Alright, after spending far too much time researching this, and now knowing exactly where the property is located, it's pretty obvious it's part of a wetland system that has been in confirmed to existence for nearly 100 years. The major issue is that if you don't understand how wetlands work, then you would consider the property isolated from the main wetland on the other side of the road which feeds into a drainage channel, that feeds into a large creek, which feeds directly into the lake (US Waters); because it's intersected by a man made road. Just one look on google maps tells you that these two systems are historically and currently one. They no longer have an above ground connection, since the flow was diverted by the road and drainage channel, but there is no other way for the wetland on the property in question to exist unless it's linked to the major wetland on the other side of the road underground some how (that's basically what the EPA's field report said as well).
While I agree that there needs to be a reasonable limit to how far the EPA can take their claims of US Waters, Alito is an idiot and this ruling literally doesn't pass the eye test. That being said, there should have been better communication with the property owners since they got the necessary permits from the state, but the EPA came in after the fact with threats and no realistic form of resolution outside of a massive cost to the owners. Clearly it wasn't a major environmental issue as the land still hasn't been cleared some 15 years later.
This could be your worst take yet, and that's really saying something... Remember that Erin Brockovich movie? Remember Flint? Try searching for stories around the Detroit area about chemicals being dumped into creeks and streams.