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Biological Opinion Endangered Species Act Section 7 Consultation on the U.S. Army Corps of Engineers Mobile District Update of the Water Control Manual for the Apalachicola- Chattahoochee-Flint River Basin in Alabama, Florida, and Georgia and a Water Supply Storage Assessment Prepared by: U.S. Fish and Wildlife Service Panama City Field Office, Florida September 14, 2016 USFWS Log No: 04EF3000-2016-F-0181 1 Biological Opinion for ACF Water Control Manual September 14, 2016 EXECUTIVE SUMMARY The action evaluated in this consultation is the U.S. Army Corps of Engineers’ (USACE) Update of the Water Control Manual (WCM) for the Apalachicola-Chattahoochee-Flint River Basin (ACF) in Alabama, Florida, and Georgia. The proposed action is primarily the operation of the five federal facilities, individually and in concert, under the WCM. The USFWS recognizes that the ACF River basin is a working river basin that provides water, transportation and livelihood for residents of three states. The USACE uses its WCM to balance these uses, for recreation, water supply, navigation, hydroelectric generation, flood control, drought reduction, fish and wildlife habitat, and endangered species. The USACE determined in its Biological Assessment (BA) that the proposed action may adversely affect the fat threeridge, purple bankclimber, and Chipola slabshell, but is not likely to adversely affect (NLAA) their designated critical habitat. Additionally, USACE determined that the proposed action may affect, but is NLAA, the Gulf sturgeon and its designated critical habitat. The USFWS incorporated new information and analysis for Gulf sturgeon and does not concur with the USACE's determination of NLAA for the Gulf sturgeon and its designated critical habitat. Therefore, mussel and sturgeon effects on the species and their critical habitats are addressed in this biological opinion (BO). In the WCM, the USACE adopts a modified version of its preferred alternative action (PAA) from the Draft Environmental Impact Statement (DEIS). The WCM includes actions for fish and wildlife conservation, including actions for federally-listed species (e.g., water releases below Woodruff Dam on the basis of spawning, non-spawning, and winter requirements), tailrace dissolved oxygen levels, fish passage, reservoir fish spawning, and management of Eufaula National Wildlife Refuge. The WCM also includes actions for drought operations, flood risk management, hydroelectric power generation, navigation, recreation, water quality, and water supply. Compared to existing management, the USACE proposes to modify 1) the action zones, 2) drought operations, 3) storage relocation at Lake Lanier, 4) ramping during prolonged flow, and 5) navigation. The current status of Gulf sturgeon and the three mussel species and the critical habitat for all four species is discussed in detail in this BO. The principal factor we examine is the flow regime of the Apalachicola River and how the flow regime affects habitat conditions for the listed species. In the BA, environmental baseline was defined as the observed flows of the river since the full complement of the USACE's reservoirs were completed and for which an unimpaired data set was available, so that the proposed action could be modeled (calendar years 1975 to 2012). In this BO, an alternative strategy is being employed as discussed in the Environmental Baseline – Physical Environment section. Under this approach, the modeled effects of the WCM are compared to the modeled effects of the USACE’s no action alternative (NAA) for 1939- 2012. The NAA includes the RIOP management implemented from 2012-present and is the baseline for this consultation. Relative to the baseline, the proposed update to the WCM provides both beneficial and adverse effects to the species and designated critical habitats we have assessed. The WCM will 2 Biological Opinion for ACF Water Control Manual September 14, 2016 negatively affect Gulf sturgeon by providing more time under which appropriate flow conditions for hydropeaking will occur during the spring spawning season and less inundation of floodplain habitats in late summer, fall, and winter. The WCM may affect four of the six primary constituent elements (PCEs) of sturgeon critical habitat: 1) food items in the riverine and estuarine environments, 2) riverine spawning areas, 3) flow regime, and 4) water quality. However, the WCM would not appreciably change the quantity or quality of the PCEs to the extent that it would appreciably diminish the habitat’s capability to provide the intended conservation role. It is the U.S. Fish and Wildlife Service’s (USFWS) biological opinion (BO) that the proposed action: 1) will not jeopardize the continued existence of the Gulf sturgeon, and 2) will not destroy or adversely