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Endangered and Threatened Species; Recovery Plans

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National Marine Fisheries Service (NMFS), National Oceanic and Start Printed Page 162Atmospheric Administration, Commerce.


Notice of availability; request for comments.


The National Marine Fisheries Service (NMFS) announces the availability of the Proposed Columbia River Estuary Endangered Species Act (ESA) Recovery Plan Module for Salmon and Steelhead (Estuary Module) for public review and comment. The Estuary Module was developed to meet the estuary recovery needs of all ESA-listed salmon and steelhead in the Columbia River Basin. The Estuary Module will be incorporated by reference into all Columbia Basin salmon and steelhead recovery plans to guide salmon and steelhead recovery in the Columbia River estuary. The Estuary Module was prepared by the Lower Columbia River Estuary Partnership, under contract to NMFS. At this time, NMFS is soliciting review and comment from the public and all interested parties on the proposed Estuary Module.


NMFS will consider and address all substantive comments received during the comment period. Comments must be received no later than 5 p.m. Pacific Daylight Time on March 3, 2008.


Please send written comments and materials to Patty Dornbusch, National Marine Fisheries Service, 1201 NE Lloyd Boulevard, Suite 1100, Portland, OR 97232. Comments may also be submitted by e-mail to: Include in the subject line of the e-mail comment the following identifier: Comment on Columbia River Estuary Recovery Plan Module. Comments may be submitted via facsimile (fax) to (503) 872-2737.

Persons wishing to review the Estuary Module may obtain an electronic copy (i.e., CD-ROM) by calling Sharon Houghton at (503) 230-5418 or by emailing a request to, with the subject line “CD-ROM Request for Columbia River Estuary Module.” Electronic copies of the Estuary Module are also available online on the NMFS website:

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Patty Dornbusch, NMFS Lower Columbia Recovery Coordinator (503-230-5430), or Elizabeth Gaar, NMFS Salmon Recovery Division (503-230-5434).

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The Endangered Species Act of 1973 (ESA), as amended (16 U.S.C. et seq.), requires that a recovery plan be developed and implemented for species listed as endangered or threatened under the statute, unless such a plan would not promote the recovery of a species. Recovery plans must contain (1) objective, measurable criteria which, when met, would result in a determination that the species is no longer threatened or endangered; (2) site specific management actions necessary to achieve the plan's goals; and (3) estimates of the time required and costs to implement recovery actions. NMFS is the agency responsible for developing recovery plans for salmon and steelhead, and the agency will use the plans to guide efforts to restore endangered and threatened Pacific salmon and steelhead to the point that they are again self sustaining in their ecosystems and no longer need the protections of the ESA.

To accomplish recovery planning in the Columbia River Basin, NMFS organized the eight listed salmon evolutionarily significant units (ESUs) and the five listed steelhead distinct population segments (DPSs) into two geographic recovery domains, the Lower Columbia/Willamette and the Interior Columbia. (The latter was further divided into the Snake, Mid-Columbia, and Upper Columbia sub-domains.) Recovery plans are either complete or in development to address all listed salmon ESUs or steelhead DPSs within each domain.

Because NMFS believes that local support for recovery plans is essential, the agency has approached recovery planning collaboratively, with strong reliance on existing state, regional, and tribal planning processes. For instance, in the Columbia Basin, recovery plans have been or are being developed by regional recovery boards convened by Washington State, by the State of Oregon in conjunction with stakeholder teams, and by NMFS in Idaho with the participation of local agencies. NMFS reviews locally developed recovery plans, ensures that they satisfy ESA requirements, and makes them available for public review and comment before formally adopting them as ESA recovery plans.

Recovery plans must consider the factors affecting species survival throughout the entire life-cycle. The salmonid life cycle includes spawning and rearing in the tributaries, migration through the mainstem Columbia River and estuary to the ocean, and the return journey to the natal stream. In the estuary, juvenile and adult salmon and steelhead undergo physiological changes needed to make the transition to and from saltwater. They use the varying sub-habitats of the estuary - the shallows, side channels, deeper channels, and plume of freshwater extending offshore - at varying times of the year. While local recovery planners appropriately focus on the tributary conditions within their jurisdictions and domains, NMFS recognized the need for consistent treatment of the factors in the estuary that affect all of the listed salmonids in the Columbia Basin.

