Status and Trends Monitoring of the
mainstem Columbia River – Sample
frame development and review of
programs relevant to the development of
an integrated approach to monitoring
Timothy D. Counihan, Jill M. Hardiman, and Steve Waste
US Geological Survey, Western Fisheries Research Center, Columbia River Research
Laboratory, 5501A Cook-Underwood Road, Cook, WA 98605
PNAMP Report Series 2013-003
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Contents
Executive Summary ................................................................................................................................. 6
Introduction ............................................................................................................................................ 7
What steps are needed to formulate a mainstem Columbia River ISTM? ................................................. 8
Identify Decisions and Questions that Aquatic Resource Monitoring is intended to inform .................. 8
Federal Columbia River Power System Biological Opinion ................................................................ 9
Northwest Power Act..................................................................................................................... 10
Recovery Plans............................................................................................................................... 11
Columbia River Treaty.................................................................................................................... 12
Identify and document the extent to which existing monitoring programs support and align with the
priority monitoring objectives............................................................................................................ 13
Smolt Monitoring Program – Fish Passage Center .......................................................................... 13
Northern Pikeminnow Management Program................................................................................ 14
Draft Monitoring, Evaluation, Research, and Reporting Plan (MERR Plan) - Northwest Power and
Conservation Council ..................................................................................................................... 15
Resident Fish Monitoring Strategies ........................................................................................... 17
White Sturgeon Population Monitoring .................................................................................. 17
Other resident fishes .............................................................................................................. 18
Draft Anadromous Salmonid Monitoring Strategy, Viable Salmonid Population Criteria, and
Subset of Tributary Habitat and Hatchery Effectiveness ............................................................. 18
Vital Sign Indicators – Columbia River Gorge Commission .............................................................. 19
Regional Environmental Monitoring and Assessment Program: 2009 Lower mid-Columbia River
Ecological Assessment – Oregon Department of Environmental Quality......................................... 20
Zooplankton Monitoring – Washington State University and USGS ................................................ 22
Other studies ................................................................................................................................. 22
Conclusions ................................................................................................................................... 23
Sample Frame Development – USGS and PNAMP .............................................................................. 23
Develop information on the pros and cons and costs associated with different monitoring design and
field protocol combinations. .............................................................................................................. 25
Examples of long-term monitoring programs in other large river systems.............................................. 27
Mississippi River ................................................................................................................................ 27
Illinois River ....................................................................................................................................... 27
Colorado River ................................................................................................................................... 27
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Summary ............................................................................................................................................... 28
Acknowledgements ............................................................................................................................... 29
References ............................................................................................................................................ 30
List of Figures
Figure 1. The geographic extent of the sample frames developed for the mainstem Columbia and Snake
Rivers. Sample frames comprise the individual reservoir and associated floodplain to the next upstream
dam (black squares). For the Columbia River the upper most extent is the Grand Coulee Dam and for the
Snake River it is the Hells Canyon Dam. ................................................................................................. 25
List of Tables
Table 1. Sub-basin plans that pertain to reaches of the mainstem Columbia River that have been
formulated as part of the Northwest Power and Conservation Council’s coordination of activities under
the Northwest Power Act Fish and Wildlife program. ............................................................................ 11
Abbreviations and Acronyms
Abbreviation
Meaning
ASMS
Anadromous Salmonid Monitoring Strategy
BiOp
Biological Opinion
CGNSA
Columbia Gorge National Scenic Area
CHaMP
Columbia Habitat Monitoring Program
CRB
Columbia River Basin
CRE
Columbia River Estuary
CRITFC
Columbia River Intertribal Fisheries Commission
CRT
Columbia River Treaty
DEM
Digital Elevation Model
DEQ
Oregon Department of Environmental Quality
EMP
Environmental Management Program
EPA
Environmental Protection Agency
ESA
Endangered Species Act
FCRPS
Federal Columbia River Power System
FPC
Fish Passage Center
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GCDAMP
Glen Canyon Dam Adaptive Management Program
GCPA
Grand Canyon Protection Act
GRTS
Generalized Random-Tessellation Stratified
HLI
High Level Indicator
ISAB
Independent Science Advisory Board
ISTM
Integrated Status and Trends Monitoring program
LMC
Lower Mid-Columbia
LTRMP
Long Term Resource Monitoring Program
MERR
Monitoring, Evaluation, Research, and Reporting Plan
NOAA
National Oceanic and Atmospheric Administration
NPCC
Northwest Power and Conservation Council
NPMP
Northern Pikeminnow Management Program
ODFW
Oregon Department of Fish and Wildlife
PNAMP
Pacific Northwest Aquatic Monitoring Partnership
RARE
Regional Applied Research Effort
RME
Research, monitoring, and evaluation
RPA
Reasonable and Prudent Alternatives
SMP
Smolt Monitoring Program
UMC
Upper Mid-Columbia
US
United States
USGS
United States Geological Survey
VSI
Vital Signs Indicator
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Executive Summary: Implementing an Integrated Status and Trends Monitoring program (ISTM)
for the mainstem Columbia River will help identify trends in important natural resources and
help us understand the long-term collective effects of management actions. In this report, we
present progress towards the completion of a stepwise process that will facilitate the
development of an ISTM for the mainstem Columbia River. We discuss planning and regulatory
documents that can be used to identify monitoring goals and objectives and present existing
monitoring and research activities that should be considered as the development of a Columbia
River ISTM proceeds. We also report progress towards the development of sample frames for
the Columbia and Snake Rivers and their floodplains. The sample frames were formulated using
Digital Elevation Models (DEM’s) of the river channel and upland areas and a Generalized
Random-Tessellation Stratified (GRTS) algorithm for an area based resource to generate
“master sample(s).” Working with the Pacific Northwest Aquatic Monitoring Partnership
(PNAMP) we facilitated the transfer of the sample frames to the PNAMP “Monitoring Sample
Designer” tool. We then discuss aspects of response and survey designs as they pertain to the
formulation of a mainstem Columbia River ISTM. As efforts to formulate an ISTM for the
mainstem Columbia River proceed, practitioners should utilize the extensive literature
describing the planning and implementation of fish and wildlife mitigation and recovery efforts
in the Columbia River Basin. While we make progress towards establishing an ISTM framework,
considerable work needs to be done to formulate an ISTM program for the mainstem Columbia
River. Long-term monitoring programs have been established for other large rivers systems;
scientists that have experience planning, implementing, and maintaining large river monitoring
efforts such as those in the Colorado, Illinois, and Mississippi Rivers should be consulted and
involved as efforts proceed.
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Introduction
The lack of integrated long-term monitoring data for the mainstem Columbia River
confounds interpretation of the long-term effects of current and past fish, hydropower, and
water management strategies on recovery efforts for endangered and threatened Pacific
salmon, Pacific lamprey (Entosphenus tridentatus), white sturgeon (Acipenser
transmontanus), and other important natural resources. Recovery efforts for Pacific salmon
in the mainstem Columbia River are ongoing and have focused on altering dam operations,
improving bypass structures, managing fisheries, and predator removal programs to increase
survival of migrating adult and juvenile salmonids. However, little is known about how
efforts to recover anadromous fish populations are affecting resident fish species or other
components of the Columbia River ecosystem that could have direct or indirect effects on
Pacific salmon. Similarly, fisheries for native and non-native resident fish are managed to
provide recreational opportunities (ODFW 2011) or address salmon predation issues
(Sanderson 2009) but little is known of how the structure and function of the resident fish
community is responding to these management strategies.
Assessing trends in most ecosystem services (ESA 1997) provided by the Columbia River is
not possible because there is no established baseline or dedicated monitoring program. The
mainstem Columbia River provides many important ecosystem services to anadromous and
resident fishes, people, and wildlife. For instance, the importance of sustaining freshwater
habitats for salmonid abundance or viability, especially when ocean productivity is low, has
been acknowledged in the literature (ISAB 2011, Naiman et al. 1995, Ruggerone et al. 2009).
