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NOAA Fisheries

2009 FCRPS Adaptive Management Plan


2009 Adaptive
Management Plan

Federal Columbia River Power System
Biological Opinion

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Adaptive Management Plan


The 2008-2017 FCRPS Biological Opinion (BiOp) included an adaptive management and
contingency plan framework should there be a significant decline in listed species or should the
survival improvements assumed in NOAA Fisheries’ Supplemental Comprehensive Analysis not
be realized. The framework incorporated into the BiOp includes biological triggers at the ESU
level for implementing contingencies and an “All H Diagnosis” to determine appropriate
contingency actions. It is supported by a research and monitoring program, a transparent process
for progress reporting, and full involvement of the sovereigns’ Regional Implementation
Oversight Group (RIOG). This contingency plan was based on the adaptive management
platform described in the 2007 FCRPS Biological Assessment (BA) (Adaptive Management; pp.
2-1 through 2-16) and referenced in the Reasonable and Prudent Alternative (RPA) for the BiOp
(Actions 1-3 and 50-73). The adaptive management process in the FCRPS BA defines what
steps the Action Agencies will take if performance standards are not met.

The new administration thoroughly considered this framework in the context of the BiOp, the
available science on which it was based, the issues raised by the litigants and independent
scientists, and the Court’s letter of May 18, 2009. Its review highlighted a number of important
questions regarding the implementation of contingencies, centered on precautionary
implementation and rapid response to indications of declining fish status. What conditions are
we monitoring? How rapidly would the Action Agencies and NOAA Fisheries be able to
respond to a precipitous decline in a listed species? What if climate change leads to extreme
swings in habitat and fish status? Are available mitigation actions that might have immediate
fish survival benefits -- such as more aggressive control of predators or invasive species, harvest
reductions, hydro operation measures, and re-establishment of extirpated populations -- getting
sufficient attention and could they be quickly implemented? The administration leadership has
concluded that implementation of the contingency framework in the FCRPS BiOp would benefit
from more structure and detail, so that these questions can be more fully answered.

In response, the Action Agencies, with the full support of NOAA Fisheries and the
administration leadership, are proposing additional structure and details for the BiOp
contingency framework. Through adaptive management, the federal agencies are clarifying and
committing to the Court and to the region how the agencies will plan for and implement
contingencies for all Columbia Basin ESUs/DPSs within the BiOp framework (see Figure 1,
General FCRPS BA / BiOp Adaptive Management Framework). Including the newly proposed
modifications, the adaptive management framework would generally consist of:

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▪ Targeting Action Agency and NOAA Fisheries Research, Monitoring, and Evaluation
(RM&E) programs to ensure that key priorities, including fish status and climate change
conditions, are met;
▪ Providing BA/BiOp performance standard and action effectiveness monitoring (Hydro,
Habitat, Hatchery, and Predation) and implementing additional actions, if necessary, to
achieve these standards;
▪ Using the BA/BiOp contingency process in connection with the 2013 and 2016
Comprehensive Reports, including All-H Diagnostics, to determine effective (applicable)
contingency actions;
▪ Adding Early Warning and Unexpected Severe Decline triggers, designed to enhance the
BiOp’s potential to respond to declines in fish numbers or natural disasters;
▪ Developing Rapid Response Plans by 2011, for use in the event that 2013 and 2016
Comprehensive Analysis, Early Warning, or Unexpected Severe Decline triggers are
▪ Developing longer term Contingency Plans by 2013, for use in the event that the existing
hydro and habitat measures contained in the FCRPS BiOp are insufficient to respond to
unexpected declines.

The addition of the Early Warning and Unexpected Severe Decline triggers will ensure
precautionary implementation of the BiOp and increase its responsiveness to emerging climate
change information. Most importantly, together with the Rapid Response and Contingency
Plans, they will ensure that there is a rapid response by the Federal agencies collectively in the
event of a precipitous fish decline and/or extreme habitat disturbance affecting interior Columbia
Basin fish.

Implementation of rapid response and longer term contingency actions will be taken by Action
Agencies, NOAA Fisheries, and U.S. Fish and Wildlife Service (FWS), depending on the
responsive action(s) in question. Collaboration with the States and Tribes would also occur
through the RIOG to inform the implementation decision.

Figure 1 (Proposed Contingency Process Flow Chart) displays the expanded Contingency
Implementation process, including additional triggers for rapid response. The following sections
provide further detail regarding each element.

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1. New Actions Being Taken

1.1 Immediate Actions

1.1.1 Conservation Measures: Washington Memorandum of Agreement

All salmon and steelhead stocks in the Columbia River Basin spend time in the estuary before
migrating to sea. Estuarine habitats must be available throughout time and space at sufficient
quantities to support more that 150 distinct salmon and steelhead populations, which represent 13
Evolutionary Significant Units (ESU), each capable of expressing a variety of different fresh-
water and ages of estuary entry; periods of estuary residence; and times, sizes, and ages of
seaward migration. For example, recent genetic studies have revealed that all Colombia River
Chinook salmon ESUs produce subyearling migrants that rear in the estuary for weeks or months
before entering the ocean (Bottom et al. 2008).

A proposed Estuary habitat Memorandum of Agreement (MOA) with the State of Washington
has been developed to help ensure that survival benefits established in the 2008 BiOp are
achieved. The proposed MOA would add to the federal commitment to ESA-listed steelhead and
salmon in the BiOp – nearly doubling estuary habitat funding – and provide extra assurance that
actions to address fish survival will occur.

While this MOA has not yet been executed, it will establish a new avenue for implementing
large-scale habitat restoration projects. The MOA will provide BPA funding to the Washington
Department of Fish & Wildlife (WDFW) to match the US Army Corps of Engineers’ Section
536 funding to implement ecosystem restoration projects that support salmonids. It is expected
that major projects will result from this new partnership and will be implemented in the out-years
between 2013 and 2017; however, some of these projects will likely be implemented in the 2010
– 2012 timeframe.

The draft MOA with the State of Washington provides additional funding from the Action
Agencies for estuary habitat projects, to the order of $4.5 million annually committed to
Washington. Through the implementation of the MOA the Action Agencies will be providing an
increase in funding for all estuary habitat actions of approximately $40.5 million over the nine
year term of the MOA. Completion of the MOA is expected later this summer. BPA has decided
to support planning work now, so that Washington will be positioned to obtain other funds and
build partnerships in the immediate near term for projects that benefit fish and wildlife. Project Selection and Benefits

In identifying the projects for inclusion in the MOA, WDFW identified a suite of potential
projects, which were later refined to the 21 sites as identified in Attachment 1: Estuary Habitat
MOA Projects. WDFW coordinated with PC Trask & Associates to gain an understanding of the

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process used in the BiOp estuary survival benefits. Project concepts were then refined and
physical project sites were established in a GIS layer. Project concepts were evaluated in terms
of certainty of success based upon a scoring process outlined below.

Survival units were assigned to each of the 21 project concepts. This was accomplished by
identifying the appropriate sub-action in the Estuary Module Recovery Plan to each project
concept. WDFW and PC Trask collaborated to assign preliminary survival unit estimates for
each project. After initial assignment of survival benefits, each project concept was compared
and sometimes adjusted to survival unit scores for similar projects evaluated in the 2008 BiOp to
ensure consistency. Scores (0 – 5) were based upon the following guidelines:
ƒ (5 pts) Larger project that are on or very near mainstem making the project benefits
accessible to both tributary and upstream ESUs; making existing habitats available.
ƒ (4 pts) Smaller mainstem projects/parcels; Less than ideal benefits for upstream and
tributary populations, but still good; improving habitat that may already be accessible;
specific smaller projects that focus on important rearing areas.
ƒ (3 pts) Projects that are generally smaller or less feasible for full benefit; focused more on
tributary populations than upstream.
ƒ (2 pts) Potentially good projects that require further research or study; may include
experimental methods.
A potential benefit score was assigned by WDFW for each of the 21 project sites. The scores
ranged from a high of 5 to a low of 2. The average potential benefit score for the projects was
between 3 and 4 points. The process used was similar to the process described in the 2008 BiOp.

The Hump – Fisher Island Restoration is an example of project that was evaluated with this
method before inclusion in the MOA. The 337 acre site is located in Reach C downstream of
Longview. Hump – Fisher Island is co-owned by WDFW and the Department of Natural
Resources. The site contains important juvenile salmonid rearing habitat, used by juvenile
migrants from both upriver and downriver ESUs, in a complex of channels and mosaic of tidal
and upland wetlands adjacent to Fisher Slough. The proposed project at Hump – Fisher Island is
to enhance the existing embayment wetlands to improve hydrology and tidal and upland wetland
habitat complexity within and around the existing embayment.

