One of the biggest botches in U.S. Supreme Court history came about five years ago in what's known as the Rapanos case. Just how big is only now becoming clear, thanks to a series in the New York Times and a study of Texas wetlands reported this week.

In the Rapanos decision, delivered in June 2006, the high court broke 4-1-4. In the case a Michigan farmer named John Rapanos had argued that his land was not a wetland and so he was not breaking the law when he dumped fill dirt on it for a development without getting a U.S. Army Corps of Engineers wetlands permit -- even though his own consultant and Michigan state employees had both told him that he was wrong.

Four of the justices sided with Rapanos and four with the federal government. The crucial swing vote was Justice Anthony Kennedy, who wrote in his separate opinion that there needs to be a "significant nexus" with navigable waters, defined as situations when the wetlands "significantly affect the chemical, physical, and biological integrity of other covered waters."

Wetlands such as the ones in dispute on Rapanos' land were not under government jurisdiction when the effect on water quality is "speculative or insubstantial," he added.

Regulators and judges have come to regard the Rapanos decision as a thick, murky swamp in which even an expert can get lost. "The short answer is that the state of post-Rapanos wetlands jurisdiction is a mess," said Richard Frank, director of the California Environmental Law & Policy Center at University of California, Davis, told the Times. "Rapanos produced a broad consensus of opinion, virtually unheard of when it comes to wetlands regulation, that the Supreme Court had made things worse, rather than better."

One of the results has been that the Corps has avoided claiming jurisdiction over any wetland that appears to lack that "significant nexus." One area it's dropped regulation over is what Texans call "prairie potholes," seemingly isolated wetlands that appear unconnected to any navigable waterway.

Except now comes a study that says they are, in fact, connected. Whenever the shallow wetlands exceeded their normal storage capacity - a frequent occurrence, even in dry years - the runoff flowed through to nearby bays, rivers and streams "in significant amounts." At least 17 percent of the water that falls on the prairie potholes winds up in a navigable waterway over a four-year period, the study found.

"The bottom line is these isolated wetlands are critical to the watershed of Galveston Bay," John Jacob, one of the researchers, told the Houston Chronicle. "The federal government needs to take a second look."

In "Paving Paradise" we documented a similar situation in Florida, where the Corps has dropped any regulation of wetlands that appear to funnel water straight down into the underground aquifer. Yet, we found, that water frequently pops back up to the surface again miles away in gushing springs.

“There are a lot of areas where what’s been classified as an isolated wetland
pops up somewhere else,” a Corps of Engineers regulator told us. But does the Corps consider that? “Once it goes underground,” he said, “for the most part, not a lot.”

Efforts by congressmen to remedy this botched Supreme Court decision have failed repeatedly, as big business groups have claimed -- falsely -- that this was an attempt to expand government power, and not an effort to fix something the high court fouled up.

Ironically, in 2009, Rapanos agreed to pay a $150,000 civil penalty and spend an estimated $750,000 to mitigate for 54 acres of wetlands that were filled without authorization under the Clean Water Act.