The Estuary Module is intended to address limiting factors, threats, and needed actions in the Columbia River estuary for the 13 ESUs and DPSs of salmon and steelhead listed in the basin. Each locally developed recovery plan will then include or incorporate by reference the Estuary Module as its estuary component. This approach will ensure consistent treatment across locally developed recovery plans of the effects of the Columbia River estuary as well as a system-wide approach to evaluating and implementing estuary recovery actions. The planning area of the Estuary Module overlaps to some extent with the planning areas for locally developed plans for lower Columbia River tributaries. This overlap occurs in the tidally influenced portions of the tributaries, and in such instances the local plans will reflect the Estuary Module but may contain a higher level of detail in terms of specificity of actions.

NMFS contracted with the Lower Columbia River Estuary Partnership (LCREP) for development of the Estuary Module. LCREP was established in 1995 as part of the Environmental Protection Agency's National Estuary Program. LCREP's major roles are to convene common interests, help integrate conservation efforts, increase public awareness and involvement, and promote information-based problem-solving. LCREP is the primary organization focused on conserving and improving the environment of the Columbia River estuary. In addition to having completed development, and begun implementation, of its Comprehensive Conservation and Management Plan in 1999, LCREP completed the Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan and Supplement in 2004. The LCREP's expertise in assessment, planning, and stakeholder connections made it uniquely suited to develop this proposed Estuary Module for NMFS.

NMFS has reviewed the Estuary Module and is now making it available for public review and comment.

Upon approval of the Estuary Module, NMFS will make a commitment to implement the actions in the Estuary Start Printed Page 163Module for which it has authority, to work cooperatively on implementation of other actions, and to encourage other Federal agencies to implement Estuary Module actions for which they have responsibility and authority. NMFS will also encourage the States of Washington and Oregon to seek similar implementation commitments from state agencies and local governments.

NMFS expects the Estuary Module to help NMFS and other Federal agencies take a more consistent approach to future section 7 consultations and other ESA decisions. For example, the Estuary Module will provide greater biological context for the effects that a proposed action may have on a listed ESU or DPS. Science summarized in the Estuary Module will become a component of the ''best available information'' for section 7 consultations as well as for section 10 habitat conservation plans and other ESA decisions.

The Estuary Module

The purpose of the Estuary Module is to identify and prioritize management actions that, if implemented, would reduce the impacts of the limiting factors that salmon and steelhead encounter during migration and rearing in the estuary and plume ecosystems. To accomplish this, changes in the physical, biological, or chemical conditions in the estuary are reviewed for their potential to affect salmon and steelhead. Then, the underlying causes of limiting factors are identified and prioritized based on the significance of the limiting factor and each cause's contribution to one or more limiting factors. These causes are referred to as threats and can be either human or environmental in origin. Finally, management actions are identified that are intended to reduce the threats and increase the survival of salmon and steelhead during estuarine rearing and migration. Costs are developed for each of the actions using an estimated level of effort for implementation.

The Estuary Module is a synthesis of diverse literature sources and the direct input of estuary scientists. The following key documents were used extensively as a platform for the Estuary Module: Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan and Supplement (Northwest Power and Conservation Council, 2004); Salmon at River's End (Bottom et al., 2005) and Role of the Estuary in the Recovery of Columbia River Basin Salmon and Steelhead (Fresh et al., 2005). Many primary sources were also consulted, including experts from the NMFS Northwest Fisheries Science Center, other NMFS staff, LCREP staff, and Lower Columbia Fish Recovery Board staff. Additionally, modifications to the Estuary Module were influenced by interactions with the Northwest Power and Conservation Council, the Mid-Columbia Sounding Board, the Upper Willamette Stakeholder Team, and the Lower Columbia River Stakeholder Team.

Planning Area and ESUs and DPSs Addressed

For the purposes of the Estuary Module, the estuary is broadly defined to include the entire continuum where tidal forces and river flows interact, regardless of the extent of saltwater intrusion (Fresh et al. 2005; Northwest Power and Conservation Council 2004). For planning purposes, the upstream boundary is Bonneville Dam and the downstream boundary includes the Columbia River plume. These two divisions-the estuary and plume-were used extensively in the Estuary Module.

