A federal judge based in Corpus Christi has found Texas officials responsible for the deaths of nearly two dozen whooping cranes and ordered the state to develop a conservation plan that would protect the last naturally migrating flock of the endangered birds.Senior U.S. District Judge Janis Graham Jack ruled Monday that the Texas Commission on Environmental Quality was responsible for the deaths of 23 whooping cranes in the winter of 2008-09 because its management of the rivers that feed San Antonio and Aransas bays caused their salinity to rise.The saltier water hurt blue crab and wolfberry supply, two of the cranes' primary food sources, as well as the birds' primary freshwater drinking source.Jack found that TCEQ officials violated the Endangered Species Act and ordered a conservation plan that would balance the interests of water users with the need to protect the whooping cranes' habitat."This is really about the future," Jim Blackburn, lead counsel for the group that sued the state, said Tuesday. "What has happened has happened. We were not seeking penalties. Rather we were thinking changes in the future to try to prevent these takes from occurring."In early 2010, The Aransas Project, a coalition of local governments and environmental advocates, sued TCEQ over its management of the rivers. Lawyers for all the parties packed a courtroom in December 2011 for an eight-day bench trial in which the judge would make the final decision, in place of a jury."This ruling says that among the factors to be balanced by the state of Texas are inflows to Aransas and San Antonio bays and protection of the whooping crane and the bay health," Blackburn said.The cranes winter in and around the Aransas National Wildlife Refuge, about 170 south of Houston along the Gulf Coast.TCEQ chairman said Tuesday that the agency was considering its options, including appeal."I am disappointed with the outcome of the case, but not deterred," TCEQ Chairman Bryan W. Shaw said in a statement. "The science and law will prove out in the end."The agency considered the lawsuit "an unconstitutional attempt to use the Endangered Species Act as cover for rewriting the Texas Water Code."TCEQ had challenged the evidence on the number of whooping cranes that had died that winter. Late last year, the state tried to reopen the case to submit a new U.S. Fish and Wildlife Service report, which raised questions about the aerial survey methods used for decades to count the birds. But in December, Jack canceled a scheduled hearing on that motion to reopen the trial.The judge's order also prohibits the state from issuing any new water permits on the rivers until assurances are in place. Blackburn said he interprets that to maintain the status quo until the habitat conservation plan is in place. TCEQ said it would seek relief from that prohibition.The flock of whooping cranes travels between Canada and Texas every year. In the 1940s, its numbers dwindled to 16 cranes, but they peaked in 2008 with 270. The flock lost 57 birds in 2008-09, with 23 of those deaths coming in Texas that winter, according to The Aransas Project. The Sierra Club and National Wildlife Federation also praised the decision Tuesday.