The Hump – Fisher Restoration project concept was developed by the WDFW and the Army
Corps of Engineers – Portland District. Hump – Fisher received a score of 4 for certainty of
success and a 5 for potential benefit. Table 2 provides additional details regarding its estimate of
survival benefits. 1

The WAMOA used the latest draft version of the Estuary Recovery Plan Module; as a result there are some
modifications in sub-actions from the module version used to evaluate federal projects.

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Hump – Fisher Island Restoration – Assignment of Survival Benefits

Estuary Total Possible Preliminary Estimated

Certainty Potential Module Survival Units By Survival Units By
Total Sub-Action Project
of Success Benefit Sub-
Ocean Stream Ocean Stream

CRE 1.4 2 2 0.12 0.12

4 5 20
CRE-6. 0.3 0.15 0.1 0.03 Estuary Habitat RM&E

The intent of RM&E efforts in the estuary is to provide data and information to evaluate progress
toward meeting program goals and objectives and support decision-making in the estuary for
actions being taken by the Action Agencies and regional partners. An adaptive management
process will be utilized to identify RM&E efforts and habitat actions. Estuary actions under the
Washington MOA will be integrated into the Action Agencies’ evaluations of the cumulative
effects of individual habitat restoration actions on the entire estuarine ecosystem. RPA 37
establishes an expert regional technical group to support and guide these actions.

1.1.2 Summer Spill Program

The BiOp specifies the use of a biological trigger for determining when voluntary summer spill
will be terminated in August at the four Snake River projects (see RPA Action 29 and RPA
Table 2). Namely, when fish collection numbers of subyearling Chinook fall below 300 fish per
day for 3 consecutive days at Snake River collector projects. In the event that collection numbers
exceed 500 fish per day for 2 consecutive days after spill termination, spill would resume until
the 300 fish per day trigger was tripped again. Thus, under this program spill could be terminated
as early as August 4, but no later than August 31. The LRT Fish Accords modify the
implementation of this requirement so the trigger is applied at each dam and the cessation of spill
progresses downstream so that spill ceases at Little Goose no earlier than 3 days after cessation
at Lower Granite, Lower Monumental ceases no earlier than 3 days after Little Goose and Ice
Harbor ceases no earlier than 2 days after Lower Monumental.

In 2008, the use of this trigger would have resulted in spill being terminated at Lower Granite on
August 30. Recent fish passage data indicates that the 2009 migration is earlier than in 2008 –
thus use of the trigger would likely result in spill termination in early to mid-August in 2009.

This measure was been vetted through the Regional Collaboration Process and is supported by
the non-plaintiff parties.

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Since 2005, a Court-ordered spill program continues spill at the four Snake River projects
through August 31 – regardless of the number of smolts that are observed at these projects.
While continuing spill through August would not harm SR fall Chinook salmon, it also fails to
provide a substantial benefit as there are simply too few fish affected (as a proportion of the
entire ESU) to influence the productivity (Recruits per Spawner, etc.) of the ESU in any
significant way. For example, the date by which 95% of the PIT tagged natural origin fish from
the Snake River (not the Clearwater River) have passed the Snake River collector projects has
ranged from July 8 (2005) to Aug 5 (2008) since 2002.

Continuing spill through August as an immediate action would likely be viewed favorably by the
court and plaintiffs, but unfavorably by many supporting parties in the litigation. This action
would be expensive and ineffective as it would likely have an insignificant benefit to the SR fall
Chinook ESU. Continuing spill through the entire month of August may be considered in the
event that the abundance of SR fall Chinook salmon is (BiOp / BA Trigger, or Unexpected
Severe Decline Trigger) or is likely to (Early Warning Trigger) decline to levels that are unlikely
to occur if our understanding of these fish and their habitat (as articulated in the BiOp) are

1.1.3 Pikeminnow Sport Reward Fishery

BPA and the Corps of Engineers are committed to the ongoing implementation of the enhanced
Northern Pikeminnow Management Program (NPMP), as articulated in RPA Action 43. This
commitment includes a general increase in the reward structure of the sport-reward fishery and
an evaluation of the effectiveness of focused removals (dam angling) at lower Columbia FCRPS
projects. The Action Agencies will work with Pacific States Marine Fisheries Commission,
Oregon Department of Fish and Wildlife, WDFW, and USDA (Animal Damage Control (Dam
Angling)) to ensure full implementation of this program.

The current NPMP deploys USDA employees to conduct dam angling in forebay and tailrace
areas at two FCRPS projects. Increasing the dam angling effort at more FCRPS projects will
increase the overall catch to contribute to the program’s exploitation rate and potentially improve
within year dam passage survival of outmigration juvenile salmon. There is also a small
increased benefit of removals at the dam relative to the general public fishery because
pikeminnow removed from these areas tend to be larger and therefore able to consume more
juvenile salmonids. The proposal would increase the dam angling program from one crew to
three crews with the mobility and flexibility to fish all eight mainstem dams.

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1.1.4 Research, Monitoring, & Evaluation Needed to Implement Management Activities

Before we can take immediate actions such as reducing threats from predators and invasive
species and reintroducing populations to historically occupied habitat, RM&E will be needed to
determine which actions provide the greatest benefits with the least risk. Predator Control & Invasive Species

Regional partners are currently working on a strategy to reduce non-native piscivorous predation
on juvenile salmonids consistent with RPA Action 44 of the BiOp.

At the regional scale, it is necessary to assess the impacts of non-native species. This will include
combining spatially explicit information on non-native species populations (abundance, size,
etc.) and mechanisms and magnitudes of impact to identify areas where risks to salmon are the
greatest and where management strategies are needed to minimize these impacts. We will
evaluate multiple mechanisms of impact (predation, competition) for a number of key taxa
(including but not excluded to smallmouth bass, largemouth bass, channel catfish, walleye, shad,
brook trout). These assessments are needed to identify regions in the Columbia with greatest
potential impacts from non-native species. In addition, results of this effort can be linked with
proposed climate studies that will identify ESUs that are most susceptible to the effects of
climate change to help identify potential synergistic interactions between climate and non-native

The Action Agencies hosted a predation workshop in the fall of 2008 with approximately 100 in
attendance representing 18 federal, state and tribal entities, and several regional universities. A
report on the proceedings identified a number of predation management strategies, most
requiring a level of basic field research as a first step in implementing full-scale management
actions. A smaller follow-up meeting occurred in May of 2009 to narrow the focus to a few high
priority approaches warranting further development. The following briefly describes the three
highest priority subject areas that received regional consensus.

Current non-indigenous piscivorous predation activities include developing a research proposal

to be submitted to the ISRP to increase our understanding of some key uncertainties regarding
predation by introduced predators on juvenile salmonids. Key objectives include: 1)
documentation of the influence of juvenile shad on the growth and condition of introduced
predators in the fall as they prepare for overwintering. 2) Documentation of the predatory impact
of channel catfish, 3) Document whether localized removals of smallmouth bass may reduce the
predatory impact on juvenile salmonids in areas of intense predation.

