from logging, grazing, water diversions, railroads, and roads. Climate change and low lake levels are a growing concern that reduces available habitat, increases water temperature, and changes the water chemistry.