During their life cycles, all listed salmon and steelhead in the Columbia River basin rely for some period of time on the Columbia River estuary. The Estuary Module is therefore intended to address all eight listed ESUs and all five listed DPSs.

Recovery Goals, Objectives, and Criteria

Because the Estuary Module addresses only a portion of the species life-cycle and is intended to be incorporated into locally developed recovery plans that will be adopted by NMFS as ESA recovery plans, it does not contain recovery goals and objectives or de-listing criteria. Those will be provided in the domain-specific recovery plans that this Estuary Module is intended to complement.

Causes for Decline and Current Threats

The estuary and plume are considerably degraded from their historical condition. The Estuary Module identifies these changes, evaluates their potential effects on salmon and steelhead, and discusses their underlying causes. The causes of decline and current threats may be broadly categorized as habitat-related threats, threats related to the food web and species interaction, and other threats.

Habitat: The estuary is about 20 percent smaller than it was historically (Northwest Power and Conservation Council, 2004). This reduction is due mostly to diking and filling practices used to convert the floodplain to agricultural, industrial, commercial, and residential uses. Flows entering the estuary also have changed dramatically: spring freshets have decreased and other aspects of the historical hydrograph have been altered. These changes are the result of flow regulation by the hydropower system, water withdrawal for irrigation and water supplies, and climate fluctuations.

Flow alterations and diking and filling practices have affected salmon and steelhead in several ways. Access to and use of floodplain habitats by ocean-type ESUs (salmonids that typically rear for a shorter time in tributaries and a longer time in the estuary) have been severely compromised through alterations in the presence and availability of these important habitats. Shifts in timing, magnitude, and duration of flows have also changed erosion and accretion processes, resulting in changes to in-channel habitat availability and connectivity.

Elevated temperatures of water entering the estuary are also a threat to salmon and steelhead. Degradation of tributary riparian habitat by land-use practices, in addition to reservoir heating, has caused these increased temperatures. Water quality in the estuary and plume has also been degraded by toxic contaminants. Many contaminants are found in the estuary and plume, some from agricultural pesticides and fertilizers and some from industrial sources. Salmon and steelhead are affected by contaminants through short-term exposure to lethal substances or through longer exposures to chemicals that accumulate over time and magnify through the food chain.

Food Web and Species Interactions: Limiting factors related to the food web and species interactions can be thought of as the product of all the threats to salmon and steelhead in the estuary. Examples include relatively recent increases in Caspian tern and pinniped predation on salmonids, due at least in part to human alterations of the ecosystem, as well as the more complex and less understood shift from macrodetritus-based primary plant production to phytoplankton production. The introduction of exotic species is another ecosystem alteration whose impacts are not clearly understood.

Other Threats: The estuary is also influenced by thousands of over-water and instream structures, such as jetties, pilings, pile dikes, rafts, docks, breakwaters, bulkheads, revetments, groins, and ramps. These structures alter river circulation patterns, sediment deposition, and light penetration, and they form microhabitats that often benefit predators. In some cases, structures reduce juvenile access to low-velocity habitats. Ship wake stranding is Start Printed Page 164an example of another threat to salmon and steelhead in the estuary whose full impact is not well understood.

Recovery Strategies and Actions

The Estuary Module identifies 23 management actions to improve the survival of salmon and steelhead migrating through and rearing in the estuary and plume environments. Table 1 identifies these management actions and shows their relationship to threats to salmonid survival.

