Apalachicola-Chattahoochee-Flint Drought: Species and Ecosystem Management

Apalachicola-Chattahoochee-Flint Drought:
Species and Ecosystem Management
Updated July 22, 2008
M. Lynne Corn
Specialist in Natural Resources
Resources, Science, and Industry Division
Kristina Alexander
Legislative Attorney
American Law Division
Eugene H. Buck
Specialist in Natural Resources Policy
Resources, Science, and Industry Division

Apalachicola-Chattahoochee-Flint Drought:
Species and Ecosystem Management
Drought in the Southeast has brought congressional attention to an ongoing
interstate water conflict among Alabama, Florida, and Georgia over water allocation
and management of the Apalachicola-Chattahoochee-Flint (ACF) basin. Reservoir
drawdown and predictions for a continued drought have Georgia’s upper basin
municipal and industrial customers concerned about depleting their principal (in
some cases, their only) water supply, Lake Lanier in northern Georgia. Alabama,
Florida, and Georgia’s lower basin interests are concerned about sustaining river
flows to meet their municipal, agricultural, electrical, recreational, and ecosystem
needs. In addition, four federally protected species, once widely distributed but now
confined to the lower basin, are caught in the controversy.
The issue for the U.S. Army Corps of Engineers (Corps) is how to manage ACF
federal reservoirs, now at record low levels, to meet needs in the upper and lower
basin equitably. The challenge includes complying with federal law (e.g., the
Endangered Species Act (ESA)); minimizing harm to the ACF basin and
Apalachicola Bay species, ecosystems, recreation, fishing, and oyster industry; and
providing flows for hydropower and thermoelectric cooling, while also meeting water
needs of the Atlanta region, other communities, and industries.
To varying degrees, the ACF drought has lasted for several years, depleting
water supplies, with Lake Lanier being the largest source for downstream needs. The
Corps has released water at various times from Lake Lanier to meet minimum flow
requirements in the lower basin — to the consternation of upper basin users. As an
emergency drought response in 2007, the Corps began to reduce flows in the
Apalachicola River, thereby slowing the drawdown of Lake Lanier, though heavy
rains in early 2008 in the lower basin temporarily halted extra releases from Lake
Lanier. The Corps’ Revised Interim Operating Plan (RIOP) calls for three
operational seasons, contingencies for drought operations, and additional water
storage before and after a drought phase. It differs from previous plans in allowing
water flows to fall to a specified level during drought without additional ESA
consultation. In addition, a previous agreement to limit the rate of reduction in flow
(to allow species to move to deeper water) will end under certain conditions. Judging
that the Corps’ actions would not jeopardize the continued existence of listed species
or adversely modify their critical habitat, the Fish and Wildlife Service issued a
Biological Opinion on June 1, 2008, that approved the RIOP.
Four species protected under the Endangered Species Act — three mussels and
a sturgeon — depend on Apalachicola River flows. The impacts of the RIOP on
these species continue to be the subject of study and debate. Yet the four are not the
focus of debate. Rather the law itself acts as a hammer, forcing parties to reach
decisions that may produce winners and losers. As climate change and population
growth continue to affect ecosystems, ESA controversies may be at the center of still
more stormy debates. Responses of the various parties in the ACF and species
protection controversy may presage responses to future river management
controversies in other regions.

ACF Ecosystem from Top to Bottom..................................2
Oysters and Fisheries...........................................3
Oysters ..................................................4
Marine Commercial Fishing.................................5
Marine Sport Fishing.......................................5
Freshwater Sport Fishing....................................5
The Four Species: A Sturgeon and Three Mussels....................6
Consultation Under the Endangered Species Act.........................6
Consultation in 2006-2007.......................................6
Consultation in 2007...........................................7
Biological Opinion and Species Analysis.......................9
No Long-Term Analysis Provided, or Expected.................13
Incidental Take Statement and Reasonable and Prudent Measures...17
Consultation in 2008..........................................17
Conclusions of the BiOp...................................18
Effects on Other Species...................................19
Consistency with Previous Court Decisions....................21
What Does a Species Need?.....................................22
Appendix A. How the Endangered Species Act Works: Consultation........24
Other Options for Federal Agencies Under Section 7.................26
Dim Prospects Under the Disaster Provision....................26
An Outright Exemption: The Long Road......................27
Appendix B. NEPA in the Context of the Exceptional Drought Operations
and ESA....................................................28
Timing and Content...........................................28
Emergency Exception.........................................29
The Right to Sue Under NEPA..................................30
List of Figures
Figure 1. Critical Habitat and Historic Range of Gulf Sturgeon in
ACF Basin..................................................11
Figure 2. Current Range and Additional Range of Fat Threeridge in
ACF Basin..................................................14
Figure 3. Current and Additional Range of Purple Bankclimber in
ACF Basin..................................................15
Figure 4. Current and Historic Range of Chipola Slabshell in ACF Basin.....16

Apalachicola-Chattahoochee-Flint Drought:
Species and Ecosystem Management
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,1 through apportionment by the courts,2 or
through allocation by Congress.3 (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, coordinated by Nicole T.
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

1 Generally, interstate compacts, which create a binding agreement between two or more
states, require congressional approval in addition to approval by the states involved in the
agreement. (U.S. Const., Art. I, § 10, cl. 3.)
2 The U.S. Supreme Court has original jurisdiction to hear disputes between states. (U.S.
Const., Art. III, § 2, cl. 1.) In the case of the ACF litigation, no state has sued another state,
and therefore the cases must be heard first by lower courts.
3 Congress may apportion interstate waters under its power to regulate interstate commerce.
(See U.S. Const., Art. I, § 8, cl. 3; Arizona v. California, 373 U.S. 546 (1963).) Although
Congress has the authority to act in the interest of interstate commerce, congressional
allocation in such conflicts is rare.

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.
ACF Ecosystem from Top to Bottom
The ACF basin is geographically varied, with population density highest at the2
north end of the basin around metropolitan Atlanta (2,483 people/mi in DeKalb
County and 1,544 people/mi2 in Fulton County), lowest near the mouth of the system22
in Florida (8.4 people/mi in Liberty County and 20.3 people/mi in Franklin County),
and at intermediate densities in Alabama and southern Georgia.4 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,”5 and the state designated a 104,000 acre Apalachicola
Bay Aquatic Preserve.6 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.7 At the lower end of the ecosystem, the
estuarine and coastal area comprising Apalachicola Bay was named a Biosphere
Reserve in 1983.8
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

4 U.S. Census Bureau, Census 2000 Summary File 1.
5 According the state’s website, “This special designation ... is intended to protect existing
good water quality.” See [http://www.dep.state.fl.us/water/wqssp/ofw.htm].
6 See [http://www.dep.state.fl.us/coastal/sites/apalachicola-ap/]. The designation occurred
in 1969 (although the same website states that enabling legislation was passed in 1975).
7 See [http://nerrs.noaa.gov/Apalachicola/].
8 See [http://www.unesco.org/mabdb/br/brdir/directory/biores.asp?mode=all&code=USA
+37]. The recognition comments, “Increased demand for water by large upstream cities and
agriculture now puts pressure on the floodplain ecosystem.” A biosphere reserve is “an area
that has been nominated by the locality and the country in which it is located for
participation in the worldwide U.S. Man and the Biosphere Program (MAB), and accepted
for such recognition by the United Nations Educational, Scientific, and Cultural
Organization (UNESCO) ... on the basis of [its] significance for research and study of
representative biological regions of the world” (CRS Report 96-517, Biosphere Reserves:
Fact Sheet, by Susan R. Fletcher).

the RIOP to the Fish and Wildlife Service (FWS).9 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.
Oysters and Fisheries
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.10 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.11
(Specific fisheries are discussed below.) Salinity changes in Apalachicola Bay could

9 For more information on the revised plan, see CRS Report RL34326, Apalachicola-
Chattahoochee-Flint (ACF) Drought: Federal Water Management Issues, coordinated by
Nicole T. Carter.)
10 Florida Department of Environmental Protection, About the Apalachicola National
Estuarine Research Reserve and Associated Areas, available at [http://www.dep.state.fl.us/
coastal/sites/apalachicola/info.htm] .
11 K. F. Drinkwater and K. T. Frank, “Effects of River Regulation and Diversion on Marine
Fish and Invertebrates,” Aquatic Conservation: Marine and Freshwater Ecosystems, vol.

4, no. 2 (1994), pp. 135-151.

