The concurring opinion by Justice Thomas (joined by Justice Gorsuch) was in reality a dissent.
It argues that "waters of the US", even if it leaves off the word "navigable" in the law, still refers to only navigable waters since the term "waters of the US" has always been used in only that way. That would narrow the scope of the Clean Water Act even further.
From the "concurrence":
"the agencies have 'asserted jurisdiction over virtually any parcel of land containing a channel or conduit through which rainwater or drainage may occasionally or intermittently flow,' including 'storm drains, roadside ditches, ripples of sand in the desert that may contain water once a year, and lands that are covered by floodwaters once every 100 years.'...The agencies’ definition 'engulf[s] entire cities and immense arid wastelands' alike...Indeed, because 'the entire land area of the United States lies in some drainage basin, and an endless network of visible channels furrows the entire surface,' 'any plot of land containing such a channel may potentially be regulated.'...
If this interpretation were correct, the only prudent move for any landowner in America would be to ask the Federal Government for permission before undertaking any kind of development."
Then, getting to the real meat of the not-really-a-concurrence "concurrence":
"What happened to the CWA is indicative of deeper problems with the Court’s Commerce Clause jurisprudence.
The eclipse of Congress’ well-defined authority over the channels of interstate commerce tracks the Court’s expansion of Congress’ power '[t]o regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes.'...As I have explained at length, the Court’s Commerce Clause jurisprudence has significantly departed from the original meaning of the Constitution"
That's what Justice Thomas is going for. To kill the New Deal expansion of federal power through the commerce clause. That's why to progressives, he is public enemy number one. He got one other justice to go along for the ride on this one.
It argues that "waters of the US", even if it leaves off the word "navigable" in the law, still refers to only navigable waters since the term "waters of the US" has always been used in only that way. That would narrow the scope of the Clean Water Act even further.
From the "concurrence":
"the agencies have 'asserted jurisdiction over virtually any parcel of land containing a channel or conduit through which rainwater or drainage may occasionally or intermittently flow,' including 'storm drains, roadside ditches, ripples of sand in the desert that may contain water once a year, and lands that are covered by floodwaters once every 100 years.'...The agencies’ definition 'engulf[s] entire cities and immense arid wastelands' alike...Indeed, because 'the entire land area of the United States lies in some drainage basin, and an endless network of visible channels furrows the entire surface,' 'any plot of land containing such a channel may potentially be regulated.'... If this interpretation were correct, the only prudent move for any landowner in America would be to ask the Federal Government for permission before undertaking any kind of development."
Then, getting to the real meat of the not-really-a-concurrence "concurrence":
"What happened to the CWA is indicative of deeper problems with the Court’s Commerce Clause jurisprudence. The eclipse of Congress’ well-defined authority over the channels of interstate commerce tracks the Court’s expansion of Congress’ power '[t]o regulate Commerce with foreign Nations, and among the several States, and with the Indian Tribes.'...As I have explained at length, the Court’s Commerce Clause jurisprudence has significantly departed from the original meaning of the Constitution"
That's what Justice Thomas is going for. To kill the New Deal expansion of federal power through the commerce clause. That's why to progressives, he is public enemy number one. He got one other justice to go along for the ride on this one.