Since resident fishes use freshwater habitats in the Columbia River for feeding, migration, and
shelter, they also rely on the productivity of these habitats to provide the foods needed for
growth and survival. Despite the acknowledged importance of freshwater food webs to
resident fish and salmon recovery efforts, very little is known of how the Columbia River
ecosystem functions, whether current management is improving or degrading ecosystem
function, or how altered ecosystems in turn influence the survival and production of native
fishes and wildlife (ISAB 2011). In addition, despite the fact that exposure of fish, wildlife, and
people to contaminants within the Columbia River Basin has caused concern (USEPA 2009),
there is currently no dedicated contaminants monitoring program for large portions of the
mainstem Columbia River.
While integrated monitoring programs are being established in other areas of the
Columbia River Basin, efforts to establish an integrated monitoring framework for the
mainstem Columbia River upstream of the estuary are lacking. Recently, the Pacific
Northwest Aquatic Monitoring Partnership (PNAMP) initiated efforts to scope and
implement an Integrated Status and Trend Monitoring program (ISTM) for tributaries to the
Columbia River Estuary (CRE) (PNAMP 2009, Rawding and Rodgers 2013, Puls et al. In
review). Monitoring programs for tributaries upstream of the estuary have also been
established (Ward et al. 2011). With respect to the mainstem Columbia River, a preliminary
framework for ecosystem monitoring has been established for the CRE (Simenstad et al.
2011). The advent of these programs suggests that the importance of monitoring for tracking
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the trajectory of managed aquatic resources in the Columbia River Basin is being recognized
by management agencies within the region. In this report, we describe progress towards
establishing a framework that would facilitate the development of an ISTM for the mainstem
Columbia River. We also report on our efforts to develop and make available sample frames
for the mainstem Columbia and Snake Rivers. This report is not intended to be a
comprehensive accounting of all of the factors that would need to be considered when
formulating a Columbia River ISTM but rather constitutes a starting point for further
discussion.
What steps are needed to formulate a mainstem Columbia River ISTM?
The PNAMP has suggested a step-wise process for the development of an ISTM. Although
some management questions are unique to particular agencies and organizations, the need for
comprehensive and efficient collection of information on metrics and indicators on all or certain
aspects of the status and trend of fish, habitat, and watershed health is shared by the entities
involved in monitoring in the Pacific Northwest. By applying well-coordinated monitoring
approaches, technical and fiscal resources can be more effectively shared among interested
parties, data can be shared, and resulting information can provide increased scientific
credibility, cost-effectiveness in use of limited funds, and greater accountability to
stakeholders. The steps recommended by PNAMP are as follows:
1. Identify decisions and questions that aquatic monitoring is intended to inform, and
identify associated prioritized monitoring goals and objectives.
2. Identify and document the extent to which existing monitoring programs support and
align with the priority monitoring objectives in #1 above.
3. Identify and/or develop monitoring designs, sampling frames, field and data
management protocols, and analytical tools to meet priority aquatic status and trend
monitoring objectives identified in #1 above.
4. Develop information on the pros and cons and costs associated with different
monitoring design and field protocol combinations.
5. Recommend mechanism(s) to implement and report the monitoring results from
implemented monitoring programs.
Proceeding through the steps outlined above will provide a solid foundation to the
formulation of an ISTM for the mainstem Columbia River. While it is beyond the scope of this
report to complete all of these steps, we describe progress towards addressing components of
the step-wise process or recommend sources that could be used to address them.
Identify Decisions and Questions that Aquatic Resource Monitoring is intended to inform
Formulating an ISTM that addresses the diverse needs and priorities of stakeholders in the
Columbia River Basin will benefit from an understanding of the management and regulatory
contexts that dictate the use of Columbia River resources. The Columbia River is one of the
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largest river systems in North America and flows through multiple jurisdictions and originates in
in British Columbia, Canada; approximately 15 percent of the 259,500 square miles of the
Columbia River Basin is located in Canada. The flows from Canada account for about 38 percent
of the average annual volume, and up to 50 percent of the peak flood waters at The Dalles Dam
on the Columbia River between Oregon and Washington. The operations of the Federal
Columbia River Power (FCRPS) are subject to multiple international treaties and other national
legislation that govern aspects of water usage in the Columbia River. Columbia River water
provides benefits to multiple user groups and provides for: flood control, habitat for fish and
wildlife including some species listed as endangered or threatened under the Endangered
Species Act, fisheries for tribes, and provides water for irrigation of agricultural crops,
municipalities, power generation by hydroelectric facilities, and shipping and barge navigation.
Below we provide brief synopses of some of the management and regulatory processes
currently driving the management of the Columbia River.
Federal Columbia River Power System Biological Opinion
A mainstem Columbia River ISTM would help provide a long-term context to mitigation
strategies implemented as part of the Federal Columbia River Power System Biological Opinion
(FCRPS BiOp). The Endangered Species Act (ESA) requires that any federal agency proposing an
action that may affect an ESA-listed fish – issuing a permit, spending money, taking a direct
action on fish habitat – consult with the U.S. Fish and Wildlife Service or NOAA Fisheries (i.e.,
regulatory agencies). The agency proposing the action (known as the action agency) will
commonly complete a biological assessment on potential effects to the fish or its habitat and
submit it to the regulatory agency(ies). The regulatory agency then renders a Biological Opinion
(BiOp) to the action agency making the proposal. The BiOp is intended to ensure that the
proposed action will not reduce the survival and recovery of ESA-listed species. A BiOp typically
includes conservation recommendations to advance the recovery of the specific ESA-listed
species, includes Reasonable and Prudent measures needed to minimize harmful effects, and
may require monitoring and reporting to ensure that the action is implemented as described.
The FCRPS BiOp (NOAA 2008) contains many proposed mitigation strategies. The
implementation of these strategies is intended to have a desired outcome; progress towards
the desired outcome of some strategies are being tracked (Fish Passage Center 2010) while
other aspects are not (ISAB 2011).
As of the writing of this report, the most recent version of the FCRPS BiOP was in 2008
(NOAA 2008) and contains 73 Reasonable and Prudent Alternatives (RPA’s). As part of a remand
of this version of the BiOP, federal agencies integrated the Adaptive Management
Implementation Plan into the 2008 FCRPS BiOp resulting in the 2010 FCRPS Supplemental BiOp
(NOAA 2010). The RPA’s listed in the BiOp stipulate mitigation to improve conditions of ESA
listed species. Clearly, there are many actions being undertaken to monitor the progress of
some of the RPA’s. However, other factors that may affect the desired outcomes of RPA’s, such
as climate change effects, food-web processes, and non-indigenous species remain poorly
understood. A systematic review of the food web processes currently not being monitored as
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part of the Fish and Wildlife Program (ISAB 2011) would help inform the development of
indicators and metrics that could be monitored as part of a mainstem Columbia River ISTM.
Northwest Power Act
The Northwest Power Act of 1980 addresses the effects of Columbia River hydroelectric
dams on fish and wildlife. The Act establishes the Pacific Northwest Power and Conservation
Council (NPCC) to prepare and adopt a regional conservation and electric power plan and a
program to protect, mitigate and enhance fish and wildlife. The Northwest Power and
Conservation Council is an interstate compact agency of Idaho, Montana, Oregon and
Washington. The Act specifically directs the NPCC to develop a program to “protect, mitigate,
and enhance fish and wildlife, including related spawning grounds and habitat, on the Columbia
River and its tributaries … affected by the development, operation, and management of
[hydroelectric projects] while assuring the Pacific Northwest an adequate, efficient, economical,
and reliable power supply.” This program is referred to as the “Columbia River Basin Fish and
Wildlife Program” (NPCC 2009).