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
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.13
Oysters. 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.14
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 geologic15
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

12 Army Corps of Engineers, Biological Assessment: Temporary Modifications to the Interim
Operating Plan for Jim Woodruff Dam and the Associated Releases to the Apalachicola
River, Document #CESAM-PD-E1, pp. 22, 24, available at [http://www.sam.usace.army.
mil/ACF%20W a t e r % 2 0 R e s o u r c e s % 2 0 M a nagement/ACFDr ought_Consultation2007/Fin
alBiologicalAssessment_1_Nov_2007.pdf]. This document was amended on November 7,
2007; the amendment is available at [http://www.sam.usace.army.mil/ACF%20Water
%20Resources%20Management/ACFD r o u gh t _ C o n s u l t a t i o n 2007/BA_Ame ndmentLetter

11_7_2007.pdf]. Hereafter the two documents are referred to as the BA and the amended BA.

13 Ron Word, “Apalachicola sues Corps over Chattahoochee,” Atlanta Journal-Constitution,
January 17, 2008. Available at [http://www.ajc.com/metro/content/metro/stories/2008/01/

17/apalachicola_0117.html ].

14 Apalachicola Bay Chamber of Commerce, at [http://www.apalachicolabay.org/
15 D. Twichell, “Habitat Mapping to Assess Health of Oyster Fishery in Apalachicola Bay,
Florida,” Sound Waves (USGS, June 2005).

freshwater inflow decreases16 — 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.”17
Apalachicola town officials asserted in their lawsuit that four oyster beds had died
due to high salinity.
Marine Commercial Fishing. In addition to oysters, important commercial
species include shrimp, blue crabs, and striped mullet. Blue crabs may migrate as
much as 300 miles to spawn in Apalachicola Bay, and the bay serves as a major
nursery for juvenile penaeid shrimp, blue crabs, and many fish (e.g., striped bass,
grouper, redfish, speckled trout, flounder, and various species of sturgeon). In
addition, Apalachicola Bay is a major forage area for offshore fish such as gag
grouper and gray snapper. In 2006, the total value of commercial fish landings at
Apalachicola, FL, was about $33 million.18
Marine Sport Fishing. Species that can be caught in the bay include spotted
seatrout, flounder, cobia, sheepshead, redfish, Spanish mackerel, pompano, speckled
trout, tripletail, black drum, whiting, bluefish, grouper, jack crevalle, snapper,
amberjack, king mackerel, and tarpon. Fish that spend their juvenile stages in
Apalachicola Bay waters include striped mullet, spotted seatrout, red drum,
flounders, and sharks. Most of these open ocean sport fish enter the bay primarily
for foraging. Changes in the estuarine environment could cause changes in the
distribution of these species, their prey, and their predators, to uncertain effect in the
complex exosystem.
Freshwater Sport Fishing. A total of 131 species of freshwater and
estuarine fish have been identified in the Apalachicola River, with 40 of these species19
found only in the lower tidal reaches of this river system. The Apalachicola River
has the only know reproducing Gulf population of striped bass. Southern stocks of20
this species tend to be primarily riverine and rarely undertake coastal migrations.
Important sport species in the lower river include largemouth bass, striped bass,
sunshine bass, white bass, and river bream (redbreast sunfish). In addition, speckled
trout and redfish move into the lower river during the winter, and young grouper and
snapper inhabit wetlands and marshes of the Apalachicola basin before moving into
marine waters. The Florida Fish and Wildlife Conservation Commission and FWS
annually stock striped bass and sunshine bass in the lower River.

16 R. E. Turner, “Will Lowering Estuarine Salinity Increase Gulf of Mexico Oyster
Landings?,” Estuaries and Coasts, vol. 29, no. 3 (June 2006), pp. 345-352.
17 Florida DEP November 8 letter, p. 2.
18 National Marine Fisheries Service, Fisheries of the United States 2006, p. 7.
19 Helen M. Light, Melanie R. Darst, and J. W. Grubbs, Aquatic Habitats in Relation to
River Flow in the Apalachicola River Floodplain, Florida, U.S. Geological Survey
Professional Paper 1594 (1998), p. 45.
20 U.S. Department of the Interior, Fish and Wildlife Service, Life History Requirements of
Selected Finfish and Shellfish in Mississippi Sound and Adjacent Areas, FWS/OBS-81/51
(March 1982), p. 51.

The Four Species: A Sturgeon and Three Mussels
A focal point of the debate on management of the ACF basin during drought has
been protection of four notably uncharismatic protected species: the threatened Gulf
sturgeon (Acipenser oxyrinchus desotoi), the endangered fat threeridge mussel
(Amblema neislerii), the threatened Chipola slabshell mussel (Elliptio chipolaensis),
and the threatened purple bankclimber mussel (Elliptoideus sloatianus). Water flow
rates, temperature, dissolved oxygen, and other aspects of water quality are important
to all four. The biology of each species is discussed below, along with the
conclusions of FWS in its 2007 Biological Opinion.
Consultation Under the Endangered Species Act
Under §7 of the ESA, federal agencies are obliged to consult with FWS when
their actions may affect listed species. The most recent formal consultations by the
Corps on ACF management took place in 2006 and 2007. FWS issued Biological
Opinions and Incidental Take Statements regarding the actions.
Consultation in 2006-2007
In March 2006, the Corps requested formal consultation with FWS on the
Interim Operating Procedure (IOP) of the Corps’ Jim Woodruff Dam on the Georgia-
Florida border; the Corps submitted a Biological Assessment (BA) on the IOP. (For
a brief description of earlier consultations, see CRS Report RL34326, Apalachicola-
Chattahoochee-Flint (ACF) Drought: Federal Water Management Issues.) FWS
responded with a Biological Opinion (BiOp), and included reasonable and prudent
measures (RPMs) to modify the IOP to reduce incidental take of listed species.
Among the five RPMs, one specified that the Corps develop a set of trigger points
(of the reservoir, climatic or hydrologic conditions, and species conditions) and water
management measures to take effect when drought conditions were reached. The
Corps submitted a revised BA on February 16, 2007. FWS issued a BiOp and
incidental take statement approving these changes to the IOP on February 28, 2007.
Among the conditions set in the 2006 IOP to protect listed species were these:
!Minimum flow in drought conditions: 5,000 cfs (cubic feet per
second) daily average, but 6,500 cfs daily average considered
!Maximum fall rate during drought conditions: 0.25 feet/day (i.e., the
height of the river to drop no more than 3 inches in the course of any
given day), but a lower rate considered desirable.
The first figure was intended to provide a certain minimum of available habitat. This
flow rate was chosen because no rate below 5,000 cfs had ever been recorded in the
Apalachicola River.21 The maximum fall rate was set to allow the sturgeon, and the

21 Fish and Wildlife Service, Biological Opinion and Conference Report on the U.S. Army
Corps of Engineers, Mobile District, Interim Operating for Jim Woodruff Dam, and the

very slowly moving mussels, some chance to relocate to more suitable habitat before
a given location dried out.
Consultation in 2007
As the drought continued, on November 1, 2007, the Corps proposed
Exceptional Drought Operations (EDO, amending the IOP) for the Jim Woodruff
Dam. It requested a new, expedited formal consultation with FWS concerning the
EDO’s effects on listed species, and submitted a new BA to FWS. In it, the Corps
proposed to reduce flows from the Jim Woodruff Dam still further:
!Minimum flow: 4,150 cfs (down from 5,000 cfs, and from the 6,500
cfs considered “desirable” in the previous IOP).
!Maintenance of the 0.25 ft/day maximum fall rate, until 4,200 cfs is
According to the Corps BA, “adverse impacts to listed species (especially the listed
mussel species) are reasonably certain to occur as flows on the Apalachicola River
drop below 5,000 cfs.”22 As noted previously, any flow below that rate would be less
than any previous record for the Apalachicola River. Among the issues mentioned
in the rationale for adopting EDO and its lower minimum flows was reducing “the
demand of storage in order to ... provide greater assurance of future ability to sustain
flows for listed species during a severe multi-year drought, as currently being
experienced in the ACF basin.”23 The result of the proposal was that the listed
species would face a reduced water flow this year to reduce risks in later years, if the
drought continues.24 The Corps requested a BiOp from FWS on an expedited basis,
and both agencies agreed to a goal of November 15, 2007 for a BiOp and the
associated Incidental Take Statement from FWS.
Commonly, when another agency (e.g., Forest Service, Environmental
Protection Agency) requests formal consultation with FWS, the other agency’s BA
may provide considerable information not only about its own project, but also about
the range, food, known distribution, laboratory studies, etc., of the species in
question, and that information is site-specific. While the Corps BA included
relatively little new information about the listed species (e.g., distribution changes

