Abstract: In January 2001, the U.S. Supreme Court ruled that the U.S. Army Corps of Engineers exceeded its statutory authority by asserting Clean Water Act (CWA) jurisdiction over non-navigable, isolated, intrastate waters based solely on their use by migratory birds. The Supreme Court’s majority opinion addressed broader issues of CWA jurisdiction by implying that the CWA intended some “connection” to navigability and that isolated waters need a “significant nexus” to navigable waters to be jurisdictional. Subsequent to this decision (SWANCC), there have been many lawsuits challenging CWA jurisdiction, many of which are focused on headwater, intermittent, and ephemeral streams. To inform the legal and policy debate surrounding this issue, we present information on the geographic distribution of headwater streams and intermittent and ephemeral streams throughout the U.S., summarize major findings from the scientific literature in considering hydrological connectivity between headwater streams and downstream waters, and relate the scientific information presented to policy issues surrounding the scope of waters protected under the CWA. Headwater streams comprise approximately 53% (2,900,000 km) of the total stream length in the U.S., excluding Alaska, and intermittent and ephemeral streams comprise approximately 59% (3,200,000 km) of the total stream length and approximately 50% (1,460,000 km) of the headwater stream length in the U.S., excluding Alaska. Hillslopes, headwater streams, and downstream waters are best described as individual elements of integrated hydrological systems. Hydrological connectivity allows for the exchange of mass, momentum, energy, and organisms longitudinally, laterally, vertically, and temporally between headwater streams and downstream waters. Via hydrological connectivity, headwater, intermittent and ephemeral streams cumulatively contribute to the functional integrity of downstream waters; hydrologically and ecologically, they are a part of the tributary system. As this debate continues, scientific input from multiple fields will be important for policymaking at the federal, state, and local levels and to inform water resource management regardless of the level at which those decisions are being made. Strengthening the interface between science, policy, and public participation is critical if we are going to achieve effective water resource management.