TABLE 1 Management Actions to Address Threats

ThreatManagement Action
Flow-related threatsClimate cycles and global warming2CRE1-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.2
CRE-2: Modify hydrosystem operations to reduce the effects of reservoir surface heating, or conduct mitigation measures.2
CRE-3: Establish legal instream flows for the estuary that would help prevent further degradation of the ecosystem.2
Water withdrawalCRE-3: Establish legal instream flows for the estuary that would help prevent further degradation of the ecosystem.
Flow regulationCRE-4: Adjust the timing, magnitude and frequency of flows (especially spring freshets) entering the estuary and plume to provide better transport of sediments and access to habitats in the estuary, plume, and littoral cell.
Sediment-related threatsEntrapment of sediment in reservoirsCRE-5: Study and mitigate the effects of entrapment of sediment in reservoirs, to improve nourishment of the littoral cell.
Impaired sediment transportCRE-6: Reduce the export of sand and gravels via dredge operations by using dredged materials beneficially.
CRE-4: Adjust the timing, magnitude and frequency of flows (especially spring freshets) entering the estuary and plume to provide better transport of sediments and access to habitats in the estuary, plume, and littoral cell.
DredgingCRE-7: Reduce entrainment and habitat effects resulting from main- and side-channel dredge activities in the estuary.
Structural threatsPilings and pile dikesCRE-8: Remove pile dikes that have low navigational value but high impact on estuary circulation and/or juvenile predation effects.
Dikes and fillingCRE-9: Protect remaining high-quality off-channel habitat from degradation through education, regulation, and fee simple and less-than-fee acquisition.
CRE-10: Breach or lower dikes and levees to improve access to off-channel habitats.
Reservoir heatingCRE-2: Modify hydrosystem operations to reduce the effects of reservoir surface heating, or conduct mitigation measures.Start Printed Page 165
Over-water structuresCRE-11: Reduce the square footage of over-water structures in the estuary.
Food web-related threatsReservoir phytoplankton productionCRE-10: Breach or lower dikes and levees to improve access to off-channel habitats.
Altered predator/prey relationshipsCRE-13: Manage pikeminnow, smallmouth bass, walleye, and channel catfish to prevent increases in abundance.
CRE-14: Identify and implement actions to reduce salmonid predation by pinnipeds.
CRE-15: Implement education and monitoring projects and enforce existing laws to reduce the introduction and spread of noxious weeds.
CRE-16: Implement projects to redistribute part of the Caspian tern colony currently nesting on East Sand Island.
CRE-17: Implement projects to reduce double-crested cormorant habitats and encourage dispersal to other locations.
CRE-18: Reduce the abundance of shad entering the estuary.
Ship ballast practicesCRE-19: Prevent new invertebrate introductions and reduce the effects of existing infestations.
Water quality-related threatsAgricultural practicesCRE-20: Implement pesticide and fertilizer best management practices to reduce estuary and upstream sources of toxic contaminants entering the estuary.
Urban and industrial practicesCRE-21: Identify and reduce industrial, commercial, and public sources of pollutants.
CRE-22: Monitor the estuary for contaminants and/or restore contaminated sites.
CRE-23: Implement stormwater best management practices in cities and towns.
CRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.
Other threatsRiparian practicesCRE-1: Protect intact riparian areas in the estuary and restore riparian areas that are degraded.
Ship wakesCRE-12: Reduce the effects of vessel wake stranding in the estuary.
1 CRE = Columbia River estuary.
2 It is unclear what the regional effects of climate cycles and global warming will be during the coming decades. In the absence of unambiguous data on the future effects of climate cycles and global warming in the Pacific Northwest, this recovery plan module takes a conservative approach of assuming reduced snowpacks, groundwater recharge, and stream flows, with associated rises in stream temperature and demand for water supplies. The climate-related management actions in this table reflect this assumption.

Identifying management actions that could reduce threats to salmon and steelhead as they rear in or migrate through the estuary is an important step toward improving conditions for salmonids during a critical stage in their life cycles. However, actual implementation of management actions is constrained by a variety of factors, such as technical, economic, and property rights considerations. In fact, in some cases it will be impossible to realize an action's full potential because its implementation is constrained by past societal decisions that are functionally irreversible. An important assumption of the Estuary Module is that the implementation of each of the 23 management actions is constrained in some manner.Start Printed Page 166

The Estuary Module makes another important assumption about implementation: although implementation of actions is constrained, even constrained implementation can make important contributions to the survival of salmonids in the estuary, plume, and nearshore.

It is within the context of these two fundamental assumptions that recovery actions are evaluated in the Estuary Module, in terms of their costs and potential benefits.