Management plans have been developed for reaches of the mainstem Columbia River that
could serve as a starting point for identifying decisions and questions associated with the Fish
and Wildlife Program that could be informed by a mainstem ISTM. In 2005 the NPCC completed
one of the largest locally led watershed planning efforts of its kind in the United States, an
effort that resulted in separate plans for 58 tributary watersheds or mainstem segments of the
Columbia River. These sub-basin plans were developed collaboratively by state and federal fish
and wildlife agencies, Indian tribes, local planning groups, fish recovery boards, and Canadian
entities where the plans address trans-boundary rivers. The planning effort was guided by the
NPCC and funded by the Bonneville Power Administration. The sub-basin plans were developed
collaboratively by multiple stakeholders and presumably represent the collective priorities of
the entities that contributed to their development. If workshops were convened to garner input
into the development of a mainstem ISTM, contacting the entities listed as contributors to the
reports would be a good starting point for enlisting participation.
The sub-basin plans developed for the mainstem Columbia River (Table 1) could be used to
help identify metrics that would characterize the status of biological objectives resulting from
the priority restoration and protection strategies for key habitats and fish species identified in
the plans. The sub-basin plans were formulated to guide the future implementation of the
NPCC’s Columbia River Basin Fish and Wildlife Program, which directs funds in excess of $200
million per year from the Bonneville Power Administration. The sub-basin plans outline a
sequential process of providing 1) an assessment of the sub-basin being described including
aquatic and terrestrial focal species and habitats and factors that limit them; 2) an inventory of
existing activities including a description of existing legal protection and management plans for
the area; 3) a gap analysis of existing legal protection and management plans; and 4) the
development of a management plan that includes biological objectives and strategies for
managing focal species in the area. Evaluating the efficacy of these strategies will require
periodic assessments of progress towards the underlying biological objectives. Based on the
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outcome of these periodic assessments the probability of success of strategies can be
determined. If the probability of success is low, the strategies can then be altered adaptively.
Establishing a long-term mainstem Columbia River ISTM would help to assess the long-term
effects of these activities on important aquatic resources, including resources not specifically
targeted.
Table 1. Sub-basin plans that pertain to reaches of the mainstem Columbia River that have
been formulated as part of the Northwest Power and Conservation Council’s coordination of
activities under the Northwest Power Act Fish and Wildlife program.
Subbasin Plan
Columbia Gorge
Subbasin Plan
Reach description
The Columbia River
between Bonneville
and The Dalles Dams
River km range
232-306
Web address
http://www.nwcouncil.or
g/fw/subbasinplanning/co
lumbiagorge/plan/
Lower MidColumbia
Mainstem
Subbasin Plan
The Columbia River
306-505
from The Dalles Dam to
the mouth of the Walla
Walla River
http://www.nwcouncil.or
g/fw/subbasinplanning/lo
wermidcolumbia/plan/
Upper Middle
Mainstem
Subbasin Plan
The Columbia River
from Wanapum Dam
to Chief Joseph Dam;
contains Wells, Rocky
Reach, Rock Island and
Wanapum reservoirs.
669-877
http://www.nwcouncil.or
g/fw/subbasinplanning/u
ppermidcolumbia/plan/
Upper Columbia
Subbasin Plan
Grand Coulee Dam to
border with Canada
954-1205
http://www.nwcouncil.or
g/fw/subbasinplanning/ad
min/level2/intermtn/plan
/uprcol.pdf
Recovery Plans
Recovery plans developed as part of the Endangered Species Act (ESA) can also be used to
identify decisions and questions that could be addressed by a mainstem Columbia River ISTM.
For instance, the NOAA Fisheries has adopted a Recovery Plan for the Middle Columbia River
Steelhead Distinct Population Segment. This recovery plan was developed to guide the recovery
of the Middle Columbia steelhead (Oncorhynchus mykiss) that are listed as Threatened under the
ESA. The steelhead spawn and rear in freshwater tributaries then migrate to the ocean. Of the
17 extant populations of Middle Columbia steelhead, five are considered at high risk of
extinction over the next 100 years, nine are at moderate risk, and three populations are
currently considered viable. The recovery plan addresses major factors currently limiting the
viability of Middle Columbia River steelhead populations; that is, degraded tributary habitats,
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impaired fish passage in the mainstem Columbia River and tributaries, hatchery-related effects,
and predation/competition/disease. The plan then develops strategies for recovery that include
improving juvenile and adult steelhead migratory passage and survival in the FCRPS and
reducing predation on steelhead in the Columbia River and estuary. Progress towards achieving
these objectives are being addressed in part by components of the Army Corps of Engineers
Anadromous Fish Evaluation Program, namely by studies documenting the passage and survival
through mainstem hydroelectric facilities (Adams and Counihan 2009) but others such as
reducing predation effects of non-indigenous predators remain poorly understood (Sanderson
et al. 2009).
Columbia River Treaty
The Columbia River Treaty (CRT) with Canada will expire in 2024, and a ten year period for
renegotiation of the treaty prior to its expiration commences in September of 2014. The Pacific
Northwest recognizes the value of the CRT to facilitate shared water resource management in
the Columbia River Basin to maximize benefits to both countries. The regional goal is for the
U.S. and Canada to develop a new framework for the Treaty that retains Flood Risk
Management and Hydropower as primary purposes while incorporating Ecosystem Function as
a third primary purpose. The intent is to ensure a more resilient and healthy ecosystem-based
function throughout the Columbia River Basin while maintaining an acceptable level of flood
risk and providing reliable and economic hydropower benefits. In addition, the CRT should
include both short- and long-term mechanisms that allow for adapting the treaty and/or build
in flexibility of operations as conditions change or as new information becomes available.
Implementation of the CRT should be modernized to incorporate a coordinated operations
plan based on power production, flood risk management, and ecosystem-based function as
primary drivers. In general, the intent is to ensure the greatest shared benefits across the U.S.
and Canada for these primary drivers while considering potential impacts to recreation,
navigation, cultural resources, water supply, and water quality – all important issues to
Columbia River Basin (CRB) entities dependent on the mainstem of the Columbia River, such as
the Columbia Gorge National Scenic Area (CGNSA). The Department of the Interior proposes
that specific flow targets and anticipated ecological gains be identified, refined, and quantified,
to the extent necessary, from 2014-2024. This period would also be used to develop and
organize an ecosystem flow development process, to determine sideboard provisions for
ecosystem flow requests, and to assess other ecosystem benefits of interest to Canada.
In support of this effort, regional sovereigns will develop a scope of work addressing
necessary studies and monitoring to implement the operation of the CRT post-2024. These
studies will include multiple scenarios designed to test and compare a range of possible
situations with varying: 1) study time horizons, 2) maximum flood control flow objectives, 3)
Assured Operating Procedures, and 4) observed and forecast mode water supply and inflow
model simulations.
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To successfully implement a modernized CRT will require that the expected benefits from
prescribed management actions, such as flow management, be validated to ensure that was
predicted to happen is actually occurring. The ISTM could help improve management of the
Columbia River under a new CRT, by providing information to help validate predicted outcomes
or that suggests a new management strategy is warranted.
Identify and document the extent to which existing monitoring programs support and align
with the priority monitoring objectives
Existing monitoring efforts in the mainstem Columbia River should be examined to
determine the potential for synergy amongst the programs. We submitted a query to a variety
of regional agencies requesting information regarding current monitoring efforts in the
mainstem Columbia River; the response to this query was limited. We requested a listing of
known monitoring activities within the mainstem Columbia River. We assumed a lack of a
response indicated that there were no known activities. Below, we describe existing monitoring
activities in the mainstem Columbia River based on these limited responses and also report on
other programs or known activities in the mainstem Columbia River based on professional
knowledge and other less formal queries to other scientists.
