Alkali Flats Creek originates in the mixed rangeland of SE Washington and terminates in the Lower Snake River. The creek is designated as a Minor Spawning Area mSA for steelhead encompasses the watershed from the confluence with the Snake River up to the town of Hay. The creek supports populations of wild Snake River ESU Steelhead and spring Chinook.
Alkali Flats has undergone habitat degradation from the removal of riparian trees, dewatering, elevated water temperature, channel straightening and floodplain confinement. Limiting factors in Alkali Flats have not been determined due to data gaps in areas needed to determine limiting factors.