Smallmouth Bass, Walleye, Channel Catfish and American Shad are all introduced species in the
Columbia Basin. With the exception of American shad, they are also predators on juvenile
salmonids. American shad do not consume juvenile salmonids, but are thought to substantially
affect food webs in the mainstem migration corridor. In addition, the nutrients provided by

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juvenile American shad in the fall may serve to increase condition and survival of predators,
therefore increasing net predation on juvenile salmonids. Conversely, they may reduce predation
rates on subyearling Chinook salmon by providing an abundant, alternative source of food to
Basic research is needed to achieve the objectives stated above. If the research supports the
management action, then site-specific removals of smallmouth bass and adult shad exclusion
from upper mainstem dams could occur as early as 2012. Reintroduction
Currently, efforts are being made to reestablish functioning populations where extirpation is
occurring is expected to occur in several Columbia basin locations. These plans include the
development of passage facilities or removal of large barriers (e.g., dams on the Cowlitz, Lewis,
Willamette, Deschutes, and White Salmon rivers). Other areas from which salmonids have been
extirpated are being actively repopulated with fish. These include spring Chinook salmon into
the Okanogan River basin, chum salmon in Duncan Creek (lower Columbia), and sockeye into
Lake Cle Elum (Mid-Columbia) and Pettit and Alturas Lakes (Snake River). The first step
toward the reintroduction of interior Columbia basin ESUs into large, blocked areas has been
taken by the ICTRT, which assessed the change in risk at the ESU level that would result from a
successful reintroduction into historically occupied areas. However, a thorough and systematic
evaluation of the benefits to population status (reduction in extinction risk) and the necessary
actions to affect a reintroduction successfully has not occurred. Proposed Enhancements

Using the Interior Columbia TRT’s memo evaluating the likely change in risk resulting from
reintroductions as a starting point, we will continue to evaluate the benefits from reintroductions
in the Columbia basin and identify actions necessary before reintroductions can take place. This
evaluation will include the following elements:

▪ Conditions under which reintroductions would be suitable versus unsuitable responses to

unexpected declines in abundance. Reintroducing fish to high-quality habitat in times of
high abundance is likely to be successful. In some situations, however, such as when
unoccupied habitat has been severely degraded or current abundance is extremely low,
there are likely to be significant costs to a reintroduction attempt. We will evaluate the
conditions under which reintroduction is a robust strategy and describe the relative costs
and benefits in other situations.

▪ Reintroduction techniques. “Re-introductions” can occur naturally, by allowing fish to

stray as they normally would; alternatively, artificially propagated fish can be outplanted in
currently unoccupied areas. We will therefore evaluate the costs and benefits of alternative
reintroduction strategies and techniques.

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In some cases, removal of or passage over a barrier could be insufficient to support a successful
reintroduction. We will identify the suite of actions that are likely to be required for a
reintroduction effort to be highly likely to succeed and that could be undertaken before a
reintroduction is needed.

Reintroductions, by making unoccupied but historically accessible habitats available has the
potential to enhance population abundance and productivity as well as spatial structure and
diversity. Thorough evaluation of the potential for reintroduction and the conditions under which
a reintroduction is most likely to be successful will both increase the likelihood of success and
reduce wasted effort and expense.

1.1.5 Research, Monitoring, & Evaluation Needed to Evaluate Progress and Increase Basic
RM&E is an essential component of the adaptive management framework in the BiOp. NOAA
Fisheries’ analysis included a number of assumptions about the way that fish populations will
respond to RPA actions, and how the actual results could change their risk of extinction.
Although the invited scientists thought that these assumptions were reasonable, they noted that
many lacked an empirical basis. This section describes enhanced RM&E efforts to provide these
data, adding greater certainty to NOAA Fisheries’ conclusions, allowing NOAA Fisheries and
the Action Agencies to adapt the RPA where these assumptions are not upheld. Based on the
new administration’s science review and adaptive management revisions for contingency
planning, the Action Agencies and NOAA Fisheries are expanding current RM&E actions.
These RM&E enhancements will address uncertainty and support evaluation of long term
contingency actions.

Currently, the FCRPS BiOp includes a large RM&E commitment totaling approximately $75
million per year from the Action Agencies (including status monitoring, effectiveness monitoring
such as IMWs, and critical uncertainties research in each of the “All H” categories). NOAA
Fisheries also has a major RM&E program linked to the ESA in the Columbia Basin. RM&E
results can lead to adaptive management changes to optimize fish survival, and will be reported
each year to the region and the RIOG in annual BiOp Progress Reports. This will include
reporting on the annual abundance of natural fish at the ESU/DPS level based on dam counts, the
metric used for the new contingency triggers. The research and modeling enhancements that
follow will fit within the larger BiOp framework.

NOAA Fisheries and the Action Agencies have been jointly reviewing existing federal RM&E
efforts to identify and address critical gaps in, or potential enhancements to, these programs.
This review is being conducted in partnership with the Northwest Power and Conservation
Council and the Columbia Basin Fish and Wildlife Authority. This summer, BPA, CBFWA,
NOAA Fisheries and NPCC are convening a series of sub-regional workshops with state and

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tribal co-managers to develop a shared Columbia Basin Monitoring Strategy. These
workshops will develop an efficient monitoring framework and project specific
implementation strategy for salmonid VSP monitoring (including fish-in/fish-out), and habitat
and hatchery effectiveness monitoring that meets the needs of recovery plans, BiOp
requirements, identified adult and juvenile contingency triggers, as well as other program and
regional fisheries management objectives. By October 2009 this collaborative process will
have prioritized population-specific monitoring needs, and identified project modifications
or new projects needed to fill remaining gaps. Life-Cycle Model

The BiOp used a combination of life-cycle modeling and passage modeling (COMPASS) to
estimate how changes in life-stage specific survival affect long term viability metrics
(productivity, mean abundance and probability of quasi-extinction). These analyses adequately
expressed population viability and effects of hydropower system operations and configurations
on smolt survival and alternative ocean/climatic scenarios.

The existing models can be expanded further in order to explicitly evaluate a variety of other
factors, described below. In addition, the expanded models can be developed to estimate the
likelihood that early-warning and contingency triggers might be met under alternative scenarios
of climate change and management strategies.

Starting immediately, the existing model will be expanded in the following ways: First, we will
update the Interior Columbia Technical Recovery Teams (ICTRT) stochastic life-cycle models to
incorporate most recent population data (abundance of adults and juveniles, stage-specific
survival, etc.) and expand the number of populations considered where possible (Snake River
spring/summer Chinook; Snake River steelhead; Upper Columbia spring Chinook; and Middle
Columbia steelhead). We will also explore data availability and, to the extent possible, develop
data-supported models for populations within ESUs that have not been modeled to date (Snake
River fall Chinook; Snake River sockeye; and Upper Columbia steelhead). Second, we will
expand the current models to address each of the following: Climate – Sensitivity of ESUs. Analyzing the potential effects of climate change is a key
element to the Adaptive Management Plan of the BiOp. Ultimately, as part of the spatially
explicit modeling discussed below, we want to identify which ESUs are most sensitive to climate
variability and which restoration actions are most resilient to climate change. Results will be
used to guide BiOp implementation decisions and cost effectiveness. Climate – Adaptive Management. We will evaluate effects of climate variability and
change in the near term (1-2 years) by incorporating predicted climate conditions, such as
freshwater conditions (e.g., snow pack), mainstem conditions (flow and temperature), and ocean
conditions on survival through the life cycle. Outputs will inform the early warning component
of the Adaptive Management Plan, as will our existing monitoring of marine ecosystem

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productivity each year. Longer term effects of climate will be modeled based on model studies
of biological responses to projected changes in freshwater and marine climate conditions from
various scenarios (IPCC, NOAA Fisheries, UW-CIG). Outputs will be considered qualitatively
in the context of the running 4-year averages in adult escapement “triggers” in the Adaptive
Management Plan and used to further judge trend patterns. Hatchery Effects. A critical uncertainty is the effect of hatchery spawners on the success
of wild spawners, the impact of hatchery releases on wild populations, and density-dependent
effects of hatchery production on the productivity of wild fish. Each of these issues has been
evaluated to some degree, and we will model the effects of hatcheries on populations under
various ocean productivity regimes and climate scenarios. This will provide a sensitivity analysis
of the potential role of hatchery production in recovery and to possibly identify alternative
production release timing strategies that increase survival of wild fish and hatchery fish. Habitat Actions & Monitoring. The potential effects of habitat improvements on
population viability metrics will be incorporated into the life cycle models as the information
becomes available from IMWs and RM&E activities. Results of analyses of key assumptions on
how fish populations respond to habitat alterations will be used to guide future RM&E and IMW
activities, and used qualitatively as part of the 2-year early warning and 4-year trigger
components of the Adaptive Management Plan. Spatially Explicit Modeling. As stated above, we will expand the number of populations
and ESUs considered in Leslie matrix models, as available data allow. This comparative
approach will allow us to more fully identify similarities and differences in how populations
respond to factors such as variability in freshwater and marine productivity, differing levels of
habitat restoration across watersheds, and influences of total hatchery composition on the wild
component of the ESU. Interspecific Interactions. We will evaluate the availability of data on the effects of
other native species (competitors, piscivorous and avian predators, and prey), invasive species
(competitors, predators, or pathogens), or other salmon populations (i.e., tradeoffs among ESUs)
on target salmon populations. If sufficient data exist, we will evaluate the potential effects
through food web or bioenergetics models, or other analyses, to estimate the magnitude of their
impact. Intensively Monitored Watersheds (IMWs)

IMWs are large watershed-scale studies intended to resolve the effectiveness of restoration
efforts, as well as the effects of freshwater and marine habitat conditions on fish abundance and
productivity. BPA currently funds IMW pilot basin studies in the John Day, Wenatchee, Entitat,
Methow, Lemhi and South Fork Salmon river Basins, while NOAA Fisheries also funds
approximately $1.2 million annually for IMW studies in Oregon, Washington, and Idaho.