The list we provide below is likely to be a partial listing; we encourage those with additional
information to contact the authors or PNAMP staff. The monitoring efforts we describe here
would provide context and possibly synergy to a larger mainstem Columbia River ISTM. Most of
the programs we describe rely on fixed sites, such as hydroelectric projects, to implement
monitoring; few employ a probabilistic framework. As efforts to formulate a mainstem
Columbia River ISTM proceed, there will be a need to provide a framework for the inclusion of
these long standing monitoring efforts.
Smolt Monitoring Program – Fish Passage Center
The Smolt Monitoring Program (SMP) was initiated in 1987 and is coordinated by the Fish
Passage Center. The Fish Passage Center (FPC) was formed by fisheries agencies and tribes to
interact with hydro system operators and regulators in managing anadromous fish passage. The
FPC developed the SMP to assess daily information for in-season management decisions. As
part of this assessment various biological parameters including juvenile salmonid survival,
passage timing, and passage indices by species, dissolved gas trauma monitoring, hatchery
releases and fish condition are compiled and reported. Included in the annual report are counts
of adult anadromous fish that pass hydroelectric projects on the mainstem Columbia River that
provide important information to managers responsible for managing sport and commercial
fisheries for these fish. Additionally, environmental passage conditions, flow, spill water
temperature, project operations, studies and research that occurred and that may have
affected passage conditions are compiled and reported. These parameters are compiled and
reported in-season and are also reported in an FPC annual report. The purpose of the FPC
annual report is to document the hydrosystem operations, environmental conditions and the
resulting fish passage characteristics that occurred during the year. The report consolidates
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other information that is helpful in describing the year in terms of Columbia Basin salmon and
steelhead passage through the hydrosystem; reservoir operations and weather that resulted in
migration flows are documented. The annual report also presents prevailing fish passage
management concerns, questions and decisions for that year. The SMP presents environmental
and fishery information with an emphasis on how these data pertain to salmonids, though the
reported environmental data would have applicability to other aspects of the Columbia River
ecosystem.
Northern Pikeminnow Management Program
The Northern Pikeminnow Management Program (NPMP) has been monitoring aspects of
fish predator populations for 22 years (Porter 2011). The NPMP was started in 1990 with the
intent to harvest northern pikeminnow (Ptychocheilus oregonensis) to reduce predation of
juvenile salmonids during their emigration from natal streams to the ocean via the Columbia
and Snake Rivers. The impetus for the program was research in the Columbia River Basin that
suggested predation by northern pikeminnow on juvenile salmonids might account for 10-20%
of the juvenile salmonid mortality in each of eight Columbia River and Snake River reservoirs.
Modeling simulations based on work in John Day Reservoir from 1982 through 1988 indicated
that, if predator-size northern pikeminnow were exploited at a 10-20% rate, the resulting
restructuring of their population could reduce their predation on juvenile salmonids by 50%.
Data collected as part of the NPMP includes fisheries data from angler catches, fisheries data
from electrofishing efforts, summaries of monetary disbursements from the NPMP program,
and fisheries data from angling near hydroelectric projects.
Information describing angler catches is collected at twenty-one registration stations
located on the Columbia and Snake Rivers to provide anglers with access to the Sport-Reward
Fishery (Hone et al. 2011); ten of these stations were located in the Columbia River estuary
leaving the remaining 11 stations dispersed at locations on the mainstem Columbia and Snake
Rivers. The established angler registration stations are understandably selected to
accommodate angler participation. The data collected for the dam angling component is
collected using hook and line angling within the boat restricted zones of the tailraces of
hydroelectric projects within the study area. The stated purpose of these collection efforts is to
deplete the number of fish predators within these areas (Dunlap et al. 2011). The reporting of
monetary disbursements from the NPMP summarizes the financial aspects of the NPMP based
on the returns of northern pikeminnow of the appropriate size to the angler registration
stations.
The NPMP electrofishing survey collects fish predators at sites from river kilometer (rkm)
76 (near Clatskanie, Oregon) upstream to rkm 639 (Priest Rapids Dam), and in the Snake River
from rkm 112 (Little Goose Dam) to rkm 248. The number of sites sampled per year is
expressed as the number of sites sampled per river mile. The number of sites sampled per river
mile can vary from year to year; in 2010 two 15 min electrofishing efforts were conducted per
river mile (Porter 2010) while four efforts per river mile were conducted in 2011 (Porter 2011).
How the sites are chosen within river mile is not clear from the reports; the fact that they occur
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at varying numbers of sites implies that sampling doesn’t occur at the same locations from year
to year. The predators collected in these efforts are either measured, tagged and released to
provide recapture data or are sampled for diet and other biological characteristics. The
collection of diet and other biological information does not occur system-wide annually but
does occur annually in particular reaches within the larger study area. For example, in 2009 diet
data were collected for The Dalles and John Day Reservoirs and during 2011 was collected for
Bonneville Reservoir. The data reported focuses primarily on northern pikeminnow,
smallmouth bass (Micropterus dolomieu), and walleye (Sander vitreus) and the fish species they
consume. Whether data is collected on other species collected in these efforts is not clear from
the reports. The information from these efforts would help to inform the formulation of an
ISTM by providing information on the relative abundance of predators and the composition of
their diets in a spatial and temporal context. If information is not collected on other fish species
captured, there may be a way to provide opportunities to do so.
Draft Monitoring, Evaluation, Research, and Reporting Plan (MERR Plan) - Northwest
Power and Conservation Council
In 2010, in response to the perceived need to expand monitoring and evaluation as a
means to facilitate decision-making and reporting on the Columbia River Fish and Wildlife
Program (Program), the Northwest Power and Conservation Council (NPCC) developed the draft
Monitoring, Evaluation, Research, and Reporting Plan (MERR Plan) (NPCC 2010). The MERR Plan
was developed over a one-year period by NPCC staff. The impetus for the MERR Plan came
from the primary strategies for research, monitoring, evaluation and reporting adopted in the
2009 Program, which are:
• Identify priority fish, wildlife, and ecosystem elements of the Program that can be
monitored in a cost-effective manner, evaluate the monitoring data and adaptively
manage the Program based on results
• Research and report on key uncertainties
• Make information from this Program accessible to the public; and
• To the extent practicable, ensure consistency with other processes.
The MERR (NPCC 2010) outlines specific draft management questions that Research,
Monitoring, and Evaluation (RME) conducted through the Program should answer. To this end,
NPCC (2010) identify the following ten management questions:
1. Are Columbia River Basin fish and wildlife abundant, diverse, productive, spatially
distributed, and sustainable?
2. Are Columbia River Basin ecosystems healthy?
3. Are ocean conditions affecting Columbia River Basin anadromous fish in a biologically
positive manner?
15
4. Are land use changes and climate change affecting fish and wildlife in the Columbia River
Basin in a biologically positive manner?
5. Are the actions implemented by the Council’s Fish and Wildlife Program having the
expected biological effect on fish and wildlife and their habitat?
6. Are Council Program actions coordinated within the Program and with other programs?
7. Are mainstem hydro operations meeting the Council’s Fish and Wildlife Program’s
survival and passage objectives?
8. Is harvest supportive of the Council’s Fish and Wildlife Program’s vision of restoring fish
and wildlife impacted by the development and operation of the Columbia River Basin’s
hydrosystem?
9. Does artificial production complement resident and anadromous recovery and harvest
goals within the Columbia River Basin?
10. Are the fish and wildlife losses associated with the development and operation of the
Columbia River Basin’s hydrosystem being mitigated as described by the Council’s Fish and
Wildlife Program?
The NPCC has developed a list of High Level Indicators (HLI) that they propose will address
the status of the answers to these questions. Most, if not all, of the HLI can be tied to
components of the ecosystem in the mainstem Columbia River.
