This case wasn’t about a farm or rivers or lakes. It was about a lot with a ditch that someone wanted to build a house on. The EPA wanted the law to cover any property with any kind of feature to control rainwater or runoff, which is basically every piece of property in the country:
> Within a few years, the agencies had “interpreted their jurisdiction over ‘the waters of the United States’ to cover 270-to-300 million acres” of wetlands and “virtually any parcel of land containing a channel or conduit . . . through which rainwater or drainage may occasionally or intermittently flow.” Rapanos, 547 U. S., at 722 (plurality opinion).
All the court did here was rule that the law doesn’t cover ditches which might occasionally have rainwater in them. The EPA will have to go back to the older definition that includes navigable waterways, such as rivers, lakes, and seas that carry interstate or international trade, as well as the wetlands adjacent to them.
As usual, Congress retains the power to amend the law to give it a more precise definition. They could even amend it so that it does cover any random ditch that might occasionally have water in it if they wanted. Congress could have made that choice at any time in the last 50 years, but they have chosen to leave the law vague instead. If you think that the Clean Water Act _should_ be applied to every single ditch in America, then write your Representative and tell them off for not doing their job.