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As pointed out by Dr. Lubchenco’s scientific workshop with independent expert scientists,
existing adult and juvenile status and trend monitoring needs to be better integrated and
expanded in geographic scope to be cover of all Interior Columbia Chinook salmon ESUs and
steelhead DPSs at the population scale. Coordinating juvenile abundances with adult
abundances (i.e., “fish in/fish out”) within populations will allow for a better understanding of
productivity in freshwater life stages and the ability to better inform life-cycle modeling. The
expert panel also emphasized the need for rapid responses to sharp population declines, and
enhanced monitoring of adults and juveniles with quicker dissemination of data can better inform
adult and juvenile contingency triggers.

Informed by the findings and recommendations of the collaborative workshops, the Action
Agencies will revise and/or augment ongoing fish-in/fish-out monitoring to ensure the coverage
of least one population per MPG. For some of these populations, a sample of juveniles will be
measured (length and mass) to assess growth conditions. These monitoring improvements will
be coordinated with improvements to ongoing habit monitoring as part of the FCRPS action
effectiveness evaluations (RPAs 56 and 57). It is anticipated that implementing an improved
fish-in/fish-out, fish size, and habitat effectiveness monitoring strategy will include the
implementation of additional IMW studies and other habitat monitoring programs paired with
fish-in/fish-out monitoring. To this end, BPA is supplementing existing fish-in/fish-out
monitoring activities with the addition of $9 million dollars in BiOp placeholder funds, and is
also providing an additional $100K technical support plus 0.3 FTE for annual evaluations of
fish-in/fish-out and other biological and environmental metrics relative to contingency triggers.

The Action Agencies are proposing to better coordinate tributary climate change information,
including flow and temperature monitoring and fish-in/fish-out information (i.e., censusing adult
spawners and subsequent juvenile migrants). Through expanded implementation of improved
and better-coordinated monitoring designs, population fish-in/fish-out monitoring efforts in the
Columbia Basin will afford adaptive management of climate change impacts, restoration efforts,
and other management actions in response to adult and juvenile contingency triggers. Climate Change

The FCRPS BiOp includes a commitment from the Action Agencies to report annually in their
progress reports on climate change research. The Federal agencies will expand and strengthen
this approach through joint NOAA Fisheries and Action Agency review of climate change
information, with reporting of this information to the RIOG and the public in the annual and
cumulative progress reports.

▪ Habitat and Ocean Conditions: Ongoing and enhance tributary habitat and ocean
research will provide a data base on freshwater habitat and ocean conditions, allowing
tracking of changes over time.

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▪ Annual Reports: RPA Action 2 requires inclusion of new, pertinent climate change or
research in the Action Agencies’ Annual Progress Reports. To ensure this will be
accomplished each year, by June 1, NOAA Fisheries will provide to the Action Agencies
a survey of any new climate change studies, scientific papers or modeling work relevant
to BiOp implementation and fish status.

▪ Habitat Project Priorities: RPA Actions 35 and 37 require that new climate change
information be used to guide tributary and estuary habitat project selection and
prioritization and other aspects of adaptive management. The NOAA Fisheries review
described above will also be used for this purpose.

▪ Forecasting and Modeling: RPA Action 7 requires that new climate change information
be used to update forecasting and modeling of the hydrology and operations of the
FCRPS. The Action Agencies have already made significant progress on this task and are
incorporating climate change modeling from the University of Washington’s Climate
Change Impacts Group in developing the data sets that will be used for the agencies’
longer term water management planning.

In addition, the Federal agencies collectively are coordinate an inventory of existing, ongoing
and planned climate change studies. Climate change developments will be discussed and
coordinated through the RIOG.

1.1.6 How Research, Monitoring, and Evaluation will be incorporated into FCRPS BiOp
Implementation Decisions
The FCRPS BiOp envisions a collaborative and transparent adaptive management process with
the region’s sovereigns. Each fall, the Actions Agencies will prepare and discuss annual
progress reports within the framework of the RIOG, including progress on specific performance
standards and targets and progress on implementation of the RPAs. As new data and information
becomes available from the extensive monitoring and new lifecycle analysis that information
will be also be included in the annual progress report and vetted with the RIOG technical and
senior technical teams, made up of regional scientists and experts. As discussed in the climate
section of this plan, annual progress reports will include a survey of any new climate change
studies, scientific papers or modeling work relevant to BiOp implementation and fish status.
Potential adjustments to RPA actions will be discussed by the various senior technical teams
along with specific recommendations for adaptations to the RIOG. RIOG senior policy
representatives will further discuss adaptive measures so that they may be captured in upcoming
implementation plans. The RIOG is currently in the process of developing specific operating
procedures to ensure transparency throughout this adaptive management process.

The RIOG procedures will also address dispute resolution for both scientific and policy issues.
Senior technical teams will be responsible for outlining the elements in dispute, to include
relevant science information and various sovereign viewpoints. At any time, the RIOG may seek

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independent scientific review of science disputes from the ISAB, IRSP or other body. For policy
disputes, the RIOG may also seek an opportunity for public input into a policy issue or dispute.
If so, timely notice and relevant materials will be made available to the public. If resolution
is not achieved within the RIOG process, the regional federal executives will attempt to reach a
decision to accommodate the proposed change taking into account the RIOG's recommendations.
If there is further disagreement, or if the proposed management action lies outside the authority
of the regional federal executives, the RIOG and respective agency recommendations would be
forwarded to the Administration Salmon Policy Team for ultimate resolution.

1.2 Contingency Framework

1.2.1 Adult Triggers

As part of the administration’s review of the FCRPS BiOp, scientists suggested that a refinement
of the BiOp’s adaptive management and contingency planning processes could provide
additional surety that the BiOp is implemented in a precautionary fashion through 2018.
Specifically, the scientists suggested that additional “early warning” triggers be developed that
would be sensitive to 1) unexpected declines in adult abundance and 2) natural disasters or
environmental degradation (either biological or environmental) in combination with preliminary
abundance indicators. They further advised that these triggers be based on simple metrics that are
readily available.

This document describes two triggers – as refinements of the adaptive management and
contingency planning processes – that are responsive to the scientists’ advice, are transparent to
ongoing regional processes, and are not likely to result in a series of “false-positive” events.
The first trigger (Unexpected Severe Declines) relies upon 4-year rolling averages 2 of the
estimated numbers of naturally produced adults at key locations (typically dams where fish can
readily be counted) in the Snake and Columbia Rivers.

The second trigger (Early Warning) is a surrogate for the Unexpected Severe Decline trigger
which considers both recent abundance information (in relation to the Unexpected Severe
Decline triggers) as well as biological or environmental information that strongly suggests that
substantially reduced productivity would be expected to continue for several additional years.

Note: Four succeeding years of declining abundance was considered as a Unexpected Severe Decline trigger, but
was rejected in favor of a four year average abundance trigger based on a review of the available data. A trigger
using four succeeding years of decline, regardless of the magnitude of the decline, is expected to result in many
“false negative” results (i.e., the decline during those four years would not negate the expectation that the longer-
term trend analyzed in the BiOp will remain positive). The detailed evaluation of trends is appropriately considered
at the 2013 and 2016 check-ins to evaluate the BiOp’s assumptions about the recovery prong of the jeopardy
standard, whereas the Unexpected Severe Decline trigger is more indicative of increased extinction risk and extreme
changes in trend should abundances fall to very low levels.

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The remainder of this document describes the formulation of these triggers in greater detail.

