In most quarters, conflict in the Apalachicola-Chattahoochee-Flint (ACF) basin is considered an aspect of a debate over allocation of scarce water resources. But it might also be considered an aspect of an ongoing debate over the protection of endangered species and allocation of other living resources. This second debate has increased in recent decades as the Endangered Species Act (ESA, P.L. 93-205 , as amended; 16 U.S.C. § 1531) has been invoked repeatedly in conflicts over "the ecosystems upon which endangered species and threatened species depend ..." (16 U.S.C. § 1531(b)). Water resources are even uniquely recognized in the first section of the act: "It is further declared to be the policy of Congress that Federal agencies shall cooperate with State and local agencies to resolve water resource issues in concert with conservation of endangered species" (16 U.S.C. § 1531(c)(2)). Debates over species and water allocation are generally thought of as a hallmark of western water conflicts. While the ACF debate is an eastern issue, it has several features common to many western water debates: multi-state disputes; changing demographics causing increased water demand; jobs and various economic interests lined up both against and for the protection of species; and the prospect of drought and long-term climate changes not only exacerbating demands on and tensions concerning water supplies, but also making future responses that much more difficult. Congressional involvement in such issues is specified in the Constitution: when states are the parties disputing water allocation, the conflict may be resolved by agreement in an interstate compact, through apportionment by the courts, or through allocation by Congress. (Issues concerning water management per se and the conflicts among other users (e.g., municipal use, electrical generation, irrigation, and navigation) are analyzed in CRS Report RL34326, Apalachicola-Chattahoochee-Flint (ACF) Drought: Federal Water Management Issues , by [author name scrubbed] et al.) This report outlines the species conflicts in the ACF basin, the legal status of protection for those species, and the difficulty in determining the effects of dams and their operation on listed species. It also briefly describes the implications of protecting those listed species for conservation of other living resources in the ACF basin, its estuary, and the upper Gulf of Mexico. The ACF basin is geographically varied, with population density highest at the north end of the basin around metropolitan Atlanta (2,483 people/mi 2 in DeKalb County and 1,544 people/mi 2 in Fulton County), lowest near the mouth of the system in Florida (8.4 people/mi 2 in Liberty County and 20.3 people/mi 2 in Franklin County), and at intermediate densities in Alabama and southern Georgia. A fall line marking the boundary between more ancient rocks of the Appalachian Mountains and the broad coastal plain was an ancient barrier to species movement, and later marked a line of hydropower and navigation in a string of settlements running roughly from Montgomery (AL) through Columbus to Macon (GA). (See Figure 1 .) The Apalachicola and Chipola Rivers are designated by the state as "Outstanding Florida Waters," and the state designated a 104,000 acre Apalachicola Bay Aquatic Preserve. Apalachicola Bay is the site of the Apalachicola National Estuarine Research Reserve, one of 27 research sites designated by the National Oceanic and Atmospheric Administration. At the lower end of the ecosystem, the estuarine and coastal area comprising Apalachicola Bay was named a Biosphere Reserve in 1983. Habitat in the upper basin has undergone profound alteration, while the lower basin has been less altered. A series of dams along the rivers has had the most profound effects, closing major portions of habitat to movement up and down the system. For those species that range among various river habitats, or move into the Gulf at some stage, the changes produced substantial loss of habitat. On April 15, 2008, the Corps incorporated elements of the previous Emergency Operating Plan and added other changes to form a revised IOP (RIOP); it submitted the RIOP to the Fish and Wildlife Service (FWS). The Corps proposal was to store 50% of basin inflow, instead of 30%; this was to be accomplished by eliminating a minimum flow of 6,500 cfs during wetter periods, making fish spawn releases dependent on the storage level, and switching from a two-season to a three-season operation regime. The intent was to avoid storage reaching levels that would trigger the lowering of the Apalachicola River minimum flows from 5,000 cfs to 4,500 cfs. Since the Revised Operating Plan (RIOP) could alter flows in the Apalachicola River