To facilitate Program assessment and reporting, the MERR Plan consists of a Strategic Plan,
Implementation Framework, as well as implementation strategies for anadromous fish, resident
fish, and wildlife.
Strategic Plan focuses on the Council’s research, monitoring, evaluation (RME) and
reporting needs at the policy level. The Strategic Plan sets forth the purpose and
expectations for RME and reporting implemented through the Program.
Implementation Framework contains existing, modified and new processes for
prioritizing and implementing RME and reporting at the programmatic level. The
Implementation Framework describes how the various components of RME can be used
to adaptively manage the Program and guides the development of standardized
Implementation Strategies for anadromous fish, resident fish, and wildlife.
Implementation Strategies, Anadromous Fish Implementation Strategy, Resident Fish
Implementation Strategy, and Wildlife Implementation Strategy provide additional
guidance in prioritizing and implementing RME and reporting. The Implementation
16
Strategies are intended to be developed with regional partners, and will consider
integration of regional products.
The MERR has recently been updated and separated into two components (Nancy Leonard,
NPCC; personal communication), one that pertains to monitoring and research and another
that deals with information management, evaluation, and reporting. In the “Guidance to a
balance(d) approach to Monitoring and Research” the distinction between three types of
monitoring are listed as:
Implementation and Compliance Monitoring - used to assess if actions and projects were
implemented according to contractual agreement, appropriate design requirements and
standards, and when relevant, whether it achieved its assumed functional lifespan.
Status and Trend Monitoring – used to assess status over time of fish, wildlife and habitat
that informs program evaluation and reporting needs.
Effectiveness Monitoring – used to determine, by correlation or causation, if a Program
funded action achieved the intended detectable change in environmental conditions or
population characteristics.
The Implementation Strategies listed in the MERR plan (NPCC 2010) contain components
that are relevant to mainstem Columbia River issues; below we provide a synopsis of aspects of
the Resident Fish Monitoring Strategy and a synopsis of the Anadromous Fish Implementation
Strategy
Resident Fish Monitoring Strategies
White Sturgeon Population Monitoring
Efforts to assess the status and trends of white sturgeon (Acipenser transmontanus)
populations were initiated in 1986 and are currently ongoing. The project that is funded as part
of the Fish and Wildlife Program is collaborative between the Columbia River Inter-Tribal Fish
Commission, Oregon Department of Fish and Wildlife, Montana State University, and the
Washington Department of Fish and Wildlife. As part of this project, stock assessments of adult
white sturgeon are regularly conducted and age-0 white sturgeon have been surveyed annually
in multiple mainstem reservoirs since 1989 (Counihan et al. 1999; Mallette 2011).
The adult stock assessments are conducted using traditional fisheries gear such as gill nets
and set lines. Sampling sites are not randomly selected or fixed but rather an effort is made to
spread effort “equally throughout the reservoir” (Mallette 2011). Adult abundance is estimated
every three years. Sampling for white sturgeon is divided into three periods. During Period 1,
gill nets are used to capture white sturgeon; during Periods 2 and 3, baited setlines are used to
capture fish. All reservoir sections are sampled during each period, and sampling effort during
periods 2 and 3 is distributed equally throughout the reservoirs. Overall adult abundance is
17
estimated by using a Schnabel population estimator on fish in the 70-109 cm FL size class, then
using the length-frequency distribution of the setline catch to apportion the Schnabel
population estimate by 1 cm increments within the 70-109 cm FL size class. The Schnabel
estimate is then expanded to estimate abundance of the remaining size groups based on the
relative frequency of these size classes in the total setline catch and after adjusting for size
specific differences in gear vulnerability. This method precludes the estimation of 95%
confidence intervals for sizes outside of the 70-109 cm FL size class.
Age-0 indexing is conducted at fixed sites in Bonneville, The Dalles, John Day, and McNary
reservoirs that were originally selected based on the ability to fish a bottom trawl on the
substrate (Counihan et al. 1999) but that are now sampled with gill nets (Mallette 2011). The
adult stock assessments are conducted periodically while the age-0 indexing occurs annually. As
part of the age-0 indexing efforts catches of other fish species are typically recorded and
reported and as such constitute the only long-term data on fish assemblages in benthic habitats
in the Columbia River.
Other resident fishes
In addition to white sturgeon, there are plans to develop monitoring implementation
strategies for Bull trout (Salvelinus confluentus) and other resident game fishes that could are
known to inhabit the mainstem Columbia River for at least part of their life history. As such, the
plan will likely seek to coordinate existing and future monitoring activities for these species.
However, there currently does not seem to be any dedicated effort or program to monitor the
status and trends of other resident fish species.
Draft Anadromous Salmonid Monitoring Strategy, Viable Salmonid Population Criteria, and
Subset of Tributary Habitat and Hatchery Effectiveness
The Anadromous Salmonid Monitoring Strategy (ASMS) draft has been developed by
Columbia River Basin fish managers 1i to coordinate the monitoring and evaluation of tributary
lifecycle metrics of all wild and hatchery salmonids and their habitat in the Columbia River
Basin. The strategy focuses on management decision information needs and informing policy
formulation and direction. Aspects of the ASMS pertain to monitoring the status of anadromous
salmonids during the time they inhabit the mainstem Columbia. For instance the ASMS suggests
that for both intensively and less intensively monitored salmonid populations, that the smoltto-adult survival rate of fish using different passage routes through the hydrosystem be
estimated; implying that a monitoring program should be conducted to assess passage behavior
1
A regional workshop was convened by the Bonneville Power Administration, Columbia Basin Fish and Wildlife
Authority, National Oceanic and Atmospheric Administration, and Northwest Power and Conservation Council
during October 20-21, 2009 and November 3-5, 2009 in Skamania Washington to develop Basin Coordinated
Anadromous Monitoring Strategy. The purpose of the Regional Workshop was to reach agreement among
participants on an efficient and effective framework and project specific implementation strategy for anadromous
salmon and steelhead monitoring to assess (1) Viable Salmonid Population criteria, (2) habitat effectiveness and (3)
hatchery effectiveness in the Columbia Basin.
18
as juvenile salmonids pass through the mainstem Columbia River. Other recommendations can
be construed as proposing to monitor metrics describing salmonid residence in the Columbia
River. The ASMS is not fully implemented at this stage as limitations of resources require a
prioritized approach to its implementation. A Columbia River ISTM could benefit from
coordination between ASMS and PNAMP on prioritization concepts and the development of
tools that enhance monitoring and data sharing, such as produced by PNAMP’s Integrated
Status and Trend Monitoring (ISTM) project and Coordinated Assessment process (see:
http://www.pnamp.org/project/3132).
Vital Sign Indicators – Columbia River Gorge Commission
The Columbia River Gorge Commission, in collaboration with stakeholders, has initiated a
process for developing metrics and a status and trends monitoring program for the Columbia
Gorge National Scenic Area (CGNSA). The project, entitled the “Vital Signs Indicators” (VSI)
project proposes monitoring the status and trends of 51 attributes that characterize
environmental and socioeconomic resources within the CGNSA. The VSI project was developed
over a two year period with significant public input and support including the identification of
key stakeholder groups. Nested within the VSI project are proposed indicators intended to
characterize the Economic, Cultural, Natural, Recreation, and Scenic resources in the CGNSA.
For the indicators that describe the status of CGNSA Natural resources are proposed metrics
that seek to quantify aspects of the aquatic resources within the CGNSA. Since the mainstem
Columbia River is the most prominent aquatic feature within the CGNSA, characterizing the
status of aquatic resources within the CGNSA will entail measuring metrics for the mainstem.
