The wording in the clarification (that is being thrown out) gave jurisdiction to the EPA to regulate activities on navigable streams or streams with a "significant nexus" to navigable waters. These seasonal streams are ecologically vital for a number of reasons, one of the most important being that they serve as some of the most resilient cold-water refugia for critical salmonid species (e.g. bull trout). If the current climate trends persist, and all indications say they will, these smaller, seasonal headwaters are only going to be more valuable for the viability of many aquatic and terrestrial species.
On Fresh Tracks Season 4 Episode 9 (
https://www.youtube.com/watch?v=4RHqYQZ7ACo&list=PLLdxutimd-JvGyjPUXmifah2FGEHeHwJv&index=9), the HuntTalk crew mentions a spot in the Cabinet Mountains Wilderness where mining operations threaten the ecological health of Rock Creek. This is a prime example of a stream that would have been covered under the Clean Water Act, if the amendment to the wording would have remained. However, given that portions of Rock Creek are seasonally dry, EPA won't have jurisdiction to monitor and regulate the activities effecting things like water quality, water availability, and groundwater contamination. There is a resident population of bull trout that live upstream from the intermittent section of the river. I'm speculating here, obviously, but I would bet a sizeable sum of money that you won't find those bull trout there in 5 years.
I understand that we need resources and that we have to extract them. It's possible to extract resources with minimal impact on the environment, it just takes more work (generally). Sometimes it is discouraging to think about how quickly we are willing to sacrifice something so valuable (environmental health) for more immediate gratification.