21 (...continued)
Associated Releases to the Apalachicola River, September 5, 2006, p. 11. Available at
[ h t t p : / / www.f ws.go v/ sout heast / d r ought / J WDIOP_BO_FINAL_cor r ect ed9-22-06.pdf ] .
22 BA, p. 6.
23 BA, p. 6.
24 While this tradeoff in time — some risk now, to lower a species’ risk later — is not
especially common in the consultation process, it has occurred before (e.g., spotted owls and
the Northwest Forest Plan). On the other hand, tradeoffs in general are very common in the
consultation process. Examples would include direct habitat protection (less in one area,
more acquired in another); greater intrusion before or after a nesting season and less
intrusion during it; more public access if access is more carefully controlled, etc. At issue
with the listed ACF species is not a tradeoff per se, but the degree to which the current likely
harm is balanced by potential future benefits.

since implementation of the IOP in fall 2006), the BA did provide data concerning
the effects of its operations to date on water quality. Among other things, the Corps
BA stated that under the IOP as it stood then,
impairments [due to point and non-point source pollution] identified include
turbidity, coliforms, total suspended solids, dissolved oxygen (DO), biology, and
unionized ammonia.... We lack sufficient information to determine if
implementation of the IOP has altered the baseline water quality of the action
area. However, we recognize that the extraordinary drought conditions ... have
resulted in salinity changes in Apalachicola Bay and increased temperatures and
associated localized dissolved oxygen changes due to extended periods of low25
flow (approximately 5,000 cfs).
And, after acknowledging that the Corps does not have data on water temperature or
dissolved oxygen levels, the Corps BA further noted:
However, observations made by USFWS field personnel this summer, indicate
that mussels found in isolated pools or shallow slack water habitats are showing
signs of stress or mortality likely due to high temperatures and low DO
[dissolved oxygen]. Significant reductions in river flow below 5,000 cfs would
likely exacerbate the temperature and DO conditions observed this year; as well26
as substantially increase the risk of stranding aquatic organisms.
The FWS decision concerning jeopardy appeared to turn on whether to trade rather
likely immediate harm (below then-current levels) to the four species (and especially
the mussels) to avoid a risk of still greater future harm.
While agencies are required under § 7(a) (16 U.S.C. 1536(a)) to “utilize their
authorities in furtherance of the purposes of [ESA],” FWS cannot require an action
to save a listed species that is outside of that agency’s authorities. Thus, while some
might argue that reasonable and prudent alternatives (RPAs; see Appendix A) in the
ACF basin could (or should) include water conservation measures (e.g., improving
irrigation practices, restricting outdoor watering, changing commercial or residential
building codes to improve water conservation, increasing water rates to fund
municipal water conservation projects, etc.), FWS did not require that the Corps
undertake these tasks because the Corps has no authority to implement them.27 Only
those choices legally open to the Corps were considered.

25 Corps BA, p. 21.
26 Ibid., p. 22.
27 However, the Corps would not have been prevented from volunteering such an option, if
it had found partners willing to cooperate in the effort. In the Platte River Recovery Plan,
for example, the Bureau of Reclamation consulted with FWS about a project; its partners
— Colorado, Wyoming, and Nebraska — pledged to fund (with cash or payments in kind)
a program of habitat improvement (including purchase of land from willing sellers),
improved water flow, and adaptive management. The program provides $317 million over
13 years, with the Bureau responsible for half. FWS could not have required the states to
participate, but took their efforts into account in issuing a finding of no jeopardy. (Personal
communication between Lynne Corn and Mark Butler, FWS Denver Regional Office,
November 6, 2007.)

FWS had the option of concluding that there was no way to carry out the change
without jeopardizing the species or adversely modifying critical habitat. Such
decisions are extremely rare (and often referred to as the “nuclear option”), and
would have left the Corps with three choices: (a) facing a citizen suit if it proceeded,
(b) choosing not to carry out the modification, or (c) considering asking for a formal
exemption under §7 (16 U.S.C. § 1536(e)-(p); see Appendix A). FWS did not select
this option.
On November 7, 2007, the Corps amended its BA to take into account new data
it had received from FWS indicating that a greater level of harm to the fat threeridge28
mussel could result from a reduction to 4,150 cfs than was previously thought. It
therefore proposed to reduce flows in increments — first to 4,750 cfs, then 4,500 cfs,
and finally the target of 4,150 cfs. The Corps’ letter also stated that it would consult
with FWS on the triggers and conditions that would allow it to make the incremental
reductions. It stated the Corps’ understanding “based on review of the new mussel
and modeling data and consultation with your [FWS] office, that this amendment will
result in less adverse impacts” to the listed species and their designated or proposed
critical habitat.
Biological Opinion and Species Analysis. In the BiOp issued November
15, 2007, regarding the Corps’ action, FWS analyzed the effects of the proposed
action on each of the four listed species. Its conclusions are described in detail
below, but overall, FWS concluded that the EDO would not appreciably affect the
survival and recovery of the Gulf sturgeon and would not appreciably affect the
ability of its designated critical habitat to provide its intended conservation role for
Gulf sturgeon in the wild.29 In addition, FWS concluded that for the fat threeridge,
Chipola slabshell, and purple bankclimber mussels, the Corps’ EDO would have a
measurable — but not appreciable — impact on survival and recovery. While critical
habitat primary constituent elements30 for these mussel species may be adversely
affected by reducing minimum releases to 4,500 cfs, FWS did not anticipate that this
adverse affect would alter or affect the critical habitat in the Action Area to the extent
that it would appreciably diminish the habitat’s capability to provide the intended
conservation role for these mussels in the wild.31 Triggers for incremental reduction
would have to be supplied to FWS in order to make additional reductions.

28 Letter from Corps to FWS Field Office in Panama City, FL, to amend BA of November

1, 2007, at [http://www.sam.usace.army.mil/ACF%20Water%20Resources%

20Management/ACFDrought_Consultation2007/BA_Ame ndmentLetter11_7_2007.pdf].

29 However, FWS does not state that no harm would come to these four species. Rather, it
concludes that the Corps’ action would not be sufficient to jeopardize the continued
existence of the four species, provided that certain reasonable and prudent alternatives are
carried out. Any future consultation on ACF management would occur in light of a pre-
existing harm that, if not appreciable, was still measurable according to the BiOp.
30 On the same day that the BiOp was released, FWS published the final rule for critical
habitat designation for the three mussels, but the BiOp generally refers to their critical
habitat as proposed rather than designated. See 72 Federal Register 64286; November 15,


31 BiOp, p. 56-58.

Gulf Sturgeon: Biology and BiOp. The threatened Gulf sturgeon once
spawned in streams and rivers throughout the northeastern Gulf of Mexico, and it
still does, though its distribution in the rivers has changed. (See Figure 1 for historic
and current sturgeon habitat.) In the ACF system, it once occupied 636 river miles,
well into the higher portions of the basin.32 Spawning is thought to occur in deep
waters of remaining habitat. The Gulf sturgeon are anadromous, migrating upriver
from the Gulf of Mexico in the springtime to spawn near the headwater of rivers, in
areas with coarse substrates (rocks, sand, or gravel, rather than mud). The fish then
spend the summer in the mid- to lower river before migrating back into the Gulf of
Mexico. Adult Gulf sturgeon seldom feed while in rivers, instead using stored
nutrients to supply energy needed for spawning.33 Adults feed once they return to
estuaries or the Gulf of Mexico. Once the eggs hatch, young fish remain in the river,
probably for a few months. They are a very long-lived species: females mature at
about 8-12 years, and males at 7-10 years. Adult length can exceed 6 feet. In
addition to the fish flesh itself, the fish were prized for caviar. Major limiting factors
for the population include barriers (dams) to historical spawning habitats, loss of
habitat, poor water quality, and overfishing.34
A series of dams gradually reduced spawning habitat in the ACF basin. With
construction of the Jim Woodruff Dam, spawning habitat was confined to the 107
miles below the dam. This remaining accessible portion of the ACF basin is
considered a major fraction of the species’ spawning habitat. A century ago, the ACF
system supported a major commercial fishery on Gulf sturgeon, but by the time of its
listing in 1991, FWS and NMFS stated, “Any additional decline in this population
could result in its extirpation.”35 Critical habitat was designated on March 19, 2003,
and took effect one month later; the designated critical habitat encompasses several
rivers and estuaries along the Gulf coast from Florida to Louisiana, including the
Apalachicola River.
The effects of a reduction to 4,500 cfs on the listed species are outlined in the
BiOp (pp. 39-48). Sturgeon spawning habitat is highly dependent on the proper
water depth; the EDO would cause a drop from the current 13 acres of suitable
spawning habitat to 10 to 12 acres. The reduction was judged “probably not
significant,” but the BiOp noted a paucity of data.

