You’ve heard of clouds with silver linings. Well, this week conservation news can be described as a bright sunny day–but with some threatening clouds on the horizon.

Tuesday the Environmental Protection Agency and the Army Corps of Engineers finally announced the long-awaited proposed rule for which streams and wetlands would regain Clean Water Act protection stripped by Supreme Court decisions in 2001 and 2006.

Well, the bright light of salvation is now shining down on those intermittent and ephemeral headwaters that feed 60 percent of the nation’s water supply–including most of our trout fisheries. And the sportsmen’s conservation community rejoiced.

But dark clouds are still hovering over isolated wetlands absolutely essential to waterfowl such as the prairie potholes and the playa lakes.

They were left out of the proposal, put instead into the category of “to be determined on a case-by-case basis” depending on the outcome of the public hearing process.

“The EPA is asking for feedback on how to handle those, and we think that is smart,” said Chris Wood, head of Trout Unlimited, who was otherwise thrilled with the proposal. “And we hope hunters and angers will engage in this process.”

Let’s review the good news first.

Passage of the Clean Water Act in 1972 was literally a lifesaver for fish, wildlife, and humans because it not only began cleaning up our water supplies, it also made wetlands part of the public trust. The nation had decided wetlands were critical fish and wildlife habitat, an essential element in water purification and storage as well as flood protection. And the EPA and Army Corps read that law to include isolated and seasonal wetlands because of their importance in all those functions.

Before that law, we were losing about 500,000 acres of wetlands each year. After 1972 the loss dropped to 80,000 a year.

But after those Supreme Court rulings stripped protection from isolated and seasonal wetlands–a total of 20 million wetlands acres and most streams–the loss skyrocketed by 140 percent, according to a report by the U.S. Fish and Wildlife Service.

Conservationists were shocked by those rulings, but the fix seemed simple enough. The court didn’t rule the nation could not protect those habitats, it said the 1972 Congress never intended the CWA to cover them. So they worked with concerned congressmen to introduce a number of bills to restore the Clean Water Act.

Since then sportsmen have had a chance to see just who stands with them. Turns out most of those politicians who love to come to our banquets and talk about huntin’ and fishin’ and guns and dawgs had more love for the developers and big agricultural interests fighting the regulations. None of those bills ever made it through congress.

Fortunately, those court rulings led to regulatory chaos, which was hurting farming and developers as well as fish and wildlife because no one knew exactly which wetlands were protected. So there was a push by many interests to have clarification. And now we do.

The EPA has an excellent web page on the new rule.

The rule proposes to return protection to those seasonal and rain-dependent streams, which are the headwaters for most of our rivers, and which we rely on for much of our drinking water, not just for fishing and hunting. Please take a long, hard look at this map.

This is what many of the people you send to Washington did not find important.

The proposed rule also provides farmers with plenty of relief, clearly stating it doesn’t expand existing protections, and it doesn’t include some features which clearly are not natural. Farmers now know exactly where they stand.

But there has been no such clarification when it comes to waterfowl and a host of other species that depend on isolated wetlands such as prairie potholes and playa lakes. The EPA says it will consider those wetlands on a case-by-case basis.

If they consider science, there is plenty showing the connectivity of these distance wetlands to watershed of navigable waterways.

Sportsmen’s conservation groups were right to praise the proposed rule, and to be pleased with the protections that have been reinstated. They have worked hard for many years to get to this point.

But they also know the work now falls on the individual sportsmen out there, because we already know most of the folks sent to Washington are not going to come to our aid.

“Yes, we would like to have seen the rule include those habitats, but we know if congress was going to pass an act to protect isolated wetlands they would have done that by now,” said Whit Fosburgh, head of the Theodore Roosevelt Conservation Partnership.

“Right now the action will be in the rulemaking process, in seeing what we can do to strengthen this rule to protect more wetlands.”

Barring a sudden change in congress, that’s the only option we have left to remove that cloud still hanging over potholes and playa lakes.