Specifically, the VSI project lists two specific objectives that pertain to the mainstem Columbia
River: 1) Protect and enhance the native plants and animals and the habitats which support
them and to 2) Protect and enhance <the> quality of the water and aquatic habitats. To track
whether these objectives are being met the VSI project has proposed the following indicators:
•
•
•
•
•
•
•
•
•
Habitat Quality: Percent of priority habitat types rated as properly functioning.
Habitat Fragmentation: Percent of priority habitat types that are lost or fragmented
by human activity.
Species Health: Percent of at‐risk species whose populations in the gorge are
healthy.
Species Range: Percent of native species (wildlife, plants, invertebrates) with ranges
that are declining.
Surface Water Quality: Percent of streams, including the Columbia River, whose
water quality is a) poor, b) fair, c) good, and d) excellent.
Habitat Quality: Percent of native fish habitat that is properly functioning.
Surface Water Quantity: Percent of streams with satisfactory in‐stream flows.
Groundwater Quantity: Square miles of groundwater restricted areas.
Groundwater Quality
The VSI project has not moved into the implementation phase. The Columbia River Gorge
Commission is working with the USGS, Oregon State University, Portland State University, and
19
Washington State University to more fully develop and vet metrics that characterize the CGNSA
aquatic resources, to further develop and vet the design of the long-term status and trends
monitoring of metrics, and to develop the response design for the long-term status and trends
monitoring program. As part of this effort, portions of the mainstem Columbia River will be
monitored and could feed into a larger Columbia River ISTM.
Regional Environmental Monitoring and Assessment Program: 2009 Lower midColumbia River Ecological Assessment – Oregon Department of Environmental
Quality
In 2009 the Oregon Department of Environmental Quality (DEQ) conducted a study to test
a probability-based survey design and new methods for acquiring contaminant data for large
river systems; and provides an initial assessment of contaminant conditions in the middle
portion of the Columbia River (Caton 2012). Caton (2012) divided a portion of the Columbia
River into an area from Grand Coulee Dam to just upstream of McNary Dam (Upper MidColumbia; UMC)and an area from just upstream of McNary Dam to Bonneville dam (Lower MidColumbia; LMC), which includes approximately 150 river miles. The intent of this study was to
assess the ecological condition of a portion of the Columbia River and to collect information
that supports Oregon’s Water Quality Toxics Monitoring Program. The project also intended to
demonstrate the feasibility of employing large river survey designs, sampling methods and
ecological indicators relevant to water and fish tissue contaminants. Since the study used a
probabilistic based design, Caton (2012) provides a statistically valid assessment on the
condition of the Columbia River based on these indicators.
The probabilistic sampling design used by Caton (2012) was developed by the EPA’s
Western Ecology Division and the EPA Region 10 office in Seattle, WA. Twenty three random
sites were selected along the centerline of the river channel. Each site was given an alpha
numeric identification number, which DEQ reduced to simple consecutive numbers. Odd
numbered sites were sampled along the Oregon shore, and even numbered sites along the
Washington shore. Extra random sampling sites (oversample sites) were provided in case any of
the original 23 locations could not be sampled for safety reasons, etc. Eight targeted (handpicked) sites were also selected. Six of these sites were located in the lower free-flowing
reaches of major tributaries: the Hood, White Salmon, and Klickitat, John Day, Deschutes, and
Umatilla rivers. Two sites were chosen on the mainstem Columbia in areas of concern to project
sponsors: downstream of the PGE- Boardman coal-fired power plant (a potential Hg source),
and downstream of The Dalles, Oregon (a potential urban contaminant source).
The primary objectives of the project are listed as:
1) Evaluate the feasibility of implementing a probability-based sampling design to assess
the ecological condition of the mid-Columbia River, and the potential for integration with
designs being used for:
20
a. National Rivers and Streams Assessment and the state water quality monitoring
strategy for Oregon
b. Proposed multi-agency long-term monitoring and research programs advocated by
the Columbia River Toxics Reduction Working Group.
2) Assess ecological contaminant conditions in the water column and fish tissue for this
portion of the Columbia River (based on summer sampling), to answer the following
questions:
a. What percent of this Columbia River reach is characterized by poor physical habitat
conditions?
b. What percent of this Columbia River reach has impaired water quality for
conventional parameters? (e.g., E. coli, dissolved oxygen, pH, Secchi depth, turbidity,
total PO4-P, NO2 +NO3 –N, NH3 –N, chlorophyll a, and total suspended solids)
c. What is the extent of mercury concentrations (total and methylmercury) and
methylization cofactors (redox-potential, total organic carbon, dissolved organic carbon,
sulfate, selenium, and water hardness)?
d. What is the extent of priority contaminants in the water column and common foodfish fillets?
e. What percent of the river length is potentially at risk from contaminants (i.e., that
exceed criteria for either human or wildlife consumption)?
3) Compare contaminant conditions in the mainstem Columbia River with those near the
mouths of major tributaries.
4) Evaluate stressor indicators and associated methods to assess ecological condition in a
portion of the Columbia River, specifically conventional water pollutants, the use of
semipermeable membrane.
Secondary objectives of the study were listed as:
1) Collaborate with EPA Region 10 on their Regional Applied Research Effort (RARE) study
of the UMC. The Regional Environmental and Assessment Program and RARE studies share
a common survey design, sampling period, and field collection methods.
2) Provide data on contaminants in the water column and fish tissue for potential use by
DEQ and the Columbia River Treaty Review Working Group to help address data gaps.
These water quality, biological, and habitat data may provide additional information
21
needed by EPA Region 10 and state and local decision makers to complete an ecological
condition assessment, and a contaminant source assessment for the mid-Columbia Basin.
Caton (2012) state that the study was not intended to test specific statistical hypotheses
regarding contaminant extent or severity in the Columbia River. Rather, the primary use of the
data was to produce an initial statistically-based assessment of contaminant conditions in the
LMC and UMC and evaluate the feasibility of implementing such a program for future
monitoring. Caton (2012) states that statistical confidence in the assessment depends primarily
on the study design and the number of randomly selected sampling locations in the Columbia
River. The primary data output from the survey design was an estimate of the cumulative
proportion of the target population (expressed as a percentage of reach length) with a
particular value for an ecological indicator, or the percentage of river length present in discrete
“condition classes” based on specified criteria (e.g., greater than some concentration of
concern). Data quality objectives related to “decision statements”, “alternative actions”,
“action levels”, and “decision rules” were not developed. That different data users or decision
makers will have their own “action levels” of interest for particular indicators was noted by
Caton (2012).
Given that this study is one of the only examples where multiple aspects of the aquatic
ecosystem were collected in a probabilistic design framework, any ISTM efforts conducted in
the mainstem Columbia River that encompass the area sampled during this study should review
the results of this study to identify opportunities for incorporating past, and presumably, the
ongoing results of this work.
Zooplankton Monitoring – Washington State University and USGS
Recently the Washington State University and the USGS Western Fisheries Research Center
initiated a program to scope the development of a zooplankton monitoring program in the
mainstem Columbia River from Bonneville Reservoir to Wanapum Reservoir and in the lower
portion of the Snake River. The intent of this initial phase of the monitoring program was to
assess the logistics of conducting the monitoring, to estimate the expected variability in
zooplankton samples over various spatial and temporal scales, and to provide estimates of the
community composition over the longitudinal gradient sampled and also seasonally. Samples
were collected from randomly selected stations in the forebays of hydroelectric projects and
from randomly selected locations over a wider geographic area within reservoirs. Data
collected in 2010 and 2011 that characterizes the seasonal dynamics of zooplankton has been
processed and analyzed and is reported in a master’s thesis (Emerson et al. 2012); further
analyses are in progress.
Other studies
Studies examining various aspects of Columbia River reaches by the EPA were noted in our
search; however the efforts were not necessarily designed as monitoring efforts. Two studies,
one that examines levels of contaminants in fish tissues from just below Bonneville Dam to
22
Grand Coulee Dam (US EPA 1999) and another that examines human health risks and beach
sediment contaminant burdens (EPA 2006a, 2006b, 2006c, 2006d, 2006e) were noted.
