AUSTWELL, Texas -- The endangered whooping crane has emerged as a critical species for measuring success in a planned restoration of the battered Gulf of Mexico ecosystem.

The last wild migratory flock of whooping cranes winters here at the Aransas National Wildlife Refuge, where the 300 or so birds feast on berries and crabs to fuel a return flight next spring to their Canadian breeding grounds.

Whooping cranes are an iconic species. The tallest of North American birds, with adults approaching 5 feet in height, whooping cranes can live nearly 30 years in the wild. Adults have snowy white feathers with black wingtips.

But this flock faces danger. Biologists warn that pollution and a lack of fresh water in the Guadalupe and San Antonio rivers, which flow into the marshes of San Antonio Bay, pose a series threat to these hardy holdouts. And environmentalists have put the species at the heart of a lawsuit against Texas regulators for alleged mismanagement of water resources.

Dan Alonzo, the Fish and Wildlife Service's project leader at Aransas, called managing the rivers "really critical" to the health of the refuge, which was established in 1939 as a way station for migrating birds.

Endangered whooping cranes, now the subject of two Gulf of Mexico restoration initiatives, feed at the Aransas National Wildlife Refuge. Photo by Ellie Teramoto.

Concern about the whooping cranes is helping drive parallel efforts to restore and protect the bay and refuge. Federal agencies are focusing on a small-scale initiative to reduce pollution washing off farmland, while environmentalists are pushing Texas to increase the amount of fresh water flowing into the bay, even during droughts.

The federal Gulf of Mexico Initiative features a U.S. Department of Agriculture project that will put $50 million toward encouraging farmers and ranchers to adopt conservation measures aimed at keeping silt and nitrogen fertilizers and manure out of waterways. The overfertilization of waterways creates "dead zones" -- oxygen-deprived areas devoid of aquatic life.

Just $20 million is available for the first three years of the USDA project, which begins next year and aims to clean up 16 Gulf Coast watersheds. Three projects will be in Texas with Aransas at the center.

No one yet knows how much money will go to protecting Aransas' 155,000 acres and its whooping crane population.

Salvador Salinas, a conservationist at USDA's Natural Resources Conservation Service, said his office is reaching out to landowners and offering to help design projects and prepare applications for federal funding.

The effort is small and underfunded, he conceded. Gulf of Mexico conservationists hope Congress will allocate billions of dollars from penalties paid by BP PLC for last year's massive Gulf oil spill.

Salinas said he is optimistic that initial efforts will spur larger projects all along the Gulf shoreline and bring significant benefits to Aransas' whooping cranes.

"The hope is that over a period of time we will begin to see some positive effect out in the bay with regards to water quality," Salinas said.

Early this month, the State of the Gulf of Mexico Summit in Houston served as the platform for local, state and federal officials and nonprofits to roll out plans for ecosystem restoration.

Aside from the federal Gulf initiative, there are proposed restorations of marsh and oyster habitat in coastal Louisiana, estimated to cost around $30 million. Navigational infrastructure built up over decades now prevents new sediment from being deposited, causing much of southern Louisiana to erode.

A overarching restoration plan released by U.S. EPA and other agencies proposes other projects for Mississippi, Alabama and Florida involving oyster-bed construction, artificial reefs, marsh creation and dune restoration.

Whooping cranes at heart of lawsuit

The day before the unveiling of the San Antonio and Guadalupe river basin project here, hearings concluded at a federal court in Corpus Christi over a lawsuit filed last year by a coalition of conservationists alleging that mismanagement of the basin by the Texas Commission on Environmental Quality is killing whooping cranes.

Fish and Wildlife Service officials estimate that San Antonio Bay is roughly 50 percent saltier than it should be. The coalition, the Aransas Project (TAP), maintains that a lack of freshwater flows from the rivers is disrupting populations of blue crabs, a key food for the cranes as they build up the energy needed to fly back to Canada.

According to those involved in the case, a retired FWS employee named Tom Stehn testified that at least 23 cranes perished during the winter of 2008-2009, a significant number for a population of 300 or so individual birds.

Jim Blackburn, the lead attorney for the plaintiffs, says that Stehn's testimony and other expert opinion and evidence presented at the trial prove TCEQ's water rights permitting is at fault for high salinity.

"We showed that the permitting program implemented by the TCEQ caused the deaths of whooping crane due to the reduced freshwater inflows on the habitat and food supply," Blackburn said. "We were able to put forward a very solid scientific case that was, I think, technically quite good, and hopefully the judge thinks, as well."

TCEQ disagrees. The Guadalupe-Blanco River Authority, which oversees water rights in the basin, also denies TAP's claim and has intervened in the court case on TCEQ's behalf.

"First and foremost, the TCEQ vigorously disagrees with the allegations in the TAP original complaint," said TCEQ spokesman Terry Clawson.

Clawson said TAP's allegation that Texas' water drawing rights amount to a "take" under the federal Endangered Species Act is erroneous and added that TCEQ and other state agencies are already in the midst of reviewing the water allocation system with coastal waterways and estuaries in mind.

"State law also recognizes the importance of maintaining the biological soundness of the state's rivers, lakes, bays and estuaries on the public's economic health and general well-being," he said. "To that end, there is an extensive, locally driven, science-based process for developing an environmental flow regime."

Though the trial phase concluded a week ago, a judgment is not expected until next summer. Blackburn and TAP want the court to force TCEQ to enter into discussions on designing new water rights standards that would guarantee that a minimum amount of adequate fresh water gets to San Antonio Bay and Aransas. The severe drought Texas has suffered this year makes the situation even more urgent, TAP argues, as that group fears a repeat of the spate of whooping crane fatalities seen in 2008-2009.

"We would like the judge to make the state sit down and work with all the stakeholders and come up with a process whereby fresh water can get to the bay during times of drought," Blackburn said. "Right now, virtually no water gets to the bay in times of drought."

Pollution

USDA and Fish and Wildlife Service officials caution that their new initiative does not address water supply to the bay at all and thus will be of little help on the salinity issue.

But Salinas said that high concentrations of agriculture runoff and excessive silt from upriver erosion also harm the whooping cranes' food supply. He is confident the Gulf initiative will eventually help the birds.

"This is a longer-term initiative," Salinas said. "There are a number of folks, a number of organizations, a number of entities that are really interested in what the outcomes are going to be with regard to this project here."

Many green groups in Texas complain that the state leaves too little freshwater inflows for bays all along the coastline, a reality made clearer by the drought. But Blackburn insists that the TAP effort will stay focused squarely on Aransas and the threatened whooping cranes.

Whooping crane fatalities will be closely monitored, they say, especially as state officials predict the drought will extend throughout the winter next year.

So far, the Fish and Wildlife Service's Alonzo sees indications the cranes are doing all right this season.

"They are feeding quite well, from what we're seeing in their scat," Alonzo said. "They're pretty tough birds."