32 56 Federal Register 49655, September 30, 1991.
33 U.S. Department of the Interior, Geological Survey (USGS), Gulf Sturgeon Facts,
available at [http://cars.er.usgs.gov/ Marine_Studies/Sturgeon_FAQs/sturgeon_faqs.html].
34 U.S. Department of Commerce, National Marine Fisheries Service, Gulf Sturgeon
Recovery/Management Plan, available at [http://www.nmfs.noaa.gov/pr/pdfs/recovery/
35 56 Federal Register 49655, September 30, 1991.

Figure 1. Critical Habitat and Historic Range of Gulf Sturgeon in ACF Basin

Source: FWS Field Office, Panama City, Florida; slightly modified by CRS for clarity in monochrome.

The Mussels: Biology and BiOp. The endangered fat threeridge mussel,
the threatened purple bankclimber, and the threatened Chipola slabshell live in the
sand and gravel bottoms of streams and rivers. Larvae of these mussels are parasites
on the gills and fins of freshwater fishes (e.g., darters, minnows, and bass), using
these host fish for dispersal and causing them little or no harm. All three mussels
require good water quality, stable stream channels, and flowing water. Major
limiting factors include manmade structures (e.g., dams and channel alterations) that
destroy free-flowing water habitats and restrict the three species and their hosts from
dispersing, resulting in small, isolated populations. The three species are also
threatened by point and nonpoint source pollution, such as runoff containing36
fertilizers, herbicides, and pesticides from various land-use practices. The mussels
usually move very little, but a muscular “foot” helps them burrow and allows slow
and limited movement if they are disturbed by floods or droughts. All three species
were listed on March 16, 1998. Critical habitat was designated for them on37
November 15, 2007; the designation took effect on December 17, 2007.
For all three mussels, the BiOp reported that mortality increases with low water
levels and decreases with higher levels and cooler temperatures. Mussels commonly
move downslope within the river channel as waters recede, but may encounter
problems during their slow progress. For example, if they arrive at an area that has
had too high a flow rate in the past, they may find a river bottom that is scoured and
has a substrate too coarse to be suitable for mussels. If they reach an area with a very
low flow rate, they may become smothered with silt or overheated. As a result, their
preferred habitats in a river can be very patchy, with high populations in favorable
areas and low populations in the intervening areas. In addition, mussels may become
stranded in isolated pools as water levels fall; oxygen in the isolated pools may drop
to fatal levels. Once stranded, they are unable to escape and may die unless waters
rise in time. Effects on the individual species are discussed below.
Fat Threeridge Mussel. This species was found historically in the
Apalachicola, Flint, and Chipola Rivers. (See Figure 2 for historic and current
distribution of fat threeridge mussel.) The species has never been found in the
Chattahoochee River. It is no longer found in the Flint River and occurs only in the
lowest portion of the Chipola River. Siltation above dams may have contributed to
their loss in higher parts of the river basin. While the fat threeridge mussel is found
over a large portion of the Apalachicola River, over half the population is found
between River Miles 40 and 50, even though that stretch is much less than half the
species’ range. Population densities in this portion of the river range from 5 to 77
times the densities in any other part of the river.38 Because the river margins in this
concentrated area are relatively flat, a small drop in water level exposes large
amounts of habitat. The EDO would cause suitable habitat to drop from 74 to 55
acres in this critical stretch. The mussels may respond by moving downslope. But

36 U.S. Department of the Interior, Fish and Wildlife Service, Endangered and Threatened
Mussels in the Apalachicola-Chattahoocheee-Flint Basin, available at [http://www.fws.gov/
southeast/october07/ Mussels-FactSheet-ACFBasin.pdf].
37 72 Federal Register 64286, November 15, 2007.
38 BiOp, p. 42.

deeper unoccupied habitat is subject to higher water velocities, which result in
scouring and a coarser substrate, rather than the silt and clay substrate the species
seems to prefer. Higher spring flows could wash away mussels, perhaps killing them
outright, or depositing them in unsuitable habitat. By analogy with studies on closely
related (and better studied) species, FWS concluded in the November 2007 BiOp that
the species could decline as much as 30% between 2006 and 2008.39
Purple Bankclimber. The purple bankclimber is a large mussel, once found
widely in the ACF basin, plus the Ochlocknee River (FL and GA). (See Figure 3 for
historic and current distribution of purple bankclimber.) It has nearly disappeared
in the Chattahoochee and Chipola Rivers, and is now rare in the Flint River. The
purple bankclimber is found primarily at two sites in the Apalachicola River, though
a few animals are found elsewhere. One site, at River Mile 105, is a limestone shoal,
and the species is found among jagged rocks at this site. Movement down this
surface as water recedes would be problematic. At the second site, bankclimbers are
found at various depths in a sandy substrate. FWS found that “decreasing the water
levels further will harm some fraction of the bankclimber at the [limestone] site, but
we can not determine the size of that fraction from the information we have.”40
Chipola Slabshell. The Chipola slabshell was historically found only in the
Chipola River, its headwater streams, and one creek that joins the lower
Apalachicola. It is now gone from that creek, and appears to be gone from Dead
Lake on the mainstem of the Chipola. Six subpopulations remain, all in the Chipola
River. (See Figure 4 for historic and current distribution of the Chipola slabshell.)
The BiOp expects the EDO to affect only a small fraction of the population, primarily
because the affected portion of the Chipola River, where the mussel lives, represents
only the lower end of the species’ distribution. The higher parts of its range would
not be affected by the lowered flows.
No Long-Term Analysis Provided, or Expected. As noted in these
individual species analyses, FWS commented that a lack of data prohibited drawing
long-term conclusions about effects of the EDO. To that end, it limited its opinion
to a period of only a few months. Moreover, it did not determine a minimum flow
that would avoid jeopardy indefinitely into the future; it would be surprising if it had.
Not only does FWS lack sufficient data to predict confidently the effects of such a
change in flow over the long term, it also lacks sufficient information to determine
what other factors might change in the species’ habitat. For instance, if water flows
remained low, but all communities and industries in the basin were to improve their
pollution levels markedly, might the species tolerate an even lower flow, in light of
this improvement? What would happen if pollution were to increase? Or if all farms
planted shade trees along all tributaries, thereby lowering water temperatures, would
that favor mussel populations? What if existing trees were removed, or if paved
surfaces increased, and together raised water temperatures? Such complexities make
long term analyses very difficult. (See “What Does a Species Need?” below.)

39 No studies were found to demonstrate whether the projected decline has occurred or not.
40 BiOp, p. 42.

Figure 2. Current Range and Additional Range of Fat Threeridge in ACF Basin

Source: FWS Field Office, Panama City, Florida; slightly modified by CRS for clarity in monochrome.

Figure 3. Current and Additional Range of Purple Bankclimber in ACF Basin

Source: FWS Field Office, Panama City, Florida; slightly modified by CRS for clarity in monochrome.

Figure 4. Current and Historic Range of Chipola Slabshell in ACF Basin

Source: FWS Field Office, Panama City, Florida; slightly modified by CRS for clarity in monochrome.

Incidental Take Statement and Reasonable and Prudent Measures.
In issuing the Incidental Take Statement (ITS) on November 15, 2007, FWS limited
duration of the ITS to June 1, 2008, and to a reduction to 4,750 cfs in an initial stage,
to be followed by a reduction to not less than 4,500 cfs and then to 4,150 cfs.41 The
ITS in the Amended BiOp included non-discretionary measures to determine the
appropriate triggers for these incremental reductions. It directed that the Mobile
District Corps insure that the measures become binding conditions of any contract
or permit issued to carry out the EDO. Mandatory terms and conditions were
attached to the ITS to ensure that the ITS provisions are implemented. These terms
and conditions included reporting requirements, monitoring, and assuming
responsibility for certain studies, among other things. These studies include
measurements of take of the listed species resulting from lower flows, changes in
mussel distribution, and life history studies to provide better information to inform
future decisions. The ITS also warned that failure to carry out the terms and42
conditions could invalidate the ITS.
In addition to mandatory terms and conditions, the ITS also made discretionary
recommendations to the Corps. Among other things, the ITS recommended that the
Corps work with states and other stakeholders to reduce water depletions to the ACF
basin, particularly in the Flint River; its examples included incentives to reduce
agricultural demands. It also recommended that the Corps, with other stakeholders,
“evaluate ways to ensure that listed mussel mortality due to low flows does not43
become a chronic or annual source of mortality.”
Consultation in 2008
On April 15, 2008, the Corps submitted its Revised Interim Operating Plan
(RIOP) to FWS for consultation, thus eliminating the temporary EDO by
incorporating elements of the EDO and other changes into the RIOP.44 It is generally
more complicated than previous plans, but on the whole allows for more water
retention in the upper basin. The RIOP proposal includes provisions to store
additional water during the winter and during drought periods and to release more
during spawning periods. The intent is to avoid storage reaching levels that would
trigger the lowering of the Apalachicola River minimum flows from 5,000 cfs to
4,500 cfs. The Corps proposal is to store 50% of basin inflow, instead of 30%; this
would 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. Key changes resulting from
the RIOP include

41 Amended BiOp, p. 58.
42 Amended BiOp, pp. 58-59.
43 Amended BiOp, p. 64.
44 U.S. Army Corps of Engineers. Description of Proposed Action: Modification of Interim
Operations Plan at Jim Woodruff Dam. April 15, 2008. Available at [http://www.fws.gov/
southeast/drought/ProposedActionDescription-ModificationIOP.pdf]. Hereafter referred to
as RIOP.