It is important to remember that triggering the proposed Unexpected Severe Decline or Early
Warning Triggers within the term of the 2008 FCRPS BiOp is not an expected or even likely
outcome. Indeed, under the 2008 BiOp the abundance of the ESUs on average are expected to
increase over time. However, inclusion of these triggers as part of the 2008 BiOp's adaptive
management and contingency implementation processes provides additional assurances that the
2008 BiOp is implemented in a precautionary fashion from the perspective of the ESA-listed
salmon and steelhead species. Unexpected Severe Decline Trigger for Chinook Salmon and Steelhead
The purpose of the Unexpected Severe Decline Trigger is to detect unexpected and severe
declines in the abundance of ESUs 3 so that rapid response actions can be implemented in a
timely fashion to minimize or mitigate for an unforeseen downturn. The metric of exceptionally
low abundance measured over a four-year period was selected as a trigger for rapid responses for
several reasons. First, this metric is relatively easy to measure in a rapid manner and is easily
interpretable. The four-year period corresponds approximately to a generation for most ESUs,
and the International Union for Conservation of Nature (IUCN) recommends examining
population declines over a time period representing one generation. Furthermore, the ICTRT
risk assessments incorporated a quasi extinction threshold expressed in terms of a 4-year sum of

Development of the Unexpected Sever Decline Trigger was based on the following steps:

Step 1: Identify available data. The proposed approach uses US v. Oregon Technical Advisory
Committee (TAC) run reconstructions (estimates of naturally produced adult Chinook Salmon 4
and steelhead) based on adult dam counts. Counts at Lower Granite Dam are used for Snake
River ESUs, counts at Priest Rapids or Rock Island dams are used for Upper Columbia River
ESUs and counts at Prosser Dam are used for the Yakima River MPG of Mid-Columbia River
steelhead. 5 The available data varies by ESU within the 1975 to 2008 time frame.

ESU-level adult abundance information is the most readily available information at present. Future refinements of
the Unexpected Severe Decline trigger could potentially be extended to the Major Population Group (MPG) or the
population level.
Chinook “Jacks” are excluded from this data as they are predominantly small males which return to spawn after
spending only a single year in the ocean and generally represent a minor contribution to the viability of a population.
Mid Columbia River steelhead populations pass 1-4 mainstem dams and cannot be distinguished at those dams
from other listed species traveling further upstream. Prosser Dam is an adult counting site on the Yakima River that
does provide a census of adults in this MPG. In addition to the Yakima River MPG, it may be possible to develop
MPG level indices for other MPGs in the future.

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Step 2: Evaluate the historical Abundance Pattern Relied Upon in the BiOp. The proposed
approach uses four-year rolling averages of the TAC data (e.g., the average of the 1997 through
2000 returns make up the 2000 four-year average, 1998 through 2001 returns make up the 2001
four-year average, etc.). Based on the historical period evaluated in the BiOp (approximately
1980 to present), the observed four-year rolling averages were sorted from high to low and
plotted to create exceedence curves (cumulative density functions). These depict the percent of
years in the data set in which the four-year rolling average was greater than a particular
abundance level. See Figure 1 for Chinook salmon ESUs and Figure 2 for steelhead ESUs.

Step 3: Identify Abundance Levels That Were Not Expected in the BiOp. An examination of the
resultant exceedence curves for Chinook salmon (Figure 1) indicate that of the observed four-
year average abundances, about 15-25% are relatively high; about 5-15% are relatively low, and
the remainder are close to average, showing relatively little variation. The pattern is less clear for
steelhead ESUs, whose distribution is more continuous (Figure 2).

Declines to these levels, given the analysis in the BiOp, would indicate that abundance levels are
lower than expected—triggering actions to improve survival while abundance levels are still high
enough to prevent extinction.

The Action Agencies conducted a prospective analysis of the likelihood that the Snake River
spring/summer Chinook salmon ESU would fall below certain abundance thresholds
representing four year running averages. A Beverton-Holt production function was fit to Lower
Granite Dam natural adult abundances during the 1978-1994 period and then projected forward
24 years. Four thousand simulated trajectories were used in the probability calculation. The
"future" trajectories were initialized with the geometric mean of the time series of spawners from
1994-2003. The results of this analysis indicated that an abundance threshold of 4,500 average
adults would be expected to occur in only about 10% of the years, which is very similar to the
estimate based on the exceedence curves (Figure 1). This analysis confirmed that the simpler
exceedence curve methodology is reasonable for determining the likelihood of reaching
particular abundance levels.

Step 4: Specify the Triggers. Thus, we propose that the 90th percentile (dashed vertical line on
Figures 1 and 2) be used as a “hard” trigger for implementing Rapid Response Actions (see
Contingency Planning and RM&E Document); and the 80th percentile (dotted vertical line on
Figures 1 and 2) be used as a “soft” trigger that would engage closer examination and potential
readying of Rapid Response actions for more rapid implementation if the ESU(s) in question
continue to decline.

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The 90th percentile exceedence level was selected as a threshold level because this is a level
below which mean four-year abundances for Chinook salmon dropped rapidly (Figure 1). This
level represents a marked departure from median abundance levels (especially for Chinook
salmon), but is also somewhat above the lowest observed four-year period for both Chinook
salmon and steelhead (the 1990 levels that led to ESA listings). While falling to these levels is a
cause for concern, they are precautionary in that they represent ESU abundance that is at least 3-
4 times higher than the abundance if all populations dropped to the 50 fish quasi-extinction

In addition, the Action Agencies conducted a prospective analysis of the likelihood that the
Snake River spring/summer Chinook salmon ESU would fall below certain abundance
thresholds representing four year running averages. The estimation was accomplished by fitting
a Beverton-Holt production function to the ESU level data, then projecting forward 24 years.
Four thousand simulated trajectories were used in the probability calculation. The base case
expected fraction was estimated from brood years 1978-1994. The "future" trajectories were
initialized with the geometric mean of the time series of spawners from 1994-2003. The results
of this analysis were very similar to the exceedence curves developed by NOAA Fisheries for
Snake River spring/summer Chinook salmon.

Taken together, use of the 90th percentile as a threshold protects against false negatives while
kicking in well before historic low levels are reached.

As an additional precaution, the 80th percentile will serve as a “soft” trigger requiring closer
examination of the available data and the readying of Rapid Response actions for more rapid
implementation if the ESU(s) in question continue to decline.

Table 1 summarizes the four-year average abundance levels corresponding (closest value or
average of two nearest values rounded to the nearest 25 fish) to the 90th and 80th percentiles in
Figures 1 and 2.

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Table 1. Summary of ESU-Specific Unexpected Severe Decline Triggers (Average 4-year

Abundance of Naturally Produced Adults).

Species 90th Percentile Trigger 80th Percentile Trigger

SR fall Chinook 350 400

SR spring/summer Chinook 4,850 7,575
UCR spring Chinook 450 1,125
SR steelhead (A-Run) 6,800 7,825
SR steelhead (B-Run) 1,350 1,850
UCR steelhead 975 1,100
MCR steelhead (Yakima R.) 775 975 Early Warning Trigger for Chinook Salmon and Steelhead

The purpose of the Early Warning Trigger is to detect factors indicating that the Unexpected
Severe Decline ESU 6 abundance levels are likely to be reached within one to two years so that
rapid response actions can be implemented in a timely fashion to minimize or mitigate for an
unforeseen downturn. It is intended to be a failsafe that could be triggered before the Unexpected
Severe Declines triggers are exceeded. The trigger would evaluate whether an ESU is likely to
have substantially reduced abundance (and productivity) in the future, based on two years of
adult return information, preliminary biological information and environmental indicators or
known natural disasters. These indicators may included, but are not limited to, low jack counts or
juvenile migrants (biological), indicators of ocean conditions predicting very low abundance of
adult returns for recent outmigrant (environmental indicators), or wide-spread forest fires,
increased distribution and virulence of pathogens, new invasive species, prolonged severe
droughts etc. (natural disasters).

Initial assessments suggest that juvenile monitoring (numbers, sizes, condition, etc.) of interior
Columbia River basin ESUs (or MPGs or a subset of populations) at dams and in tributaries
would likely provide information that could complement the adult monitoring information and
further enhance the Early Warning Trigger in the future. Additional work will be required in
order to inventory the current monitoring program, determine what additional monitoring might
be needed, and assess how best to collect and use this information to inform the Early Warning
Trigger at the ESU, MPG, or population scale.

ESU-level adult abundance information is the most readily available information at present. Where feasible, future
refinements of the Early Warning trigger could potentially be extended to the Major Population Group (MPG) or the
population level.

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Implementation of the Early Warning Trigger would involve the following steps:

Step 1: Determine if the most recent two-year average of adult returns is near the threshold
levels used for the Unexpected Severe Decline Trigger (above).

