The Goose Lake Basin is a unique, endorheic desert valley straddling the Oregon-California border. The Basin drains into Goose Lake—a slightly alkaline body of water that goes completely dry during periods of severe drought (such as in 2015) and spills into the Pit River during rare high-flow events. This basin is home to several endemic fish species, including the Goose Lake redband trout, Goose Lake lamprey, Goose Lake tui chub, and Goose Lake sucker. These species, which inhabit the lake and surrounding rivers, marshes, and riparian zones, coexist with both native and non-native fish populations. Increased drought frequency and other climate-mediated stressors pose a serious threat for these species, potentially reducing habitat availability and quality for native species and placing further pressure on these vulnerable populations. The goal of this project is to support agency partners (Oregon Department of Fish and Wildlife, U.S. Fish and Wildlife Service, the Lake County Umbrella Watershed Council) in conducting a comprehensive population assessment of at-risk native species within Oregon’s closed lakes basin ecosystems. By identifying the systems most at risk of population decline due to drought and other disturbances, such as invasive species, this research aims to provide critical insights into species vulnerability. This study is timely. Surveys of high desert basins in Oregon have been inconsistent for over a decade, leaving gaps in our understanding of population trends and ecosystem health. The updated abundance and distribution estimates will enable state and federal managers to make informed decisions regarding the status and management needs of these at-risk species. Additionally, population risk assessment will serve as a foundation for targeted management actions to help protect and sustain Oregon’s native desert fish species amidst mounting environmental challenges.