!change in the protocol to determine the minimum discharge from
Woodruff Dam. In times of low inflow45 that is still above 5,000 cfs,
amounts above 5,000 cfs would be released below Woodruff Dam.
If basin inflow is below 5,000 cfs, then 5,000 cfs would be released
anyway. However, if storage of water dipped to drought levels, then
water release could fall to 4,500 cfs.
!suspension of requirements for a maximum fall rate (0.25 ft/day) if
water storage drops to a specified level and the Corps is operating
under a drought plan.
Conclusions of the BiOp. FWS issued its most recent BiOp on June 1,

2008.46 FWS concludes that the RIOP would not jeopardize the four listed species,

nor would it adversely modify their critical habitat. It stated (p. 174):
Generally, it appears that the Corps would store water more often under the
RIOP (about 9% more often) than has occurred historically, which means that the
river would have less water about 9% of the time. The RIOP uses this stored
water to maintain a minimum flow of 5,000 cfs, but the frequency of flows less
than 10,000 cfs is increased by about 5%.
As is the case in other consultations, FWS compared the effects of the proposed
action to the effects that would occur on the listed species if the proposed action were
not taken. Thus, a conclusion of “no added harm” for the four species cannot be
interpreted as “no harm” to the species. In general, FWS concluded that, with certain
reasonable and prudent measures (mandatory under the terms of the new ITS), neither
jeopardy nor destruction or adverse modification of designated critical habitat would
occur. In its conclusions, FWS focused primarily on those periods when flows below
Woodruff Dam would be at or below 5,000 cfs. Because the RIOP would apply until
a new water control plan is adopted in two to five years, the BiOp would apply until
June 1, 2013, or until the RIOP is amended or superseded by a new proposed action.
The effects of the RIOP on each of the four species is discussed below, followed by
a discussion of effects on other species in the Apalachicola River and Bay.
For the Gulf sturgeon, FWS concluded that the RIOP “may have a moderate
beneficial effect by decreasing the maximum number of consecutive days/year less
than 16,000 cfs.... However, future depletions to basin inflow from non-project
related water uses might further change sturgeon estuarine habitats by increasing the
duration of flows less than 16,000 cfs during drought years” (2008 BiOp, p. 175).
For the fat threeridge mussel, FWS commented on the effects of more frequent
periods of low inflow (below 5,000 cfs, a level which had not been reported before

45 Inflow is the unimpaired runoff into the basin, minus the consumptive uses that might
occur above a reservoir. The use of inflow into reservoirs, rather than unimpaired runoff
into the basin, to guide operations is contentious because of the exclusion of consumptive
uses, such as irrigation in the Flint River sub-basin above Lake Seminole.
46 U.S. Fish and Wildlife Service. Biological Opinion on the U.S. Army Corps of Engineers,
Mobile District, Revised Interim Operating Plan for Jim Woodruff Dam and the Associated
Releases to the Apalachicola River. Panama City Field Office, FL. 211 p. Hereafter
referred to as the 2008 BiOp.

the creation of Lake Lanier) into the basin would be about 7.3% of the time under
current estimated water demands throughout the basin, and 8.3% of the time if
municipal and industrial demands increase by 27%. Under the RIOP, while
additional releases upstream would be triggered to maintain 5,000 cfs downstream
at Woodruff Dam, if inflow (not unimpaired runoff; see above) fell below 5,000, then
the RIOP’s minimum inflow provision would be triggered, which would lower the
releases below Woodruff Dam to 4,500 cfs (2008BiOp, p. 176). “We anticipate a
take of not more than 21,000 fat threeridge (9% of the population) if the 4,500 cfs
minimum release is triggered” (2008 BiOp, p. 176). Continuing, FWS concluded
that the RIOP would have a measurable but not appreciable impact on this species,
if flows fall to 4,500 cfs. It expected that drop to occur once in the next five years.
The purple bankclimber tends to occur more commonly in deeper water than the
fat threeridge. FWS concluded that, while there is evidence that the species is
declining throughout its range, they anticipated a take of about 200 animals if flows
fell to 4,500 cfs. Because of the species’ preference for deeper water, and given
models suggesting that the lower flow would occur only about once in the next five
years, FWS concluded that critical habitat would not be adversely modified.
The Chipola slabshell is found in the Chipola River, a tributary of the lower
Apalachicola River (Figure 4), and FWS reported discoveries of 12 new
subpopulations with many individuals. It concluded that the species is now
improving rangewide. FWS further concluded that the changes in the mainstem of
the Apalachicola, and a reduction to 4,500 cfs in the main river, might lead to a take
of about 2% of the population. It found that this level of additional take would not
jeopardize the species, or destroy or adversely modify its designated critical habitat.
Reasonable and prudent measures to implement the ITS were also given by
FWS. These mandatory measures included additional monitoring and evaluation of
other strategies for reducing fall rates, especially during sturgeon spawning season
from March to May. In addition, and after consulting appropriate water resource and
management agencies, the Corps was to:
provide the Service by June 1, 2009, an evaluation of methods to estimate total
surface water flow of the basin to Woodruff Dam by accounting for depletions
to basin inflow. The goal of this evaluation is to outline the steps whereby the
Corps may integrate up-to-date estimates of water depletions into its monthly47
operational decisions.
FWS made recommendations to the Corps as well. These recommendations are
discretionary, and included efforts to work with stakeholders to reduce depletions in
the ACF, especially in the Flint River; assistance for stakeholders in plans to reduce
water consumption; additional monitoring, education, and research; and other
Effects on Other Species. Change in salinity is one of the more likely
features to have observable effects on species of economic importance in
Apalachicola Bay. High flows and runoff from the Apalachicola River to

47 2008 BiOp, p. 185.

Apalachicola Bay dilute saltwater and reduce estuarine salinity, providing nursery
habitat for many marine species with early life stages that are intolerant of high
salinity, and preventing the permanent intrusion of marine predators, such as oyster
drills, that are intolerant of low salinity. Freshwater flow from the Apalachicola
River into Apalachicola Bay, as modified by winds, tides, and local rainfall runoff,
regulates the bay’s salinity and likely influences the amount of habitat available.48
The June 1, 2008, BiOp notes that extended duration of high salinity in the estuarine
environment is ecologically significant, because aquatic organisms widely differ in
their salinity tolerance. More variable salinity favors those with the widest tolerance,
and less variable salinity favors those with narrower tolerance.49
The Eastern oyster (Crassostrea virginica) is the commercial species of primary
concern in considering effects of the RIOP because it is sedentary, is affected by
changes in salinity, and has considerable economic value. Oysters grow and
reproduce optimally at intermediate salinities; prolonged exposure to freshwater
inhibits oyster growth, while higher salinity waters harbor marine predators and
correlate with an increased susceptibility of oysters to the potentially lethal parasite
Perkinsus marinus (commonly referred to as “dermo”).50 Within Apalachicola Bay,
highest oyster densities and overall growth occur in the vicinity of the confluence of
high salinity water moving westward from St. George Sound and river-dominated
(lower salinity) water moving south and eastward from East Bay. High salinity
(proximity of an oyster bar to entry points of saline Gulf water into the bay) and
relatively low-velocity currents are important factors contributing to increased oyster
mortality. River flow reduction, whether through drought or increased upstream use,
could have serious adverse consequences for oyster populations.51
A benthic survey of Apalachicola Bay conducted by the Florida Department of
Environmental Protection found that polychaetes, bivalves, gastropods, and
amphipods dominated the total abundance of this community.52 How this fauna
might respond to changes in freshwater inflow is not well known. As noted above,
the more sedentary species would likely be more detrimentally affected, while some
of the more mobile species might move to more acceptable habitat, though increased
competition for resources in these areas could result until populations stabilize at a
new level.
Thus far in 2008, investigations of Apalachicola Bay and the lower Apalachicola
River indicate conditions similar to 2007, with record duration of low flows, yielding

