Ecosystem-based management is becoming a more prevalent in federal legislative and executive mandates. Still, there are constitutional limitations to applying such measures, especially regarding federal control of certain intrastate water resources. Recent U.S. Supreme Court precedent may suggest a willingness to allow ecosystem-based principles as a foundation to support greater federal control. This paper looks at one recent U.S. Supreme Court decision to determine how far ecosystem-based principles might apply to federal control over intrastate bodies of water.