Step 2: Determine if there are any biological or environmental indicators that would suggest that
ESUs are likely to experience low abundance in the next two or more years. This information
could include, as an example, extremely low jack counts (a preliminary biological indicator that
next years returns will be much lower than average) and ocean indicators (both biological and
environmental) that indicate that recent outmigrants are likely experiencing extremely poor
ocean conditions that would be expected to result in substantially reduced numbers of naturally
produced adults in the next two years.

Step 3: Assess whether there have been any "natural disasters" such as wide-scale forest fires,
volcanic eruptions, rapid increases in the distribution or virulence of fish pathogens, or mud-
slides that would be likely to substantially reduce the productivity of freshwater habitat or
severely limit the ability of adults or juveniles to migrate to or from this habitat. Responses to
impacts affecting a specific MPG or subset of populations would be tailored to the appropriate

After evaluating each of the factors in steps 1-3, a determination would need to be made as to
whether or not there is a reasonable likelihood that future adult returns would fall to levels
triggering the Unexpected Severe Decline Trigger (see above) or the existing BA/BiOp trigger. If
the determination is affirmative, then the Rapid Response Actions would be implemented.

1.2.2 Development of Future Juvenile Triggers

NOAA Fisheries and the Action Agencies will establish a juvenile monitoring program for
Interior Columbia basin ESUs that provides for early warning of regional or population specific
changes in juvenile production or survival. The program will be designed to complement adult
monitoring, providing an early opportunity to detect substantial changes in productivity
(measured as abundance or survival) at the ESU, major population group or population level. In
addition to abundance based metrics, the program will monitor changes in parr/smolt size or
timing that might translate into changes in cumulative life cycle survival or productivity.

Juvenile out-migrant metrics would complement adult based measures and should provide an
early opportunity to detect patterns or trends than adult based approaches that might otherwise be
masked by the relatively high year to year variation in ocean survival rates typical of salmon
runs. The primary objectives for a juvenile monitoring program will be to:

ƒ Enable detection of within ESU (specific to particular MPGs, populations, major life
history groupings) sudden downturns in natural production levels.

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ƒ Complement environmental measures, jack return metrics etc. to detect sudden
downturns in abundance at the ESU/MPG level.
ƒ Detect changes in size, timing other condition factors that could be early warning signs of
regional environmental impacts (e.g., local or subregional climate change impacts, etc.)

The approach would incorporate at least three types of juvenile monitoring efforts. At the ESU
or major population group level, the monitoring framework would incorporate estimates of
aggregate juvenile abundance or productivity generated through updated sampling programs
targeting the aggregate wild run from an ESU or MPG (e.g., Lower Granite Dam smolt
sampling, Rock Island Dam juvenile sampling, Prosser Dam outmigrant monitoring in the lower
Yakima River. Sampling programs designed to estimate juvenile production from a specific
tributary would also be included (e.g., Grande Ronde River sampling programs, Yanke et al.
2007). A third major program component would include out-migrant marking/downstream
monitoring designed to collect information on the timing/size of migration from a given reach
(e.g., Achord et al. 2007). The tributary production and out-migrant evaluation programs
generate information on the size and timing of annual outmigrants. The size individuals attain
during the juvenile life stage has direct consequences for fitness through size-selective mortality
in later life stages (e.g., Zabel and Williams 2002) and enhanced reproductive success of larger
individuals (Kingsolver & Huey 2008). Further, migration timing is related to growth, with
larger individuals within a population out-migrating earlier than smaller ones (Achord et al.
2007). Thus, juvenile fish size is an indicator of habitat quality, particularly for higher elevation,
lower nutrient streams found in the interior Columbia River basin. Deviation from long-term
average fish size is potentially an indicator of deterioration in conditions related to juvenile fish

Monitoring fish size at a specific time in the season can provide several benefits:

1) A general indication of the fish and habitat status.

2) An early indication if habitat conditions have changed for the worse and further actions
are required.
3) An indication of whether habitat actions are effective.

Each population has different growth patterns, and thus annual measures of fish size should be
compared to long-term patterns of the population.

Annual results from a structured juvenile monitoring program would serve as inputs into early
warning assessments. Life cycle assessment tools would incorporate results from annual juvenile
modeling along with environmental indices and recent adult return data to generate probability
based projections of near term risks (see Section above). A second general application
would be to detect or confirm changes in production among populations within ESUs. For
example, patterns in smolt per spawner or population size characteristics could indicate impacts
of changing climate conditions or the effects of local changes in habitat conditions, etc.

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2009 FCRPS Adaptive Management Plan Implementation. As a first step, ongoing juvenile monitoring efforts will be inventoried
and evaluated as potential contributors to the annual juvenile trigger program. Some of these
metrics have been employed for past evaluations or could be implemented with information from
ongoing studies. Those metrics would be verified and updated for application beginning with the
2010 out-migration.

This step would also include defining explicit technical guidelines for metrics and triggers
considering each of the categories of juvenile monitoring listed above. The trigger guidelines for
juvenile monitoring would include an evaluation of alternative criteria applicable to each
category. For example, annual indices of total natural origin smolt production from a given
region that are generated from an effort with a relatively long historical series might incorporate
a trigger based on a statistical analysis of the time series or on stochastic modeling. The same
general approach could also be used to define specific criteria based on the size distribution of
migrants or on timing metrics. Smolt per spawner metrics could be evaluated against minimums
based on past performance or estimates generated by stochastic population modeling.

The inventory of current juvenile monitoring activities would also be a starting point for
identifying opportunities for expanding on the initial set to ensure appropriate coverage at least at
the major population group level across each ESU in the Columbia River basin. The review
would be used to identify additional monitoring sites or metrics for implementation, specifically
identifying opportunities that could begin to generate information prior to 2013 status /
implementation check-in called for in the FCRPS Biological Opinion. Selecting and
implementing additional monitoring actions for the program could be carried out in conjunction
with the ongoing process to develop annual population level fish-in fish-out monitoring
(described in accompanying attachment Fish In/Fish Out monitoring support to BiOp contingency
planning). The guidelines for early warning trigger metrics and criteria will inform the design
and selection of additional monitoring actions through that effort.
1.2.3 Rapid Response Actions Hydro Actions

The BiOp provides a systematic approach to achieving dam passage performance standards at
the mainstem dams, with accountability for specific survival results. Species response to spill,
bypass and transport varies from dam to dam therefore the RPA is structured to apply the most
effective operation at each dam factoring in species migration timing. To improve fish survival
and meet BiOp performance standards and metrics (e.g. 96% dam survival for spring migrants,
etc.), the RPA spill, bypass, and transport operations at mainstem Snake and Columbia River
projects are adaptively managed annually based on results of biological studies. These results are
discussed and operations modified in collaboration with sovereign representatives to ensure
targets are being met based on the best available scientific information.

In 2009, spill and transport operations under the adaptive management provisions of the BiOp
were modified to continue spill for two weeks in May at the Snake River collector projects as a

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result of an ISAB recommendation and agreement with RIOG. This was done for one year
despite concern about adverse affects on Snake River steelhead. The adult return information
will be reviewed in fall 2009 to determine future years’ operation based on the best available

The RPA also requires the use of Configuration and Operational Plans (COPS) to describe
existing dam configuration and operations, and identify additional dam improvements needed to
achieve the performance standards. These plans are based on the best available scientific
information in collaboration with sovereign representatives. The COPS include a process to
assess, following installation and testing of planned fish passage features, whether performance
standards are being met. In the event performance standards are not being met, Phase II
contingency actions will be discussed and implemented as long term contingency actions. Phase
II measures may include, for example, additional surface passage and other juvenile passage
improvements. In addition to the BiOp provisions, the Fish Accords include “no backsliding”
metrics for forebay delay and spill passage efficiency.

If a biological trigger is tripped, the Action Agencies and NOAA Fisheries, in collaboration with
RIOG and appropriate technical groups (hydro coordination team), will review the current status
of the biological research at the dams and discuss where additional project survival benefits
could be gained in relation to the specific ESU in question. This will include assessing whether
there are potential spill and/or transport operational adjustments that could be made to address
the problem contributing to the decline or the condition affecting survival, in order to maximize
additional survival benefits.

This discussion will inform the spill and transport operations the Action Agencies will
implement. These rapid response actions could include actions taken in the short term that may
exceed performance standards for a particular species. (e.g. increase steelhead transport or
increase spill at mainstem dams, if warranted)

The primary difference in this rapid response option is assessing which of the mainstem dams
could increase survival, potentially above the dam passage performance standard, by making an
operational adjustment such as increasing spill or transport if triggered.