Potential Survival Benefits and Time and Cost Estimates

The evaluation of survival benefits and costs is highly uncertain because it relies on estimates not only of what is technically feasible, but also of what is socially and politically practical. To help characterize potential survival improvements, the Estuary Module uses a planning exercise that involves distributing a plausible survival-improvement target of 20 percent across the actions to hypothesize the portion of that total survival-improvement target that might result from each action. The primary purpose of the survival-improvement target is to help compare the relative potential benefits of different management actions. The survival-improvement target does not account for variation at the ESU, population, and subpopulation scales, and is not intended for use in life-cycle modeling, except as a starting point in the absence of more rigorous data.

Costs are developed by breaking each action into a number of specific projects or units and identifying per-unit costs for each project. Both the survival improvements and costs reflect assumptions about the constraints to implementation and the degree to which those constraints can be reduced given the technical, social, and political context in the Columbia River basin.

The Estuary Module estimates that the cost of partial (constrained) implementation of all 23 actions over a 25-year time period is about $500 million. Costs of tributary actions and the total estimated time and cost of recovery for each affected ESU or DPS will be provided in the locally developed recovery plans.

Monitoring and Adaptive Management

As discussed in chapter 6 of the Estuary Module, several important monitoring and adaptive management activities are occurring throughout the Columbia River Basin that have a direct bearing on the estuary, plume, and nearshore. While NMFS believes that these activities provide an adequate framework for monitoring in the estuary, there remains a need to ensure consistency of existing monitoring and evaluation programs in the estuary with the NMFS document Adaptive Management for Salmon Recovery: Evaluation Framework and Monitoring Guidance (​Salmon-Recovery-Planning/​ESA-Recovery-Plans/​Other-Documents.cfm) and to review and evaluate pertinent monitoring programs to identify additional monitoring needs (including indicators, metrics, and protocols; lead entities; costs), particularly in the area of action effectiveness monitoring for the actions identified in the Estuary Module. This work is underway and expected to be incorporated into chapter 6 or as an appendix of the Estuary Module at the time it is finalized.


The Estuary Module contributes to all the Columbia Basin salmon and steelhead recovery plans by analyzing limiting factors and threats relating to survival of listed salmonid species in their passage or residence time in the Columbia River estuary, site-specific management actions related to those limiting factors and threats, and estimates of cost, to be incorporated by reference into all the basin recovery plans. NMFS concludes that the Estuary Module provides information that helps to meets the requirements for recovery plans under ESA section 4(f), and thus is proposing it as a component of Columbia Basin ESA recovery plans.

Literature Cited

Lower Columbia River Estuary Partnership. 1999. Lower Columbia River Estuary Plan (Comprehensive Conservation and Management Plan).

Northwest Power and Conservation Council. 2004. Mainstem Lower Columbia River and Columbia River Estuary Subbasin Plan and Supplement. (Adopted into the Columbia River Basin Fish and Wildlife Program).

Bottom, D.L., C.A. Simenstad, J. Burke, A.M. Baptista, D.A. Jay, K.K. Jones, E. Casillas, and M. H. Schiewe. 2005. Salmon at River's End: The Role of the Estuary in the Decline and Recovery of Columbia River Salmon. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-68, 246p.

Fresh, K.L., E. Casillas, L.L. Johnson, and D.L. Bottom. 2005. Role of the Estuary in the Recovery of Columbia River Basin Salmon and Steelhead: An Evaluation of the Effects of Selected Factors on Salmonid Population Viability. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-69, 105p.

Public Comments Solicited

NMFS solicits written comments on the proposed Estuary Module as a component of Columbia Basin ESA recovery plans. All comments received by the date specified above will be considered prior to NMFS's decision whether to adopt the Estuary Module. Additionally, NMFS will provide a summary of the comments and responses through its regional web site. NMFS seeks comments particularly in the following areas: (1) survival improvement targets and allocation of benefits among actions; (2) costs and schedule for implementing management actions; (3) strategies for monitoring action effectiveness; (4) oversight and institutional infrastructure needed for implementation of Estuary Module actions.

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Authority: 16 U.S.C. 1531 et seq.

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Dated: December 26, 2007.

Angela Somma,

Chief, Endangered Species Division, Office of Protected Resources, National Marine Fisheries Service.

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[FR Doc. E7-25401 Filed 12-31-07; 8:45 am]