and its tributaries downstream of Woodruff Dam, and alter freshwater inflow to Apalachicola Bay, many species could be affected by these changes. As many species interactions are incompletely known, the Florida Fish and Wildlife Conservation Commission, the Apalachicola National Estuarine Research Reserve (Florida Department of Environmental Protection), and the Northwest Florida Water Management District are cooperatively working to analyze the relationship of freshwater inflow to the benthic communities of Apalachicola Bay and changes in fish and shellfish abundance. Variations in freshwater runoff can cause changes in habitat features of the receiving estuaries, including (1) salinities, (2) turbidity; (3) nutrient availability, (4) pathogen exposure, and (5) sedimentation. While mobile species are able to move to avoid suboptimal habitat conditions, sedentary species are less able to move and are more likely to experience detrimental effects from changing habitat features. Although some mobile species may become less abundant in Apalachicola Bay if they are able to move to avoid newly unsuitable habitat features, other species that find the modified habitat to be more acceptable may move into the bay and increase in abundance. This species movement is a generally expected response to changing habitat features, but may present problems of crowding or competition in some areas. More than 95% of all species harvested commercially and 85% of all species harvested recreationally in the open Gulf spend a portion of their lives in estuarine waters. (For example, blue crabs may migrate as far as 300 miles to spawn in Apalachicola Bay.) In addition, Apalachicola Bay is a major forage area for such offshore fish species as gag grouper and gray snapper. Apalachicola Bay is also an unusually important nursery area for Gulf of Mexico commercial fish species. Reductions in freshwater flow change salinity downstream and are generally associated with a decline in some coastal fisheries and with overall harm to biota. (Specific fisheries are discussed below.) Salinity changes in Apalachicola Bay could affect the suitability of this habitat for forage and nursery use. In particular, higher salinity levels in Apalachicola Bay could prevent juvenile and adult Gulf sturgeon from entering the bay in the fall and winter, blocking access to productive feeding habitat. Because of the importance of the bay to commercial and recreational fisheries, the town of Apalachicola became the first Florida city to sue the Corps to block any further reductions in flows to the bay. In its argument, it said that lower flows (and therefore higher salinity) had already harmed the bay. Apalachicola Bay oysters constitute an important part of northwestern Florida's economy. More than 1,000 people are employed by the oyster industry in Florida's Franklin County, which harvests approximately $10 million in oysters annually. Historically, this county harvests more than 90% of Florida's oysters and 10% of the national supply. Within Franklin County, oysters account for almost one-third of the value of all commercial marine landings. In Apalachicola Bay, oyster distribution is controlled by both salinity and sea-floor geology. Oyster beds generally occur in areas where the salinity is 5 to 25 parts per thousand, on three types of shallow bars formed by different geologic processes. In normal circumstances, the varying salinities, over time, prevent the building up of the species of parasites and predators that can survive only in a fairly constant salinity (e.g., oyster drills, which are adapted only to salt water). Any decrease in freshwater inflow into the bay from the Apalachicola River may result in increased salinity in the bay. The potential effects of such increased salinity on oysters in the bay would depend upon several factors, including how fresh and saltwater mix within the bay, how rapidly and to what extent salinity increases, and the amount of oyster habitat in the bay that might be exposed to salinities exceeding oyster tolerance (as well as the amount of time these oysters were exposed to excessive salinities). Although some studies have found that Gulf coast oyster landings generally are inversely related to freshwater inflow—that is, oyster landings increase when freshwater inflow decreases —the Florida Department of Environmental Protection has raised concerns that the minimum flows proposed under the EDO could "precipitate a catastrophic collapse of the oyster industry in Apalachicola Bay." Apalachicola town officials asserted in their lawsuit that four oyster beds had died due to high salinity. In addition to oysters, important commercial species include shrimp, blue crabs, and striped mullet.