48 R.J. Livingston, The Ecology of the Apalachicola Bay System: an Estuarine Profile,. U.S.
Fish and Wildlife Service, USFWS/OBS-82/05 (1984).
49 2008 BiOp, p. 83.
50 Summary of literature in S. Gregory Tolley, Aswani K. Volety, and Michael Savarese,
“Influence of Salinity on the Habitat Use of Oyster Reefs in Three Southwest Florida
Estuaries,” Journal of Shellfish Research, v. 24, no. 1 (2005): 127-137.
51 R. J. Livingston, et al., “Modelling Oyster Population Response to Variation in Freshwater
Input,” Estuarine, Coastal, and Shelf Science, v. 50 (2000): 655-672.
52 Florida Department of Environmental Protection, NOAA Coastal Service Center, and R.J.
Diaz, Draft Apalachicola Bay Benthic Mapping Project Data Report (2000), 58 p.

conditions similar to an exceptional drought. Salinities are higher in most areas of
Apalachicola Bay and the lower Apalachicola River, with observed oyster dieoffs
from both predators and disease (e.g., dermo) and low oyster spat survival; reduced
density of submerged aquatic vegetation in estuarine marshes; lower white shrimp
and flounder abundance; encroachment of marine sea grasses, marine pelagic fish,
and stony corals further into the bay; and occurrence of more estuarine salt water
species higher into freshwater tributaries.53
The June 1, 2008, BiOp notes that, although two species of sea turtles and the
West Indian manatee may sometimes occur in Apalachicola Bay or the lower
Apalachicola River, any effects of the proposed action on these species would likely
be insignificant, due to their low numbers and only occasional seasonal residence in
the river and bay.54
Consistency with Previous Court Decisions. The 2008 BiOp does not
appear to contradict court decisions pertaining to the ACF. The only court to have
addressed the Corps’ ACF programs in the context of a BiOp is the Northern District
of Alabama. In that case the State of Florida sought to enjoin the Corps’ plan to
release only 5,000 cfs of water, arguing that the reduced water flow harmed species
listed under the ESA. The court held that “even assuming the loss of any mussels
qualifies as a take, Florida has not established the necessary causal link between the
actions of the Corps and the harm to the mussels,” indicating that the drought, not the55
Corps, was causing the water shortage. That decision did not address future actions
by the Corps or the FWS and this BiOp does not appear inconsistent with that56
The underlying agency action reviewed in the 2008 BiOp does not appear to be
at odds with the recent decision from the D.C. Circuit Court of Appeals. The D.C.57
Circuit Court held that, pursuant to the Water Supply Act, the Corps lacked
congressional authority to enter into the Lake Lanier storage contracts in a 200358
agreement with the State of Georgia and other parties. The disputed contracts had
not become effective and therefore have not affected operations to date.
The disputed contracts called for reallocation of storage space, not the delivery
of a specific quantity of water, from other uses to municipal and industrial water
supply. It is unclear from available information whether a reallocation of space to

53 Communication with Theodore S. Hoehn, biologist, Florida Fish and Wildlife
Conservation Commission, Tallahassee, FL, (850) 410-0656, ext. 17336, on July 2, 2008.
54 2008 BiOp, p. 2.
55 Alabama v. Army Corps of Engineers, 441 F. Supp. 2d 1123, 1134 (N.D. Ala. July 25,


56 Florida has filed suit challenging an earlier BiOp by FWS that found the Corps’ water
allocation did not jeopardize the continued existence of ESA-listed mussels. No ruling has
been made. Florida v. Fish and Wildlife Service, 4:06W410-RH/WCS (N.D. Fla. Sept. 6,


57 43 U.S.C. § 390b(d).
58 Southeastern Federal Power Customers v. Geren, No. 06-5080 (D.C. Cir. Feb. 5, 2008).

a water supply would change the quantity stored. For instance, differences in the
timing of releases from Lake Lanier for in-stream hydropower uses and releases for
off-stream, consumptive municipal uses potentially could affect the stored volume,
as well as in-stream flows, at a particular time. The BA and its BiOp describe an
operational regime that evaluates both the volume of stored water and basin inflow
to determine releases at Woodruff Dam. However, the flow amounts from the Jim
Woodruff Dam, which are the agency action underlying the BiOp, are not influenced
by the storage capacity in the Lake Lanier reservoir, but are based on basin inflow
What Does a Species Need?
The question of what a species needs is often asked by many parties in any ESA
debate — to the frustration of both the questioners and the biologists trying to
respond. How many big trees does a spotted owl need; how pure does the water need
to be to restore a run of chinook salmon; and how much water flow do mussels in the
ACF system need? The answers to such questions depend on some factors that are
obvious, though the details may differ from case to case:
!Is the minimum in question a feature that affects a species at a
critical portion of its life cycle (e.g., calving)?
!Is the species also threatened by incidental take in the course of other
human activities (e.g., fishery bycatch)?
!Are invasive species competing with the species?
!Are diseases, particularly newly introduced diseases, weakening the
species’ ability to withstand stress?
These and similar questions are a common feature of BiOps, or any other analysis of
species and threats to their welfare, whether for examining ESA issues (listing,
consultation, Habitat Conservation Plans, etc.), or for state or local conservation
matters. These sorts of questions are the most obvious reason why FWS biologists
are reluctant to pick out a single feature, such as cubic feet of water per second in a
river, and state that this particular hard number is what the species needs for all time.
But a more subtle issue also arises, and it is often less clearly stated than the
previous questions: to what end is the species being managed? In ESA terms, how
far down the road to recovery does a recovered species have to travel to be
considered recovered? The probability of a population surviving over a particular
period is usually chosen as the standard of recovery: 10% chance of becoming extinct
in the next 50 years, 15% in the next 100 years, 1% chance in the 100 years, etc. The
stronger the probability and the greater the desired time span, the more caution is
required in a species’ management. However, these probabilities (analyses of the
viability of a population) are difficult to calculate and hard to defend: FWS and
NMFS have set no generally agreed standard of recovery to be applied across the
board to all species.
While it may seem esoteric, this choice of a recovery standard has major
consequences over a long span of time. Ecologist Daniel Goodman of Montana State
University offered an interesting analysis of this problem:

We might date the beginning of civilization to 5,000 years ago, when the Upper
and Lower Kingdoms of Egypt were united. Imagine that, at that time, a global
policy had been adopted of managing the environment to a standard of 15%
probability of extinction within 100 years for all mammalian species. How many
mammal species would be left on earth now? The starting number of species
would have been about 4,400. Compounding the 15% probability per 100 years
over the 5,000 years gives a probability of about 0.0003 [0.03%, or 3 chances in
10,000] per species, of surviving to the present. If the extinction dynamics of all
the respective species were independent, the probability of no mammals
remaining would be 27%; the probability of more than three species remaining
would be about 4%. This doesn’t sound very good. Our preferred vision of
managing the environment for posterity obviously entails very low probabilities59
of extinction over large time spans.
In the ACF context, there is no river flow that would guarantee that any of the
listed species would last another 5,000 years, if only because the species could go
extinct for other reasons. More practically, though, if a guarantee is impossible, how
much of a risk is acceptable? Is a prolonged flow of 5,000 cfs sufficient for one of
the mussels to have at most a 1% chance of extinction in the next decade? Century?
Millennium? If the flow is lowered still further, how much greater does the risk to
the species become, and is that level of risk acceptable? If a higher risk is tolerated,
a lower flow could be acceptable; if only a low risk of extinction is acceptable, then
higher flows would be desirable.
In the ACF context, instead of setting itself the difficult or impossible task of
determining the minimum flow necessary for the various species, FWS instead
accepted the far more specific task of determining whether any one plan offers
sufficient flows to avoid jeopardy to the species. It is noteworthy that in the ACF
case, FWS limited its opinion to a specific period of months, not years, and further
requested additional studies and data from the Corps. Only then does FWS,
presumably with more data in hand, plan to address the risks from any further
cutbacks in flows.

