The United States Supreme Court has again waded into federal law governing protection of waters.  The 2006 opinion in Rapanos v. United States has resulted in more confusion over the scope of federal regulation under the Clean Water Act (CWA).  When Congress enacted the CWA, it defined federal jurisdiction to include all “navigable waters” which were defined as “all the waters of the United States.”  Despite this broad definition, a plurality of justices concluded that federal jurisdiction over non-navigable waters must in some way relate to the relationship of that water to traditionally navigable waters, but no single test commanded a majority of the Court.  Justice Scalia’s test would limit federal regulation to only permanent or continuously flowing waters and require a wetland to have a continuous surface water connection to permanent surface waters or traditionally navigable waters.  Justice Kennedy’s test would require a wetland or other water to have a “significant nexus” to traditionally navigable waters.  Subsequent decisions are trending toward a test that would find jurisdiction if either the Scalia or Kennedy test is met.  Scientists have an important role in defining the “significant nexus” of non-navigable waters to navigable-in-fact waters based on hydrological, chemical or ecological relationships.