The planned testing of dam passage improvements currently anticipated in the BiOp will include
assessment of the SPE and forebay delay to ensure “no-backsliding” occurs consistent with the
Fish Accords. The assessment will also consider adult passage, water quality, and other potential
environmental effects. This information will be useful in the event a rapid response is triggered
to ensure an informed quick response operation will not degrade other environmental conditions.
If the new operation has not been previously tested, the operation being implemented would
likely require a test program to confirm the operation is producing the expected increased

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2009 FCRPS Adaptive Management Plan Harvest Responses Terminal Fisheries. In the event of an early warning or severe decline, all terminal
fisheries that affect the populations or ESUs of concern would be reviewed to assess whether
existing harvest management provisions provide protection appropriate for the circumstances.
Changes to existing terminal fishery regulations can be targeted to the populations, MPGs, or
ESUs of concern. NOAA Fisheries can affect these changes through their ESA authority.
t Terminal fisheries generally refer to those that occur in areas above Lower Granite Dam on the
Snake River and McNary Dam on the upper Columbia River. These are managed by the states
and tribes and are outside of the scope of the current U.S v. Oregon Agreement. Terminal
fisheries are generally directed at hatchery-origin fish, are often mark-selective and located in
place and time to target hatchery fish, and are highly responsive to changes in abundance. There
are nonetheless some incidental impacts to natural-origin fish. The level of harvest that may
occur when abundance is very low will be populations specific depending on the location of
remaining fisheries. Impacts in terminal fisheries will be on the order of 0% to 2%. U.S. v Oregon Fisheries. U.S. v. Oregon refers to a settlement agreement between five
tribes, three states, and the federal government. The agreement establishes rules for managing
harvest and hatchery production in the Columbia Basin in areas above Bonneville Dam. The
agreement is a stipulated order and operates under the continuing jurisdiction of the federal
court. The U.S v. Oregon agreement and all its provisions are central to the overall settlement in
the FCRPS litigation, particularly for the tribes, and cannot be changed unilaterally in any detail
without substantive consultation and agreement with the affected parties.

Fisheries under the jurisdiction of the U.S v. Oregon Agreement generally occur in the mainstem
Columbia River from the river mouth up to McNary Dam. UCR spring Chinook and SR
spring/summer Chinook are caught in spring season fisheries. Under the current abundance
based management framework harvest rates vary between 5.5% and 17%. At the lowest level of
abundance, fisheries are scaled back under the agreement to 5% to provide limited opportunity
for tribal ceremonial and subsistence fisheries.

All SR fall Chinook harvest in the Columbia River occurs in fall season fisheries that are subject
to the U.S. v. Oregon agreement. SR fall Chinook in the Columbia River are managed subject to
an abundance based harvest rate schedule. Under the current schedule harvest rates on SR fall
Chinook vary between 21.5% and 45%. At the lowest level of abundance, fisheries for fall
Chinook are allocated 1.5% to the non-Treaty fishery and 20% to the Treaty fishery.

Most of the harvest of upriver steelhead in the Columbia River occurs in fall season fisheries
subject to the U.S v. Oregon agreement (additional harvest occurs in terminal fisheries as
discussed above). Under the agreement, non-Treaty fall season fisheries are subject to a 2%
mortality limit for steelhead. Treaty Indian fisheries are subject to an abundance base harvest
rate for “B-run” steelhead. B-run steelhead are a component of the SR steelhead DPS. The

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allowable harvest rate ranges from 13% to 20%. Harvest rates on “A-run” steelhead that return
to the UCR DPS and parts of the Snake River are lower, generally less than 10%.

Harvest rates on Snake River sockeye are limited to 1% in non-Treaty fisheries and 5% to 7% in
Treaty fisheries.
An early warning or severe decline may suggest the need for a harvest response affecting
fisheries subject to the U.S v. Oregon agreement. In that event, NOAA Fisheries will invoke
Section I.B.8 of the agreement that allows any party to seek modification of the agreement at any
time. NOAA Fisheries will use the procedural provisions of the agreement to seek the consensus
necessary to modify the U.S. v. Oregon agreement. If consensus cannot be reached, NOAA
Fisheries may withdraw from the agreement as a last resort. Ocean Fisheries.  Of the seven ESUs and DPSs considered here SR fall Chinook is the
only one caught in ocean fisheries. SR fall Chinook are caught in fisheries in Alaska, Canada,
and off the Washington/Oregon coast. Ocean fisheries are subject to provisions of the Pacific
Salmon Treaty; fisheries off of Washington/Oregon are also subject to regulation through the
PFMC and NOAA Fisheries. Roughly half of all harvest impacts to SR fall Chinook occur in
ocean fisheries.
If the early warning or severe decline applies to SR fall Chinook and NOAA Fisheries
determines that a harvest response Is required, NOAA Fisheries will engage the U.S. v Oregon
parties as described above, take action to reduce harvest in U.S. ocean fisheries, and seek to
negotiate further reductions in Canadian fisheries through emergency provisions of the PST
agreement. Safety-Net Hatcheries

Under RPA 41 and 42 of the FCRPS BiOp, BPA will fund ongoing and new safety net and
conservation hatchery programs to preserve genetic resources, reduce short-term extinction risk
and promote recovery of ESA-listed populations of Snake River sockeye salmon, Snake River
spring/summer Chinook salmon, Upper Columbia spring Chinook salmon, Upper Columbia
steelhead, Middle Columbia steelhead, and Columbia River chum salmon. Under RPA Action
39, the Action Agencies will continue funding FCRPS mitigation hatcheries in accordance with
existing programs and will adopt programmatic funding criteria for funding decisions. Safety Net Hatcheries Approach as a Rapid Response Action. During FY 2010, the
Action Agencies and NOAA Fisheries in consultation with the RIOG will develop Rapid
Response Contingency Plans for each ESU and DPS of the interior Columbia basin. These plans
will include mitigation actions that will immediately enhance fish survival and for which the
needed regulatory process is already largely in place. If triggered, actions will be implemented
relatively quickly and provide immediate survival benefits. Most, if not all contingencies
included in the Rapid Response Plans are intended to be temporary in nature.

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The following are immediate actions that should be taken to prepare for using hatcheries as a
safety net.

ƒ Determine whether any additional safety net programs are needed. Because there may be at
most a limited need for expansion of the existing programs. Hatchery propagation entails
risks as well as benefits to listed species, so for ESUs with numerous populations there are
both genetic and ecological reasons to “spread the risk” by identifying some populations that
would remain free of supplementation under all circumstances.
ƒ Existing hatchery facilities can provide immediate increases in the egg-to-smolt survival of
listed species (Table 1- Listing of Listed Population and associated Hatchery Programs
according to ESU). Mitigation funds (Bonneville Power Administration, U.S. Bureau of
Reclamation, and U.S. Army Corps of Engineers) and Mitchell Act monies supports these
hatchery programs. Some programs already culture listed populations as captive broodstock
where fish are retained full-term through all life stages in order to accelerate increases in
effective population size. The artificial propagation of these populations from the egg stage
through smolt stage reduces natural mortality rate as compared to the natural environment.
These programs do have risks (genetic and ecological) that are regulated and managed
through NOAA approved Hatchery and Genetic Management Plans (HGMPs). Programs
already in place can serve as a part of a short-term contingency plan.

ƒ NOAA Fisheries, the Action Agencies and the co-managers will develop a Plan of Action
(POA) for using safety net hatcheries as part of the rapid response plan, to include the

1. Identity of the species or population that has reached the “trigger” for use of a safety net
2. Action, location, anticipated production needs and goals, monitoring plan, funding
authority, cost estimate and risk assessment.
3. Approval of the safety-net conservation action by NOAA, state and tribal authorities.
4. Annual reporting requirements
5. Adaptive management plan

If necessary, the Rapid Response Plan could call for either (1) the reactivation of closed
hatchery facilities (central and/or satellite) as safety-net hatcheries and/or (2) retro-fit of existing
safety-net hatcheries in order to supplement and/or enhance fish production capabilities. Rapid Predation Responses

The FCRPS BiOp RPA identified specific actions that will be undertaken with respect to avian,
piscivorous fish, and sea lions to reduce the take on juvenile and adult listed salmon and
steelhead. The following delineates the specific measures being taken.

