State, Federal Agencies Take Case-By-Case Approach to Waterway Jurisdiction

Federal court ruling shakes up which waterways fall under state or federal law, causing some uncertainty in application of new wetlands law
October 8, 2021

A federal court ruling has further complicated the process for landowners to determine whether wetlands on their property fall under federal jurisdiction or more lenient state jurisdiction, a designation that could have an important effect on the health of Indiana’s waterways and the ability to protect against climate change-induced flooding.

The judge’s ruling repealed a 2020 Trump rule that limited which waterways fall under federal jurisdiction.

Now, regulators are trying to figure out whether waterways that were given back to state control by the Trump rule once again fall under the control of the federal government and whether that determination is permanent.

In the Hoosier state, the situation is even more complicated, as regulators try to determine how a state law removing state protections and permitting requirements for wetlands will be affected by the court ruling.

During an Oct. 5 virtual wetlands forum hosted by the Purdue University’s Center for the Environment, the White River Alliance and the Hoosier Environmental Council, representatives from the U.S. Army Corps of Engineers and the Indiana Department of Environmental Management said they will approach jurisdictional determinations on a case-by-case basis due to the fluid nature of the political and legal changes those determinations face.

“It is still case by case. Just because somebody put something on paper doesn't mean we're going to take their word for it,” said Sarah Keller, regulatory specialist for USACE.


The Clean Water Act regulates the discharge of pollutants into what the law specifies as “waters of the United States.”

The ambiguity of the phrase has fueled a decades-long partisan battle over what constitutes “waters of the United States,” defining the limit of the federal government’s reach into pollution regulation.

Between 1986 and 2015, the WOTUS definition included seven broad categories of waterways under federal protection, the bounds of which were limited by several lawsuits that reached the U.S. Supreme Court.

A Supreme Court ruling in 2001 limited the federal government’s jurisdiction over isolated wetlands, legally defined as wetlands with no apparent surface water connection to perennial rivers and streams, estuaries or the ocean.

The ruling suddenly left many of Indiana’s remaining wetlands without protections, and the Indiana Legislature moved to establish its own state protections for isolated wetlands.

The 2003 Isolated Wetlands Law established a permitting program to protect the state’s wetlands. Landowners were allowed to develop wetland areas as long as they built up new replacement wetland areas or paid the state to do so. The amount of mitigation required would be decided by the type of wetland being disturbed and ratios set by the state.

The Obama administration in 2015 attempted to expand the WOTUS definition, finalizing a rule that allowed more waterways to be governed by the Clean Water Act. Those waterways included isolated wetlands and temporary waterways known as ephemeral streams found to have a “significant nexus,” a legal test established by Supreme Court decision that finds whether a waterway has “more than insubstantial or speculative effect” on the chemical, physical or biological integrity of traditional waterways.

The rule was finalized, but a coalition of states, including Indiana, sued to stop the rule from being implemented and placed it in legal stasis until it was formally repealed by the Trump administration in 2019.

The Trump administration wrote its own WOTUS definition, the Navigable Waters Protection Rule, that limited federal protections to just four categories: territorial seas and navigable waters; perennial and intermittent tributaries; certain lakes, ponds and impoundments; and wetlands adjacent to jurisdictional waters.

The NWPR removed federal jurisdiction over some waterways formerly protected by the federal government for decades.

Indiana lawmakers, some with financial interests in the fate of waterway protections, moved to remove all state protections for wetlands through Senate Bill 389.

The legislation was amended as it made its way through both houses of the legislature, and, ultimately, the final bill signed by Gov. Eric Holcomb removed state protections for half of the Indiana’s remaining wetlands and pared permitting requirements and mitigation ratios for Class II wetlands.


Meanwhile, a group of native American tribes, along with some labor and environmental groups, sued the U.S. Environmental Protection Agency in Washington and Arizona to stop the implementation of the Trump rule in 2020.

U.S. District Judge Rosemary Marquez struck down the rule in late August 2021, saying its exclusion of isolated wetlands and ephemeral streams has resulted in “significant, actual environmental harms.” The judge said she would also review the Trump administration’s 2019 repeal of the Obama WOTUS definition.

The ruling means that, at least for now, jurisdictional determinations will be based on the 1986 WOTUS definition.

“Generally speaking, [the federal government] is going to take perennial, intermittent and ephemeral streams with the caveat that we have to do that significant nexus determination in order to be able to take jurisdiction over ephemeral streams,” Keller said.

What has yet to be seen is how the WOTUS change will affect the enforcement of the Indiana wetlands law.

The law took effect on July 1. The new permit reflecting changes in the law was finalized in late July. Some landowners developing Class II wetlands have already received five-year permits to develop the land.

Keller said changes to the WOTUS rule will not affect landowners who have already received their permits.

“Just because the regulations change, it does not change the effect. Just because we change regulations, we're not going to go back and reopen an approved jurisdictional determination or permitting action for that reason,” Keller said.

Wetland permit applications that are currently being processed could face more scrutiny.

“The Army Corps makes the determination. IDEM cannot make those determinations. We might have a very strong indicator in our minds of what it's going to be, but the Army Corps must make that call and what class is the wetland,” said Heather Parsons, special projects coordinator for the IDEM Office of Water Quality.

Parsons said IDEM has created a website,, to help landowners navigate the changing jurisdiction rules.

There, landowners can begin the application process or ask IDEM staff questions about the application process.

State, Federal Agencies Take Case-By-Case Approach to Waterway Jurisdiction