Following is an excerpt regarding the study design of the fish contaminant survey:
“This study was designed to estimate risks for a specific group of people (Columbia River
Intertribal Fisheries Commission’s (CRITFC) member tribes). Therefore, the sample location,
fish species, tissue type, and chemicals were not randomly selected. Collection sites were
selected because they were important to characterizing risks to CRITFC’s member tribes.
Chemicals were chosen because they were identified in other fish tissue surveys of the
Columbia River Basin as well as being found throughout the environment. This type of
sampling is biased with unequal sample sizes and predetermined sample locations rather
random. This bias is to be expected when attempting to provide information for individuals
or groups based on their preferences. The results of this survey should not be extrapolated
to any other fish or fish from other locations.”
The EPA further note in a report describing the state of toxics in the Columbia River (see:
http://www.epa.gov/columbiariver/pdf/columbia_state_of_the_river_report_jan2009.pdf ):
“While considerable information has been collected over the past 20 years, the data are
limited with regard to whether the contaminants are increasing or decreasing Basin-wide.
There is some trend information for specific areas of the Basin such as the Lower Columbia.”
Conclusions
Listed above are monitoring programs and other ongoing studies that we identified that
could contribute to a mainstem Columbia River ISTM in various ways. Other more localized
monitoring efforts that are ongoing and that should be evaluated for a mainstem Columbia
River ISTM likely exist. Further work needs to be done to document and coordinate additional
monitoring and research efforts when they are identified. Once the decisions and questions
that aquatic monitoring is intended to inform and associated prioritized monitoring goals and
objectives are identified, the parties conducting the monitoring programs and other activities
above should be contacted, a thorough accounting of the metrics produced by the various
programs should be done, and the extent to which the existing program align with priority goals
and objectives should be documented. Once this is done, information gaps and opportunities to
collaborate can be fully identified.
Sample Frame Development – USGS and PNAMP
We worked with PNAMP and the Sitka Technology group to facilitate the transfer of
existing and newly developed sample frames for the mainstem Columbia and Snake Rivers from
USGS to the PNAMP Monitoring Sample Designer tool. Using Digital Elevation Models (DEM’s)
of the river channel and upland areas we generated “master sample(s)” for the Columbia and
Snake Rivers and their floodplains using a Generalized Random-Tessellation Stratified (GRTS)
algorithm for an area based resource (Figure 1). A master sample is essentially a list of sites
needed for a complete census of an area and a list of attributes assigned to each site. The GRTS
23
algorithm creates a list of sites that retains randomization and spatial balance when the full list
of sites is subset for sampling. To define the sampling frame for the river channel and upland
areas of the Columbia and Snake Rivers we used the presence of hydroelectric projects to
delineate discrete geographic units. For example, we defined the sample frame for Bonneville
Reservoir as the area bounded by Bonneville Dam at the downstream extent and The Dalles
Dam as the upstream extent. We then used the forebay elevation of the upstream hydroelectric
project (e.g., The Dalles Dam in this example) as a benchmark to define the maximum elevation
for the floodplain extent. We then used the GRTS algorithm to generate a master sample list of
sites for this area. We chose this technique to define the floodplain because the extents of the
current and historic floodplains are currently undefined and because it was the same technique
to define the floodplain for the master sample previously formulated for the Columbia River
Estuary. The sample size was selected to have a sample site approximately every 30 x 30 m.
We met with PNAMP staff (Jacque Schei, USGS) and staff from the Sitka Technology Group
to coordinate the incorporation of the area based sample frames for the mainstem Columbia
and Snake Rivers into the Monitoring Sample Designer tool
(https://www.monitoringresources.org/Designer/Home/Index) that is being developed by
PNAMP. We discussed the benefits and drawbacks associated with formulating one
comprehensive master sample (for the entire Columbia River Basin) or as discrete units.
Ultimately, how the master sample is grouped or divided will be based on the user’s needs with
respect to allocating samples over an area that encompasses their monitoring program
requirements but the decision was made to present multiple sample frames corresponding to
discrete geographic units. For instance, we developed a sample frame for Bonneville Reservoir,
The Dalles Reservoir, and John Day Reservoir versus one sample frame for the entire area. If
desired, the sample frames can be regrouped to accommodate different geographic scales (for
example, mainstem sub-basins). We attributed the area based sample frames with basic
information. Attributes including State, County, Hydrologic Unit Codes, etc. will be associated
with the master sample files. Further attribution of the sample frames is possible to
accommodate various design needs; however, coordination amongst groups using the sample
frames with respect to how the sample frame is attributed would provide for efficiency and
could reduce duplication of effort. We have transferred the sample frame to PNAMP; as of the
writing of this report the sample frames for Bonneville Reservoir and The Dalles Reservoir have
been incorporated into the Monitoring Sample Designer and are available to scientists there to
create a GRTS draw. The other sample frames will be loaded into the Monitoring Sample
Designer per scheduling and resources (Jacque Schei, USGS; Written communication).
24
Figure 1. The geographic extent of the sample frames developed for the mainstem Columbia
and Snake Rivers. Sample frames comprise the individual reservoir and associated floodplain to
the next upstream dam (black squares). For the Columbia River the upper most extent is the
Grand Coulee Dam and for the Snake River it is the Hells Canyon Dam.
Develop information on the pros and cons and costs associated with different monitoring
design and field protocol combinations.
The development and implementation of a mainstem Columbia River ISTM will require the
identification of monitoring designs that provide an assessment of the status and trends of
important resources and that allow for efficient collection of data. Given the breadth of the
policy issues and the spatial and temporal complexity of the mainstem Columbia River, no one
particular response or survey design will likely meet the needs of a comprehensive mainstem
Columbia River ISTM project. For instance, in some instances, conducting Effectiveness
Monitoring (e.g., Intensively Monitored Watersheds studies) may be a better choice than Status
and Trend Monitoring for detecting the effects of specific mitigation and restoration actions. Be
that as it may, coordination amongst agencies conducting monitoring, or activities that could
contribute to a monitoring effort would help to make the most use of the information being
generated. By promoting coordination of efforts and standardizing protocols where sensible
25
and/or possible, the limited resources available for conducting the monitoring activities can be
used as efficiently as possible. Efforts to standardize collection and analyses would allow data
collected by different agencies to be used to assess changes within particular reaches of the
mainstem Columbia River and help facilitate comparisons among reaches, where comparing
and contrasting the resources (e.g., fish, water quality, etc.) makes sense. For some metrics,
such as landscape scale metrics, using remote sensing and GIS to characterize the status and
trends of habitats has the potential to census large areas in a cost-effective manner. In other
instances, such as comparing changes in fish assemblage integrity, the collection of data will be
more labor intensive and will require areas to be subsampled. In both cases, identifying a
common set of metrics that will provide similar types of information across reaches and
jurisdictional boundaries and standard ways of measuring the metrics will help to provide
valuable information to decision makers and the public about whether mitigation and habitat
restoration strategies are working and cost effective.
Simultaneously monitoring the status and trends of resources requires special survey
design considerations. Johnson et al. (2008) provide a discussion of the benefits and drawbacks
of particular survey designs to address monitoring questions in the Columbia River Estuary and
recommend a rotational panel design (McDonald 2003) for monitoring the status and trends of
habitat conditions and juvenile salmonid performance. Rotational panel designs allow for both
status and trends monitoring simultaneously. In a rotational design, some fraction of the
sample location is revisited from the previous year while new sites enter the sample each year.
Rotational pattern designs will likely have applicability to various components of a mainstem
Columbia River ISTM.
