In the winter of 2008, a good portion of the world’s only self-sustaining flock of whooping cranes starved to death. The majestic white birds, which are nearly the size of a Smart Car when they unfurl their black-tipped wings, were dropping dead along the Texas Gulf Coast. That winter was one of the driest the state has ever seen, and a lack of freshwater in the whoopers’ habitat near Aransas Pass resulted in a choked food supply and 23 whooper casualties. It was the largest single-winter decline in the species’ population, and admirers of the imposing bird came together to protect the fragile species.

A year later, a coalition of environmentalists, businesses and local governments sued the Texas Commission on Environmental Quality, blaming the state agency for the unprecedented spike in whooper deaths. The group, called the Aransas Project, claimed the agency had violated the Endangered Species Act by allowing too much water to be withdrawn from the two river basins that feed the whoopers’ habitat. The group argued that two of the whoopers’ dietary staples—blue crabs and wolfberries—had dwindled from lack of freshwater inflow into the estuaries of San Antonio Bay.

In mid-March, federal District Court Judge Janis Jack ruled that TCEQ’s inattention to the whoopers was responsible for the 23 deaths. That amounted to 8.5 percent of the wild flock, which nests and breeds in Canada’s Wood Buffalo National Park and winters in Texas’ Aransas National Wildlife Refuge. Jack ordered TCEQ to stop issuing any new water rights and told the agency to write a habitat conservation plan to ensure enough freshwater reaches the coast. (TCEQ quickly secured a stay from the 5th Circuit Court of Appeals.)

If Jack’s ruling stands on appeal, it could upend Texas’ system of allocating water rights.

“In my view, it will require the state to change existing water rights; how drastically and in what fashion is uncertain,” says Russell Johnson, a San Antonio environmental lawyer with experience in water law and Endangered Species Act litigation. “Under the [Endangered Species] Act, if Texas is required to do that for cranes, then they’re legally required to do that for [other endangered species].”

Endangered and threatened species live in river basins across the state. The San Marcos River, for example, is home to eight endangered or threatened species, including the Texas blind salamander. If the ruling isn’t overturned, groups attempting to protect other species could use it as a precedent to demand that TCEQ take similar measures to preserve those habitats, said Myron Hess of the National Wildlife Federation.

TCEQ has managed water rights for a century. But it wasn’t until 1985 that the Texas Legislature determined that the agency had to consider bays, estuaries and habitats when granting water permits. In practice, the agency has paid little heed to “environmental flows,” or the water that ecosystems and wildlife depend upon. The appeal court’s decision could force TCEQ to give much more weight to the environment.

In her 124-page ruling, Jack outlines several options. For starters, the agency could conduct a survey to determine if permit-holders are using their water rights and cancel unused rights. Another option would be to purchase water rights to ensure that water is set aside in the rivers that feed the whoopers’ habitat. TCEQ could also encourage water reuse and start keeping track of domestic and livestock withdrawals (which currently don’t require permits), among other measures.

In times of drought, TCEQ has extensive emergency powers. It can temporarily suspend existing water rights, divert water and issue emergency orders. Jack said the agency could use these emergency powers to ensure sufficient freshwater inflows for wildlife.

“Texas has already recognized that instream flows are extremely important; the whooping crane is just a measuring stick for how well we’re doing,” says Amy Hardberger, a water law professor at St. Mary’s University in San Antonio. “Apparently we’re not doing very well.”

Conservationists had hoped the state would ensure certain flows into the cranes’ critical habitat through a system set up by the Texas Legislature in 2007. The Legislature attempted to address environmental flows by creating a process whereby teams of scientists and stakeholders studied each major river basin and associated estuary to come up with water budgets. The teams were tasked with determining how much water was needed, and at what time of year, to preserve a “sound ecological environment.”

The teams started in East Texas, where there’s an abundance of rainfall, and moved westward, finishing with the arid and troubled Rio Grande. In most cases, TCEQ approved environmental flow standards dramatically lower than those recommended by the scientists and stakeholders.

Jack acknowledged the endeavor’s shortcomings, saying it did not fully “address the concerns of the whooping crane,” in part because it has no “teeth,” and in part because it governs only future permits.

Her ruling inspired cries of federal encroachment from Attorney General Greg Abbott, who says the Aransas Project is trying to federalize Texas rivers. Conservative groups echo that fear, and claim the original ruling puts whoopers above people.

In a March opinion piece in the Austin American-Statesman, the Texas Public Policy Foundation’s Kathleen Hartnett White, a former TCEQ commissioner, wrote: “In contrast to the [Endangered Species Act], the Texas programs aim to balance the needs of the environment and human beings as well as to uphold vested property rights. The [Endangered Species Act] allows no parity. The needs of the species trump human needs.”

But the Aransas Project says that protecting the whoopers would also preserve local economies. Like the whoopers, the commercial and recreational fishing industries along the Texas coast are dependent on freshwater flows, prompting at least 18 local businesses to join the ranks of the Aransas Project.

“The whooping crane is an easy target for people who want to say that we’re favoring critters over industry, but the reality is industry needs the TCEQ to do its job better, too,” Hardberger says. “If we approach water allocation in a more holistic manner, everybody will benefit. And you don’t have to do that when there’s plenty of water – but we’re not there anymore.”