What do two rivers in the Southeast and California have in common? Both are threatened by battles over their water.

The Apalachicola-Chattahoochee-Flint Basin in Alabama, Georgia, and Florida tops a new list as the most endangered river in the U.S. this year, according to an annual report from the Washington, D.C.-based conservation group American Rivers. Second most endangered is the San Joaquin River in northern and central California.

"Both rivers suffer from increasing conflict among stakeholders who depend on their water," including cities, farmers, and wildlife, says Chris Williams, a senior vice president at American Rivers. "And these issues are exacerbated by population growth and climate change."

Other rivers high on the list include the Susquehanna in Maryland and Pennsylvania, the Smith in Montana, and the Green-Duwamish in Washington.

The annual list, which dates back to 1984, is based on three criteria: A river must be under serious threat, of regional or national significance, and at a turning point in a decision related to conservation. Last year, the Colorado River was number one, and since then two of its three biggest threats have been withdrawn: a controversial development and a plan for a tram. (A uranium mine proposal remains a threat.)

Past annual lists also helped raise awareness about the Hoback River in Montana, where oil and gas leases were defeated, and the Elwha River in Washington, where a series of dams was removed to restore the ecosystem.

Water conflicts are particularly timely now, notes Williams, given several imminent regulatory and court decisions.

"It is time to move away from the old-fashioned model of fighting over water, through grabs and lawsuits, and toward a cooperative model in which stakeholders sit down together and hammer out agreements, so everybody can get what they need," Williams says.

Water Wars

In the Southeast, a pending case in the U.S. Supreme Court may decide how water from the Apalachicola system is allocated, after a fight between Florida and Georgia. At the same time, the U.S. Army Corps of Engineers is updating its management strategy for the basin.

But American Rivers says federal action is unlikely to resolve the issues for the region, which faces water shortages and rising population. For a long-term solution, communities should come together to develop a plan they can all live with. In general, more water needs to flow into the river's lower basin and out to Apalachicola Bay because the estuary has been starved of water and nutrients in recent years, harming fisheries and wildlife, the group says.

View Images An orchard dries out near Clovis, California, thanks to drought and low flow in the San Joaquin River. Can the river be saved in the face of such high demand? Photograph by Max Whittaker/The New York Times/Redux

In California, the state is expected to make some tough decisions on allocating San Joaquin water soon.

New York's St. Lawrence River and surrounding wetlands could also be revitalized if a pending plan to allow certain releases of water through a dam is approved, Williams notes. Yet that plan has languished for years. Montana's Smith River is threatened by a proposal for a copper mine.

The Big Picture

Overall, the condition of U.S. rivers remains mixed, American Rivers says. Water quality has improved dramatically in many places in the 40 years since the Clean Water Act was enacted. And some obsolete dams have come down, opening up more river miles to fish.

"That being said, we still have a lot of work to do," Williams says. "Wetlands are still disappearing, a large percentage of rivers are still not fishable and swimmable, creeks are getting plugged from mountaintop removal mining ... We have come a long way in 40 years but we still have a long way to go."

Here's the complete list of America’s Most Endangered Rivers of 2016, and their threats, as determined by American Rivers:

1. Apalachicola-Chattahoochee-Flint River Basin

Alabama, Florida, Georgia

Threat: Outdated water management

2. San Joaquin River

California

Threat: Outdated water management

3. Susquehanna River

Pennsylvania, Maryland

Threat: Harmful dam operations

4. Smith River

Montana

Threat: Mining

5. Green-Duwamish River

Washington

Threat: Outdated dam and floodplain management, pollution

View Images In the St. Lawrence River, seaweed grows over a bass spawning bed. Conservationists hope more water can be returned to the river. Photograph by Heather Ainsworth/The New York Times/Redux

6. Pee Dee River

North Carolina

Threat: Harmful dam operations

7. Russell Fork River

Kentucky, Virginia

Threat: Mountaintop removal mining

8. Merrimack River

Massachusetts, New Hampshire

Threat: Polluted runoff

9. St. Lawrence River

New York (and Canada)

Threat: Harmful dam operations

10. Pascagoula River

Mississippi, Alabama

Threat: New dams