59 Daniel Goodman, “Predicting Bayesian Population Viability Analysis: A Logic for Listing
Criteria, Delisting Criteria, and Recovery Plans,” in Steven R. Beissinger and Dale R.
McCullough, eds., Population Viability Analysis (Chicago: University of Chicago Press,

2002), p. 447.

Appendix A.
How the Endangered Species Act Works:
Under the ESA (16 U.S.C. § 1531), the taking of species listed as endangered
or threatened is prohibited. Taking is broadly defined and includes not only obvious
actions such as killing or trapping, but also harming. (See 50 C.F.R § 17.3 for a
definition of harm.) In addition, under § 7(a)(2) (16 U.S.C. § 1536(a)(2)), federal
agencies must insure that their actions are not likely to jeopardize the continued
existence of any listed species or result in the destruction or adverse modification of
designated critical habitat. To that end, they must consult with FWS. The
consultation process is described below, in simplified form.60
Federal agencies must consult with FWS on “any action authorized, funded, or
carried out by such agency” if that action may harm a listed species or its critical
habitat (16 U.S.C. § 1536(a)(2)). If FWS advises the action agency that a listed
species, or one proposed for listing, may be present in the affected area, then the
action agency must conduct a Biological Assessment (BA) describing its proposed
action. According to FWS regulations, the purpose of the BA is to “evaluate the
potential effects of the action on listed and proposed species and designated and
proposed critical habitat and determine whether any such species or habitat are likely
to be adversely affected by the action ...” (50 C.F.R. § 402.12(A)). If, with the help
of information in the BA, formal consultation between the agency and FWS is
determined to be necessary, either because of potential taking of the species or effects
on critical habitat, the action agency submits a formal request for consultation. The
action agency must provide the best scientific data available regarding its action and
potential effects of the action on the species or its critical habitat. Once a request for
formal consultation is submitted, certain deadlines apply, but these may be extended
when additional information is needed (50 C.F.R. § 402.14).
The responsibilities of FWS during consultation are various but — notably in
the ACF context — include an evaluation of the effects of the action itself as well as
cumulative effects of the action. The evaluation is called a Biological Opinion
(BiOp) or, sometimes, a jeopardy opinion. Among other things, FWS must evaluate
whether the proposed action, “taken together with cumulative effects, is likely to
jeopardize the continued existence of the listed species or result in the destruction or
adverse modification of critical habitat” (50 C.F.R. § 402.14(g)). In forming the
BiOp, FWS first consults with the agency on the availability of “reasonable and
prudent alternatives (if a jeopardy opinion is to be issued) that the agency ... can take
to avoid violation of section 7(a)(2)” (50 C.F.R. § 402.14(g)). A reasonable and

60 The discussion below omits those species under the jurisdiction of the Department of
Commerce, since the mussels are under the jurisdiction of FWS, and while the two
departments share responsibility for the Gulf sturgeon, FWS has taken the lead in this
particular case. However, regulations concerning consultation apply to both agencies, and
their procedures do not differ substantively. The discussion also omits consultations that
agencies may carry out informally. For a more general overview of the ESA, see CRS
Report RL31654, The Endangered Species Act: A Primer, by M. Lynne Corn, Eugene H.
Buck, and Kristina Alexander.

prudent alternative (RPA) must be an action that can be “implemented in a manner
consistent with the intended purpose of the action, that can be implemented
consistent with the scope of the Federal agency’s legal authority and jurisdiction, that
is economically and technically feasible, and that the Director believes would avoid
the likelihood of jeopardizing the continued existence of listed species or resulting
in the destruction or adverse modification of critical habitat” (50 C.F.R. § 402.02).
Note that even if an alternative exists that might better fulfill the purpose of the
agency action and reduce risks to the species or to critical habitat, FWS may not
specify that alternative if it is not within the authority of the action agency. In some
instances, this limitation will mean that other solutions, perhaps more desirable from
an economical, biological, social, or other point of view, may not be considered,
simply because the action agency has no authority to implement those options.
The BiOp must include a summary of the information on which the decision is
based, and a “detailed discussion” of the effects of the action on the listed species or
critical habitat (50 C.F.R. § 402.14). It must also include the opinion on whether the
agency’s action:
(a) is not likely to jeopardize the continued existence of a listed species or result in
destruction or adverse modification of critical habitat (a no jeopardy opinion); or
(b) is likely to jeopardize the continued existence of a listed species or result in
destruction or adverse modification of critical habitat (a jeopardy opinion), and if so
(1) any RPAs would avoid jeopardy or adverse modification, or
(2) there are no RPAs; i.e., there appear to be no RPAs consistent with both
the agency’s proposed action and avoidance of jeopardy and/or adverse
If the FWS BiOp concludes that jeopardy is unlikely or that jeopardy could be
avoided with suitable RPAs, then along with the BiOp, it issues an incidental take
statement (ITS), describing the impact and any reasonable and prudent measures
(RPMs). RPMs are of a lesser nature than RPAs and are simply steps that FWS
believes necessary or appropriate for the action agency to minimize any incidental
take of the species. An RPM cannot alter the project in its major aspects, such as
duration, location, timing, etc. The ITS may include mandatory terms and conditions
for the action agency. These terms and conditions may include reporting
requirements, monitoring, scientific studies, etc.
If FWS issues a jeopardy opinion but cannot offer RPAs, then the action agency
has, fundamentally, two choices: to abandon the action, or to seek an exemption for
the action (not for the species) under the terms of § 7 (e)-(p) (16 U.S.C. § 1536 (e)-
(p)). In actual practice, jeopardy opinions without RPAs are exceedingly rare over
the history of the ESA.61 Among other drawbacks to the exemption process are (a)

61 For example, see U.S. General Accounting Office, Endangered Species Act: Types and

the exemption applicant must pay for mitigation; and (b) the burden of FWS to
recover the species is not terminated by the exemption and the burden of conserving
the species will likely fall more heavily on those places where the species is still
found. Over the history of the ESA, only three exemption applications have been
considered. One was granted; one was granted in part; and one was rejected. (See
CRS Report RL31654, The Endangered Species Act: A Primer.)
Other Options for Federal Agencies Under Section 7
The ESA offers three options to manage federal agency conflict like those in the
ACF basin: (1) additional consultation by the agency under § 7(b) (16 U.S.C. §
1536(b)) to determine if taking or adverse modification would result from the agency
action; (2) an attempt to invoke § 7(p) (16 U.S.C. § 1536(p)), involving exemptions
in presidentially declared disaster areas; and (3) an exemption for management of the
basin under § 7(e)-(p) (16 U.S.C. § 1536 (e)-(p)). The first option, discussed above,
is currently being pursued by the federal agencies. The other two options are outlined
briefly below, since they may be considered at some later time.
Dim Prospects Under the Disaster Provision. In § 7(p) (16 U.S.C. §
1536(p)), the ESA allows the President to make the determinations necessary for an
exemption to be granted in a presidentially declared major disaster area. However,
the President’s authority extends only to
the repair or replacement of a public facility substantially as it existed prior to the
disaster ... which the President determines (1) is necessary to prevent the
recurrence of such a natural disaster and to reduce the potential loss of human
life, and (2) to involve an emergency situation which does not allow the ordinary
procedures of this section to be followed.
This provision could be used for quick repair of a levee after a flood, for example.
Since, on several factual grounds, these features are not present in the ACF basin, this
provision offers apparently no solution in the ESA context, and no such presidential
declaration has occurred.
Georgia Disaster Declaration Request. On October 20, 2007, the
Governor of Georgia requested a presidential drought disaster declaration. The
likelihood of a presidential drought disaster declaration is unclear: the last
presidential disaster declaration for a drought in the continental United States was in
New Jersey in 1980.62 Instead, accessing federal resources for drought disasters
largely has been limited to agricultural assistance made available by disaster
declarations by the Secretary of Agriculture. Because of the ongoing drought
conditions and the severe freeze of April 2007, the U.S. Secretary of Agriculture
already has declared 48 of the 159 counties in Georgia disaster areas as of March 18,

61 (...continued)
Number of Implementing Actions, GAO/RCED-92-131BR, May 1992, pp. 30-32.
62 See [http://www.fema.gov/femaNews/disasterSearch.do]. There have been more recent
declarations for droughts in U.S. territories in the Pacific.