Developing a common sample frame that multiple agencies can draw from could help to
coordinate disparate sampling efforts so that they can contribute to a mainstem Columbia River
ISTM. Larsen et al. (2008) suggest a framework for coordinating efforts of multiple agencies so
that the efforts can contribute to a larger monitoring effort. Based in part on a GRTS design
(Stevens and Olsen 2004), Larsen et al. (2008) suggest that the development of a very large
sample, a “master sample” (Yates 1981), that individual monitoring programs can draw
subsamples from could serve as a framework for combining individual efforts into a larger
monitoring effort. Using the “master sample” consists of a process of specifying a GRTS based
sample of a specified size, n, that is a spatially balanced random set of sites representing the
target resource, and then selecting sites from this sample frame to collect monitoring data. The
master sample then serves as a standard set of sampling points that can be organized in a
variety of ways to allow sample site selection across different geographic domains, habitat
types or sizes, or other features by which the frame can be classified. If consistent design
principles are followed, monitoring data collected from these sites can be combined if there are
overlapping geographic domains and provided that the same frame, sample elements, and
sampling protocols are used (e.g., Larsen et al. 2007).
26
Examples of long-term monitoring programs in other large river systems
Precedence exists to suggest that establishing long-term monitoring efforts on large rivers
system is accomplishable. Long-term monitoring programs have been established for other
large river systems within the US. Following are three examples of long-term monitoring
activities on large US Rivers.
Mississippi River
On the Mississippi River, a long-term monitoring program for aquatic resources was
established in 1986 when congress authorized the Environmental Management Program (EMP)
on the Upper Mississippi River System through the Water Resources Development Act (USGS
1999). The EMP funds two major components: ecosystem rehabilitation projects and long-term
resource monitoring. The Long Term Resource Monitoring Program (LTRMP) is implemented by
the USGS in partnership with the Army Corps of Engineers and state agencies. Data collected
include water quality, vegetation, invertebrates, fish, land cover, elevation, and bathymetry. A
Strategic and Operational Plan developed by the LTRMP partnership for 2010-2014 calls for
continued monitoring, but with expanded emphasis on research, modeling, communication,
and adaptive management (see:
http://www.umesc.usgs.gov/ltrmp/ateam/strategic_operational_plan_final_30june2009.pdf ).
The long-term goals of the program are to understand the system, determine resource trends
and impacts, develop management objectives and alternatives, and manage the large amount
of information collected.
Illinois River
A long-term monitoring program implemented by the Illinois Natural History Survey has
been in place on the Illinois River since 1957 (McClelland 2006). The Long-Term Illinois River
Fish Population Monitoring Program has sampled fishes in six navigation reaches of the Illinois
River with data collected annually. Over the course of the program 205,679 fishes representing
98 fish species (and seven hybrids) from 17 families have been collected. Based on the data
collected under this program it has been determined that native fish species richness has
increased over time and community analyses revealed changes in fish species composition from
a community dominated by common carp (Cyprinus carpio) and goldfish (Carassius auratus) to
one of greater species diversity.
Colorado River
The Glen Canyon Dam Adaptive Management Program (GCDAMP) was formally established
in 1997 by the Secretary of the Interior Department in response to the Grand Canyon
Protection Act of 1992 (GCPA). The GCPA is intended to improve natural resource conditions in
the Colorado River corridor in Glen Canyon National Recreation Area and Grand Canyon
National Park, Arizona. The GCDAMP fulfills the statutory requirement of the GCPA by using
science (long-term monitoring, modeling and field experiments in an adaptive framework) and
a variety of perspectives from 25 stakeholders to support the decision-making process related
27
to dam operations. Monitoring data collected by the USGS’s Grand Canyon Monitoring and
Research Center and its various cooperators since 1996, have documented improvements to
several key biotic and abiotic resources and progress toward improved understanding of the
ecosystem have resulted from the GCDAMP since its inception (Cross et al. 2011). Recent biotic
responses include (1) an estimated 50% increase in the adult population of endangered
humpback chub (Gila cypha) between 2001 and 2009, following previous declines; (2) increased
abundance of rainbow trout (Oncorhynchus mykiss) in the Lees Ferry tailwater in response to
artificial flood experiments; (3) a 90%, albeit temporary, decrease in non-native rainbow trout
below the Lees Ferry tailwater, known to compete with and prey on native fish, during a multiyear removal experiment in a reach used by humpback chub; and (4) widespread, albeit
temporary, rebuilding of eroded sandbars in response to an experimental high-flow release of
dam water in March 2008.
Summary
In this report we present progress towards the development of an ISTM for the
mainstem Columbia River and its floodplain. The development of a mainstem ISTM will
require much directed coordination and stakeholder participation to:
1. Identify decisions and questions that aquatic monitoring is intended to inform, and
identify associated prioritized monitoring goals and objectives.
2. Identify and document the extent to which existing monitoring programs support and
align with the priority monitoring objectives in #1 above.
3. Identify and/or develop monitoring designs, sampling frames, field and data
management protocols, and analytical tools to meet priority aquatic status and trend
monitoring objectives identified in #1 above.
4. Develop information on the pros and cons and costs associated with different
monitoring design and field protocol combinations.
5. Recommend mechanism(s) to implement and report the monitoring results from
implemented monitoring programs.
While much effort needs to be expended to complete the steps above, efforts by PNAMP
to establish an ISTM in tributaries to the Columbia River estuary and the Columbia Habitat
Monitoring Program (CHaMP) where long-term monitoring efforts are in process, provide
examples of the benefits of completing them (Ward et al. 2011). Fortunately, there are a
multitude of resources that could serve to inform the formulation of a mainstem Columbia
River ISTM. As such, the efforts to establish an ISTM in the mainstem Columbia should draw
upon the experiences of groups such as PNAMP and CHaMP to begin to facilitate the
formulation of the program while utilizing the wealth of planning documents and existing
programs to jump start the coordination of the effort. The ISTM that is being developed for
tributaries to the CRE by PNAMP provides an example of how proceeding through the stepwise process above can lead to the formulation of a monitoring program that addresses
priority management needs (Rawding and Rodgers 2013, Puls et al. In review). As efforts to
28
formulate a mainstem Columbia River ISTM proceed, coordinating with entities with
experience formulating, conducting, and maintaining long-term monitoring efforts on large
rivers will be informative. The large river monitoring programs listed above have dealt with
many of the issues we will encounter as we develop a mainstem ISTM program. For instance,
the involvement of multiple jurisdictions and issues associated with the logistics of sampling
in large rivers are addressed in the large river monitoring programs discussed above.
Long-term monitoring surveys will provide the foundation for assessments of current
ecological condition and provide baseline biotic data from which to measure changes in
community composition and function. The baseline and distribution data, when linked to
existing habitat conditions, will in turn facilitate the research and development of predictive
models and other decision support tools to assist managers in their decision making
processes. Currently, managers have few tools that will help them understand how
disturbance regimes and restoration actions are affecting efforts to recover endangered and
threatened species in the CRB. The framework for assessing long-term benefits of
rehabilitating degraded habitats, implementing mitigation projects to create habitats
beneficial to indigenous species (i.e. wetlands); assessing the relative vulnerability of species
and habitats to a changing environment, and mitigating the effects of environmental
stressors to create more resiliencies in CRB habitats in the future is lacking. Implementing an
ISTM for the mainstem Columbia River will help to identify trends in important natural
resources and help us understand the long-term collective effects of management actions.
Acknowledgements
We would like to thank all of the people that responded to our requests for information
regarding monitoring activities on the mainstem Columbia River. We would also like to
acknowledge and thank Jacque Schei and Jen Bayer of PNAMP for their assistance and reviews
of this document. Finally we would like to thank Amy Puls, USGS and Kirk Krieger, WDFW who
provided editorial suggestions that significantly improved this report.
29
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