On June 5, 2007, the Environmental Protection Agency (EPA) and U.S. Army Corps of Engineers (Corps) issued joint guidance (herein the Rapanos Guidance) interpreting the U.S. Supreme Court’s divided Rapanos v. United States decision on the geographic extent of regulatory jurisdiction under Section 404 of the Clean Water Act. The technical document, “Jurisdictional Determination Form Instructional Guidebook” uses ambiguous language regarding implementation of the guidance manual. Pursuant to the Rapanos guidance, traditionally navigable waters (TNW), relatively permanent tributaries to these waters, and wetlands directly abutting such tributaries are “categorically” jurisdictional, while non-navigable tributaries that are not relatively permanent, wetlands adjacent to such tributaries, and wetlands that are adjacent to but do not directly abut a relatively permanent non-navigable tributary, are jurisdictional only if they have a “significant nexus” to a TNW. A critical issue for permit applications is whether the proposed activity will be subject to a categorical assertion of regulatory jurisdiction, or to a more involved “significant nexus analysis.” The scientific and environmental analyses of permit applications encountering a significant nexus analysis is designed to undergo additional review by the EPA. At the present time, the Guidance is deficient in providing definitive instruction for determining whether a significant nexus is present between a non-navigable tributary with non-permanent flow and a TNW. Our project allowed implementation of the Guidance and involved the installation of 264 miles of pipeline and permit negotiation with three separate Corps districts. Assessment of 483 streams and 189 wetlands was performed using the newly developed Jurisdictional Determination Forms. An interdisciplinary team approach was developed by integrating the knowledge bases of geographers and ecologists. Databases and maps were developed to allow collective assessment of potential waters of the U.S. within the context of the Rapanos ruling. Because of the Guidance’s ambiguity, it was necessary to develop a defensible approach with detailed concepts and terms to adequately implement the Jurisdictional Determination process to the satisfaction of regulators responsible for the implementation of the jurisdictional determination guidance manual.