2008, making them eligible for U.S. Department of Agriculture Farm Service Agency
emergency disaster loans.63
An Outright Exemption: The Long Road. Were FWS to find no
reasonable and prudent alternatives to an agency’s action that would be consistent
with avoiding jeopardy to a species or adversely modifying its designated critical
habitat, it would issue a jeopardy opinion in the agency consultation. The federal
agency or a governor64 could ask for an exemption for the federal action (in this case,
the EDO). Under § 7 (16 U.S.C. § 1536(e)-(p)), a seven-member Endangered
Species Committee (usually called the “God Squad”) chaired by the Secretary of the
Interior is empowered to pronounce on an activity of regional or national
significance. This panel has been convened only three times in the history of the act.
In part because of the time involved, and the fact that the requestor must both
demonstrate that a variety of other options have been justifiably rejected and pay for
mitigation to balance the effects of the proposed action, this option has fallen out of
favor, and has not been used in the past 15 years. (For more on this option, see CRS
Report RL31654, The Endangered Species Act: A Primer.) It appears to be a
somewhat unlikely option, and appears not to have been mentioned in the current

63 For more information on this program, see CRS Report RS21212, Agricultural Disaster
Assistance, by Ralph M. Chite.
64 If there is a permit or license applicant involved, that person might also request an

Appendix B.
NEPA in the Context of the
Exceptional Drought Operations and ESA
Timing and Content
A factor in the Corps’ plan to release less water is whether an environmental
review document, such as an Environmental Assessment (EA) or an Environmental
Impact Statement (EIS), is required under the National Environmental Policy Act
(NEPA; 42 U.S.C §§ 4321 et seq.). NEPA requires federal agencies to comply with
its requirements “to the fullest extent possible.”65 However, NEPA does not require
any particular results, such as choosing the least harmful project. The U.S. Supreme
Court has said NEPA “merely prohibits uninformed — rather than unwise — agency
action.”66 Accordingly, where courts have found that agencies took a hard look at the
relevant areas of environmental impact and satisfied the other demands of §

4332(2)(C), the courts have upheld the NEPA process.

To comply with NEPA, the agency must show that the environmental review
informed the decisionmaking process. NEPA regulations promulgated by the
Council on Environmental Quality (CEQ) address the timing of an environmental
review. The regulations all require the environmental review before the agency
decision, indeed, as early as practical. A section discussing timing of environmental
reviews says:
An agency shall commence preparation of an environmental impact statement as
close as possible to the time the agency is developing or is presented with a
proposal (Sec. 1508.23) so that preparation can be completed in time for the final
statement to be included in any recommendation or report on the proposal. The
statement shall be prepared early enough so that it can serve practically as an
important contribution to the decisionmaking process and will not be used to67
rationalize or justify decisions already made.
Early in NEPA practice, the courts established that a NEPA review should occur
before an agency action was decided upon: “That the filing of an EIS should precede
rather than follow federal agency action has been consistently recognized by the
courts.”68 The Fifth Circuit described the harm in reversing the order:
Whenever an agency decision to act precedes issuance of its impact statement,
the danger arises that consideration of environmental factors will be pro forma
and that the statement will represent a post hoc rationalization of that decision.

65 42 U.S.C. § 4332. For a general discussion of NEPA, see CRS Report RS20621,
Overview of NEPA Requirements, by Kristina Alexander.
66 Robertson v. Methow Valley Citizens Council, 490 U.S. 332, 351 (1989).
67 40 C.F.R. § 1502.5.
68 Cady v. Morton, 527 F.2d 786, 794 (9th Cir. 1975).

NEPA was intended to incorporate environmental factors and variables into the69
decisional calculus at each stage of the process.
The courts agree that a NEPA review is intended to inform the decisionmaking
process. The Ninth Circuit addressed the timing of the environmental review in
relationship to the agency decision. It said the purpose of the review is to provide
“decisionmakers with an environmental disclosure sufficiently detailed to aid in the
substantive decision whether to proceed with the project in light of the environmental
consequences.”70 A reviewing court is likely to find that an agency failed to take a
hard look at the environmental consequences of its action when the decision on what
action to take predates the consideration of the environmental effects.
The contents of a NEPA document may also influence a court as to whether an
agency took a hard look at the environmental effects of the proposed action. The
regulations provide a general description of the contents. Environmental
Assessments (EAs) are intended to be concise, but are also required to consider the
need for the project, the environmental impacts of the project and its alternatives,
alternatives required by § 102(2)(E), and a list of the agencies and persons
consulted.71 The NEPA process should synchronize with the ESA consultation, even
though they are independent of each other. Section 7(c)(1) of ESA states that the
Biological Assessment prepared by the action agency “may be undertaken as part of”
the NEPA review. As the BA considers whether there are any endangered or
threatened species likely to be affected by the agency action, that evaluation ties
neatly with the review under NEPA to consider whether the action would have any
significant adverse environmental effects. Since both the NEPA review and the § 7
consultation must be completed before the agency makes its decision, there is no
timing issue in gathering the data for both purposes.
Emergency Exception
It has been suggested that because the Governor of Georgia declared a State of
Emergency related to the drought, NEPA could be waived. However, the statute
provides for no such unilateral waiver. NEPA emergency provisions are found
within CEQ regulations, 40 C.F.R. § 1506.11. The provision, in its entirety, states:
Where emergency circumstances make it necessary to take an action with
significant environmental impact without observing the provisions of these
regulations, the Federal agency taking the action should consult with the Council
about alternative arrangements. Agencies and the Council will limit such
arrangements to actions necessary to control the immediate impacts of the
emergency. Other actions remain subject to NEPA review.
An agency must consult with the CEQ if it is taking action without following
NEPA; without CEQ’s approval, the agency would be acting in violation of the law.

69 Sierra Club v. Lynn, 502 F.2d 43, 59-60 (5th Cir. 1974).
70 Methow Valley Citizens Council v. Regional Forester, 833 F.2d 810 (9th Cir. 1987). See
also Save Barton Creek Ass’n v. FHWA, 950 F.2d 1129, 1137 (5th Cir. 1992) (purpose of
NEPA is to inform the decision-maker).
71 40 C.F.R. § 1508.9(b).

Waiver authorization is within the CEQ’s discretion. According to one court that
considered the issue, CEQ has the authority to “waive its own regulations ... [and]
also to interpret the provisions of NEPA to accommodate emergency
circumstances.”72 If the Corps requested a waiver from strict compliance with
NEPA, and the CEQ agreed, that decision would be given substantial deference.73
The CEQ could authorize alternative arrangements under the emergency provision,
which would not waive NEPA, but provide another means of compliance.
Research did not reveal many examples of § 1506.11 being invoked by agencies
in which a court reviewed the decision. None of the actions found was similar to the
facts at hand. The cases involved waiving NEPA for an industrial project,74 night-
time use of an Air Force base during the Desert Storm military operation,75 and Navy
sonar training.76 In the case of the Navy sonar training, the court found that there was
no emergency and rejected the use of § 1506.11. In both cases where CEQ
authorized the emergency provision, alternative environmental procedures were used.
Shortly after Hurricane Katrina, CEQ issued a memorandum in which it emphasized
that NEPA should continue to be followed to “demonstrate our continuing
commitment to environmental stewardship.”77 It provided guidance on complying
with § 1506.11 as an appendix.
The Right to Sue Under NEPA
NEPA suits are brought under the Administrative Procedure Act (APA).
Therefore, courts review whether an agency’s action was arbitrary or capricious or
otherwise not in accordance with law.78 Parties have to show standing. That limits
plaintiffs to those who could show they were adversely affected or aggrieved by the
agency action and that NEPA intended to protect against that actual or threatened
injury.79 For example, a economic injury by itself is not the type of harm NEPA
protects against and could not be the basis for a lawsuit. However, the reduced use
of the river by a recreational kayaker could be the basis for standing. Plaintiffs could
include individuals and groups, provided they were able to show they suffered an
injury in fact that was different from the injury suffered by the community at large.80

72 Crosby v. Young, 512 F.Supp. 1363, 1386 (D.C. Mich. 1981).
73 Andrus v. Sierra Club, 442 U.S. 347, 358 (1979).
74 Crosby v. Young, 512 F.Supp. 1363 (D.C. Mich. 1981).
75 Valley Citizens for a Safe Environment v. Vest, 1991 WL 330963 (D. Mass. May 6, 1991).
76 NRDC v. Winter, 2008 U.S. App. Lexis 4504 (9th Cir. February 29, 2008).
77 Memo of September 8, 2005, from the Associate Director for NEPA Oversight,
“Emergency Actions and NEPA,” available at
[http://www.nepa.gov/nepa/regs /Memo_to_NEPA_Contacts_September_8_05.pdf].
78 5 U.S.C. § 706(2)(A).
79 5 U.S.C. § 702.
80 See Massachusetts v. EPA, 127 S. Ct. 1438, 1453 (2007) (a personal stake confers
standing, even when there is “widespread harm”).