Once SCOTUS ruled that anything that could presumably be sold affects interstate commerce even if there is no plan to sell it, the federal government was free to regulate, subsidize, or seize pretty much everything. Also, under the jurisdiction of the EPA and the Fish and Wildlife Service and the Endangered Species Act, very small streams and even seasonal ponds and pools have been regulated for quite some time, as the former are habitat for many species not found in bigger waters and the latter are important to migratory birds as well as many ephemeral species that live only in temporary pools (e.g. most fairy shrimp.)
The legislative change does make one wonder if an expansion in power is underway. The article specifically mentions Kelo v. New London, to me the most troubling SCOTUS decision in at least the last thirty years. Since SCOTUS has already established the right of government (at all levels, not just federal) to take your property and give it to another individual if government deems that a better use of the land, the worst case scenario would be the federal government seizing your land because you aren't managing these streamlets and temporary pools to its satisfaction and giving your land to, say, Algore to establish a tree farm selling indulgences. Sorry, carbon credits.
Kelo v. New London established that Americans are property of government. Property can't own property - although property can be encouraged to think it owns property, for political purposes - so really this change is just a progression of government establishing further control. It only remains to be seen if government uses its extra power wisely (to prevent habitat loss and extinction of otherwise viable species) or to reward its supporters and further its political agenda. Your best guess probably demonstrates how much faith you have in the integrity and wisdom of government . . .