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2009 FCRPS Adaptive Management Plan Sea lions. The current BiOp RPA calls for the Corps to install and improve as needed
Sea Lion Excluder Devices in the fishways at Bonneville annually. It also requires support for
hazing actions by NOAA Fisheries, Tribes, and the States of Oregon, Washington, and Idaho.
The BiOp assumed the continuing impact of pinnipeds at the Bonneville tailrace to be
approximately 3% for spring Chinook and 7.6% for winter run steelhead. The removal action
initiated in 2008 and 2009 should further reduce pinniped take on adult salmon and steelhead. Piscivorous Fish. Ongoing implementation of enhanced Northern Pikeminnow

Management Program (NPMP) as described in RPA 43 – general increase in the reward structure
in the sport-reward fishery; evaluation of the effectiveness of focused removals at lower
Columbia FCRPS projects. The current NPMP deploys USDA employees to conduct dam
angling in forebay and tailrace areas at two FCRPS projects.

Rapid response efforts will include increasing dam angling efforts at more FCRPS projects to
increase overall catch to contribute to program exploitation rate and potentially improve within
year dam passage survival of outmigration juvenile salmon. There is also a small increased
benefit of dam removals relative to the general public fishery because pikeminnow removed
from these areas tend to be larger and therefore more predacious. The proposal would increase
our dam angling program from one crew to three crews with the mobility and flexibility to fish
all eight mainstem dams. Avian Predation. The current RPA identifies both on the ground actions as well as
RM&E to reduce the impact of avian predators on listed juvenile salmon and steelhead (BiOp
RPA Actions 45, 46, 47, and 48). Several of the avian predation actions are underway. The
BiOp calls for reducing tern habitat in the estuary. It is anticipated that by 2010, the creation of
new habitat outside of the Columbia River will be completed that will allow for reduction in tern
habitat in the estuary from 6 acres to 1.5 to 2.0 acres. The result of this action will reduce terns
to approximately 2,500 to 3,125 breeding pairs.

The BiOp RPA requires additional actions on double-crested cormorants (RPA 46 and 47).
Cormorants numbers have been increasing in recent years with a corresponding significant take
on juvenile salmon and steelhead. Information is currently being gathered to allow for the
development of alternative actions to reduce cormorant predation both in the estuary and inland
areas. With respect to cormorant take on listed salmon and steelhead, the BiOp analysis was
based on maintaining the current level of take. Further actions on cormorants will require NEPA
documentation which will identify future potential actions.

The BiOp RPA (Action 48) requires the Corps to continue to implement and improve avian
deterrent programs at all lower Snake and Columbia River dams. Gulls and other avian
predators feed in the near vicinity of spillways and juvenile bypass outlets to feed on passing
juvenile salmon and steelhead. For instance in 2009, gull activity increased in the spillway
tailrace at John Day Dam. Several key avian wires had failed allowing for increased gull

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predation. Operations were altered during the season to decrease take on listed salmon. In 2010,
improvements in bird wires and potential for additional hazing are being discussed to improve
the condition.

Avian hazing at McNary and Lower Snake River dam currently occurs from 1 April through 1
July, eight hours per day at each dam. Activity is land based using pyrotechnics. Wire arrays are
also in place at all dams to reduce avian predation in the tailrace. They are efficient in reducing
avian activity where they are in place.

Rapid Response efforts will include increasing hazing at projects. These measures will use boats
to carry out hazing efforts, increase the hours conducted per day, and the season will be extended
though July. Lethal measures may also be employed.

1.2.4 Long-Term Actions Hydro Phase 2

The RPA’s (18- 25) require the use of Configuration and Operational Plans (COPS) to identify
additional dam improvements needed to achieve the performance standards. These plans are
based on the best available scientific information and developed in collaboration with sovereign
representatives. The COPs consider multiple alternatives and categorize those alternatives into
Phase I and Phase II actions. Phase I modifications are those that are anticipated to improve
survival levels to meet the dam passage performance standards. Phase II actions are contingency
actions to be implemented should the Phase I actions not achieve the standards. Likely
modifications for inclusion in the COPS as Phase I and Phase II actions are described in the BA
(pages B.2.1-26-48). The Phase II contingency plans will be updated when the dam specific
COPS are updated. Phase II measures may include, for example, additional surface passage and
other juvenile passage improvements

Actual implementation of Phase II actions will be dependent on results of on-going research,

regional collaboration and prioritization, and future appropriations.

As part of the refined Adaptive Management Plan for implementation of the BiOp’s adaptive
management framework, the Action Agencies will assess potential hydro actions for inclusion in
ESU-specific long-term contingency plans. The Phase II hydro actions identified in the various
COPS will be included in the long-term contingency plans. These actions could be implemented
if a biological trigger requiring the implementation of contingency actions is tripped even if the
performance standards are being met.

In the event that triggers are tripped and rapid response actions are not sufficient to put the ESU
on track, the Action Agencies will: 1) review the most recent Long-term Contingency Plan for
the ESU in question and the current status of the recent biological research at the dams with the
regional agencies and Tribes, 2) initiate a discussion with RIOG and appropriate technical groups

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regarding the additional project survival benefits that could be gained for the specific ESU in
question. In support of this discussion NOAA Fisheries will be model the contingency actions to
determine likely improvements. If these discussions and evaluations indicate improvements are
warranted, the Action Agencies will initiate the appropriate dam specific long-term contingency
actions (including additional Phase II contingency actions) as part of the overall package of
contingency actions deemed sufficient to address the triggering event for the targeted ESU. John Day Minimum Operating Pool

The Action Agencies will initiate discussions with RIOG on the relevant hydraulic and
biological information to better understand the biological benefits and/or detriments associated
with John Day reservoir operations.

A study of operating John Day Dam at its minimum operating pool (MOP), including impacts to
project uses during juvenile fish passage was initiated in 1992 and culminated with a report
entitled, John Day Minimum Operating Pool Technical Report, dated April, 1994. The study was
conducted in response to paragraph III.4.6.a.(2) of the Northwest Power Planning Council
(NPPC) publication 91-31 “Amendments to the Columbia River Basin Fish and Wildlife
Program (Phase Two)," dated December 11, 1991.The proposed operation of John Day at its
MOP level (elevation 257), from 1 May through 31 August, was evaluated for its benefits and
impacts to the existing project, anadromous fish, the environment and other uses of the reservoir.
An option to operate at MOP level year-round, to provide for partial mitigation of environmental
impacts, was also considered in the study.

In general, project facilities at John Day Dam are designed for operation at MOP as this was
within the authorized operating range for the reservoir. However, the study identified significant
impacts associated with operating at MOP, for which the Corps does not have authority to
mitigate. These include impacts to: irrigation, municipal water supplies, hatchery water supplies,
anadromous and resident fish habitat, wildlife habitat, recreation sites, cultural resource sites, and
adult passage facilities.

By 2012, the Action Agencies will prepare a detailed study plan to layout the scope, schedule
and budget for reevaluation if warranted from review of the biological analysis. The scope will
address biological, engineering, environmental, socio-economic impacts, and other necessary
tasks and activities required to assess the feasibility of implementing the planned reservoir
operation. It will include assessment of: biological effects (benefits and/or decrements); physical
impacts; funding options; alternatives; mitigation of effects on reservoir/dam users; and, other
feasibility issues. If the biological trigger is tripped, the Corps could pursue the authority to
mitigate the impacts of operating John Day Dam at MOP.

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2009 FCRPS Adaptive Management Plan Hatchery Reforms
The Actions Agencies and NOAA Fisheries will ensure that hatchery programs funded by the
FCRPS Action Agencies are not impeding recovery of ESA listed salmon ESUs or steelhead
Best Management Practices will be defined in ESA consultations with NOAA Fisheries, in
cooperation with Oregon, Washington, Idaho, the United States Fish and Wildlife Service, and
the Nez Perce, Yakama, Colville, Warm Springs, Umatilla and Shoshone Bannock Indian tribes.

NOAA Fisheries and the Action Agencies will accelerate ESA consultations to implement best
management practices and hatchery reforms including:
1. Limit hatchery fish from spawning naturally,
2. Reduce ecological effects on natural populations from juvenile and adult hatchery fish,
3. Allow natural re-colonization of rivers and streams blocked by hatchery facilities,
4. Prevent entrainment and injury of listed fish at hatchery water diversions, and
5. Monitor hatchery compliance with ESA requirements.

NOAA Fisheries and the Action Agencies will implement new studies to determine the benefits
and risks of adjusting hatchery releases based on environmental cues.

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