This article recently appeared in the San Antonio Express-News. I don't think the river flow has as much to do with the loss of Whooping Cranes as does the closing of Cedar Bayou.

In a perfect world, an expected federal lawsuit seeking to protect the endangered whooping crane would finally bring resolution to a nearly 20-year effort to better regulate Edwards Aquifer pumping rights. Downstream users, already ensured water as a result of the aquifer fight, would acquiesce that, yes, the bays downstream of them, and the critters that inhabit those bays, deserve equal consideration.
It's still a long road to utopia, but environmental lawyer Jim Blackburn and the Aransas Project, the coastal group he represents, are focusing attention on an element that's been missing in the discussion about how to manage the region's water supply: the health of the bays and estuaries downstream.
By now, most of us are familiar with the fountain darter and the Texas blind salamander. These are among the seven endangered species whose well-being forced the pumping rights battle and gave rise to the Edwards Aquifer Authority. The species often are referred to as “canaries in the coal mine,” as they depend on the Edwards-fed Comal and San Marcos springs flowing continuously.
So, too, is the whooping crane an important indicator of how well we're taking care of our rivers, in particular the Guadalupe and the San Antonio, whose management is the target of the Aransas Project's suit. While springs feed the rivers, they in turn nourish bays and estuaries with freshwater flow.
Last winter, we were starkly reminded why we need to be better attuned to this sensitive symbiotic relationship. Amid a devastating drought, restricted freshwater inflows to the bays and estuaries surrounding the Aransas National Wildlife Refuge, the cranes' wintering spot, led to fewer blue crabs and wolfberries, believed by many to be the whoopers' principal diet. The wintering population of 270 was devastated by the loss of 23 cranes, the most deaths ever recorded.
The Edwards Aquifer Alliance summarized the relationship succinctly on lawn signs sold as a fundraising project. “I'm not watering. I'm saving my water for the whooping cranes,” the signs boasted.
There is stiff disagreement over the drought's impact on the cranes' food supply. And despite last winter's high number of deaths, the cranes have rebounded from a 1960s count of fewer than 50 in North America.
Unmistakable, however, is the opportunity before us. Under federal court order, the state for the past two years has worked with 39 stakeholders to develop an Edwards Aquifer Recovery Implementation Plan — essentially a compromise over how best and most equitably to use the region's finite water resources.
Annalisa Peace, the alliance's executive director, describes the debate among stakeholders as “less contentious” than in the past. Notably, a 75 percent majority of the group's steering committee recently voted against funding a new crane study, giving a nod to established studies by the U.S. Fish and Wildlife Service. The move was incremental but highly symbolic as downstream needs receive more attention.
The Aransas Project's lawsuit puts more heat on the issue. That's not near utopia, but it's closer than we've ever been.