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In 2001, the Supreme Court in SWANCC v. U.S. Army Corps of Engineers held that the Corps lacked authority under the 1972 Clean Water Act to regulate wetlands isolated from navigable waters. The Court held that the CWA's jurisdiction is limited to non-navigable waters that have a significant nexus to navigable waters. SWANCC did not address the Corps' regulation of wetlands near non-navigable tributaries. The courts of appeals are divided over if the Corps may regulate tributary wetlands. Mank, The Murky Future of the Clean Water Act After SWANCC, 30 ECOLOGY LAW QUARTERLY 811-891 (2003).

In 2006, the Supreme Court in United States v. Rapanos addressed the question of jurisdiction over tributary wetlands. The Court fractured into a four to one to four blocs, although a majority of five agreed to vacate and remand the two cases. Justice Scalia wrote a plurality opinion that would have sharply restricted CWA jurisdiction to only those waters that are relatively permanent, standing or continuously flowing or to wetlands that have a physical surface water connection to these waters. The plurality opinion relied heavily on dictionary definitions, but ignored scientific evidence about the importance of intermittent waters. The plurality harshly criticizes the expense of Corps regulations without giving any weight to the value of the wetland resources they protect. Justice Stevens in his dissenting opinion would have upheld the Corps' broad jurisdiction over tributary wetlands because of their ecological significance and in deference to the Corps' 30-year-old regulations. The dissent failed, however, to acknowledge SWANCC's underlying philosophy that a connection to navigable waters still has some importance in defining the Act's jurisdiction.

The key opinion was Justice Kennedy's lone opinion concurring in the judgment. He concluded that the CWA's jurisdiction reached waters and wetlands with a significant nexus to actually navigable waters. Justice Kennedy had to remain true to SWANCC's underlying principle that the Act is limited to waters that have some meaningful connection to navigable waters, but he took the broad view that ecological connections may be significant, not just actual hydrological connections. His choice of the significant nexus language as the basis for his new jurisdictional test is reasonable because commentators and several lower courts had recognized that it provided the best test for applying the Court's precedent in Riverside Bayview and SWANCC to cases involving tributary wetlands. Justice Kennedy appropriately took a middle position that was closer to the purposivist dissenting opinion than the textualist plurality opinion.

There is disagreement about which opinions in Rapanos are binding on lower courts. Some argue the holding is where the plurality opinion and Justice Kennedy agree and that lower courts may not consider the dissenting opinion. Others argue lower courts may consider the numerous points upon which the dissenting opinion and Justice Kennedy's opinion form a five vote majority. The Department of Justice (DOJ) agrees with Justice Stevens' dissent that the government should have jurisdiction over wetlands if the wetlands at issue meet either the plurality's test or Justice Kennedy's significant nexus standard. This article argues that at least six circuits will follow Justice Kennedy's significant nexus standard, although the Fifth Circuit is likely to adopt an approach closer to Justice Scalia's test.

The Corps and EPA (the agencies) have promised to issue new joint guidance in the near future to address the scope of the Act in the wake of Rapanos, but it is unclear whether the agencies will issue detailed regulations in this area. After SWANCC, the agencies tried to develop new regulations, but were unable to reach consensus. Because of strong public pressure, the agencies will likely produce new guidance addressing Rapanos. Under the significant nexus test, the agencies will likely retain jurisdiction over most, but not all, tributary wetlands. It is less likely that Congress will be able to achieve sufficient consensus to pass legislation defining the Act's jurisdiction.