modify designated critical habitat for the Gulf sturgeon. The WCM will negatively affect all three mussel species by providing longer durations of low flows (<5,000 cfs). The WCM may affect three of the five PCEs of mussel critical habitat: 1) permanently flowing water, 2) water quality, and 3) fish hosts. The WCM does appear to reduce the amount of floodplain habitat available to fish hosts for spawning. However, the WCM would not appreciably change the quantity or quality of the PCEs to the extent that it would appreciably diminish the habitat’s capability to provide the intended conservation role. It is the USFWS' biological opinion that the proposed action: 1) will not jeopardize the continued existence of the fat threeridge, purple bankclimber, and Chipola slabshell; and 2) will not destroy or adversely modify designated critical habitat for the fat threeridge, purple bankclimber, and Chipola slabshell. The Incidental Take Statement issued exempts USACE from take under the Act. During conditions appropriate for hydropeaking during the Gulf sturgeon spawning season and during late summer, fall and winter by decreasing floodplain inundation, take of Gulf sturgeon will occur and the magnitude of this take will be estimated using surrogate measures and monitored. Hydropeaking will not occur on more than 32 days on average during the sturgeon spawning season. Floodplain inundation will not be reduced below 655,000 ac-day on average during late summer and fall or below 131 days on average during winter and spring. During each low flow event (flow reduction to 4,500 cfs and exposure at > 5,000 cfs following recolonization) and due to reduced floodplain inundation, a maximum of the following mussel species may be taken: 34,000 fat threeridge total, 90 purple bankclimbers total, and 106 Chipola slabshell total. The biological opinion also outlines three mandatory, reasonable, and prudent measures necessary and appropriate to minimize the impacts of incidental take of Gulf sturgeon and the three mussel species. 1) Adaptive management, where USACE will identify ways to avoid and minimize take and implement alternative management strategies within the scope of the authorities of the WCM as new information is collected. For example, USACE will provide pulses of water in late summer, fall and winter months to inundate the floodplain and monitor the effects of these releases on Gulf sturgeon food production and mussel host fish populations. 2) Water flow and water quality stations, where USACE will develop and implement a monitoring program associated with permanent monitoring stations in the Apalachicola, Chattahoochee, and Flint rivers. Discharge, stage, temperature, dissolved oxygen, and salinity will be monitored related to listed species and critical habitat effects. 3) Species monitoring, where USACE will monitor the level of take associated with the WCM by monitoring the distribution, abundance, 3 Biological Opinion for ACF Water Control Manual September 14, 2016 survival, growth, and fecundity of the listed mussels and Gulf sturgeon in the action area. RPMs to address the effects of hydropeaking during the Gulf sturgeon spawning season are not included as part of this BO because this activity is nondiscretionary at this time. These effects will be addressed through later consultation with the Southeast Power Administration. This BO evaluates the WCM, with a consideration that the WCM is reviewed every 5 years pursuant to USACE South Atlantic Division policy; therefore, we issue this BO with the understanding that the WCM may be revised or updated within 5 years (i.e., in 2021), and that this BO will be reviewed, or consultation reinitiated at that time. No further consultation is needed unless the USACE operates its projects covered in the WCM in a way that is different than described in its BA, new information indicates that the WCM may affect listed species or their critical habitat to an extent not considered in the BO, a new species is listed in the basin that may be affected by the action, or if more mussels or sturgeon are taken under the USACE's operations than anticipated. Furthermore, the proactive adaptive management approach adopted under the BO will allow the USACE to continue to improve how it implements the WCM to protect endangered species and their habitats in response to changing flows, and changing climate. This is an opportunity for the USACE to better understand the impacts of its operations, and to contribute to the recovery of these species and conservation of their habitats in the ACF Basin. 4 Biological Opinion for ACF Water Control Manual September 14, 2016 TABLE OF CONTENTS EXECUTIVE SUMMARY ...........................................................................................................
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