EPA/600/R/13/028
  EPA Region 10 Climate Change  and
                       TMDL Pilot


              Project Research  Plan

                     Project Leader: Steve Klein1
          Co-Authors: Jon Butcher2, Bruce Duncan3, Hope Herron2
                 1 U.S. Environmental Protection Agency
                  Office of Research and Development
                      Ecological Effects Branch
                      Western Ecology Division
                      Ecological Effects Branch
                         200 SW 35th Street
                        Corvallis, OR 97333

                          2 Tetra Tech, Inc.
                     10306 Eaton Place, Suite 340
                          Fairfax, VA 22030

                 3 U.S. Environmental Protection Agency
                            Region 10
                  Office of  Environmental Assessment
                          1200 6th Avenue
                         Seattle, WA 98101

The information in this document has been funded wholly by the U.S. Environmental Protection
Agency under Contract Number EP-C-08-004 to Tetra Tech, Inc. It has been subjected to review
by the National Health and Environmental Effects Research Laboratory's Western Ecology
Division and approved for publication. Approval does not signify that the contents reflect the
views of the Agency, nor does mention of trade names or commercial products constitute
endorsement or recommendation for use.
                 Final Report: February 12, 2013

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              i



Contents

ACKNOWLEDGMENTS	ii
ABBREVIATIONS AND ACRONYMS	iii
EXECUTIVE SUMMARY	1
INTRODUCTION	3
PROJECT OBJECTIVES	5
STAKEHOLDER ENGAGEMENT	6
RESEARCH APPROACH	8
  Task 1 -Process Roadmap	8
  Task 2 - Quantitative Assessment	12

  Task 3 - Qualitative Assessment	20
  Task 4 - Climate Change Considerations for TMDL Development in the SFNR	24
  Task 5 - EPA Final Report	29
RELEVANCY TO EPA DECISION MAKING	30
SCHEDULE AND OUTCOMES	31
MANAGEMENT PLAN AND QUALITY ASSURANCE	34
LITERATURE CITED	36


Figures

Figure 1. Process roadmap: TMDL process and elements	9
Figure 2. Climate change assessment process and elements	10
Figure 3. Process roadmap: Illustrative linkages, TMDL and climate change assessment
       processes	11
Figure 4. The SFNR and known temperature impairments (Kennedy and Butcher 2012)	13
Figure 5. Climate change ecological risk assessment	22
Figure 6. Adaptive Management Framework	25
Figure 7. Illustrative decision-tree for evaluating climate change considerations in the
       SFNR TMDL	26
Figure 8. EPA Region  10 climate change TMDL pilot schedule and deliverables	32
Figure 9. EPA Region  10 climate change TMDL pilot and temperature TMDL—parallel
       study strategy	33

Tables

Table 1. Quantitative assessment milestone schedule	20
Table 2. Qualitative assessment milestone schedule	24
Table 3. Climate change considerations for TMDL development in the SFNR milestone
       schedule	28
Table 4. EPA final report milestone schedule	30

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
ACKNOWLEDGMENTS
EPA extends a special acknowledgment to the contributors for their support and
participation in the workshop held at EPA Region 10 on June 25, 2012, and in developing
this research plan.

Tim Beechie, NOAA Fisheries, NW Fisheries Science Center
Stephanie Brock, Washington Department of Ecology
Ben Cope, EPA Region 10
Dave Croxton, EPA Region 10
Oliver Grah, Nooksack Indian Tribe
Alan Hamlet, University of Washington, Climate Impacts Group (CIG)
Dan Isaak, U.S. Forest Service, Rocky Mountain Research Station
Laurie Mann, EPA Region 10
Nate Mantua, University of Washington, CIG
Teizeen Mohamedali, Washington Department of Ecology
Dave Olszyk, EPA ORD, Western Ecology Division
Claire Schary, EPA Region 10
Amy Snover, University of Washington, CIG

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
in
ABBREVIATIONS AND ACRONYMS
CCA          Climate Change Adaptation
CIG          Climate Impacts Group
CWA         Clean Water Act
DPS          Distinct Population Segment
Ecology       Washington Department of Ecology
EPA          Environmental Protection Agency
ESA          Endangered Species Act
ESU          Evolutionarily Significant Unit
GCM         Global  Climate Model
GIS           Geographic Information System
IPCC         Intergovernmental Panel on Climate Change
LA           Load Allocation
LIDAR        Light Detection and Ranging
MOS          Margin of Safety
NOAA        National Oceanic and Atmospheric Administration
NPDES        National Pollutant Discharge Elimination System
NWP         National Water Program
ORD          EPA's Office of Research and Development
OSP          Office of Science Policy
OW          EPA's Office of Water
PNW         Pacific Northwest
QAPPs        Quality Assurance Project Plans
SFNR         South Fork Nooksack River
TMDL        Total Maximum Daily Load
USFS         U.S. Forest Service
USGCRP      United  States Global Change Research Program
USGS         U.S. Geological Survey
VIC          Variable Infiltration Capacity model
WLA         Wasteload Allocation
WQS          Water Quality Standard
WRIA 1       Water Resources Inventory Area Number 1

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
EXECUTIVE SUMMARY
Global climate change affects the fundamental drivers of the hydrological cycle.
Evidence is growing that climate change will have significant ramifications for the
nation's freshwater ecosystems, as deviations in atmospheric temperature and
precipitation patterns are more frequently recorded across the United States (Bates et al.
2008; Karl et al. 2009). For example, stream temperature is projected to increase in most
rivers under climate change scenarios due in part to increases in air temperature, which,
in turn, could adversely affect coldwater fish species such as salmon (Brekke et al. 2009).
It is critical that watershed management, planning, and regulatory approaches incorporate
climate change science and understanding to ensure holistic and accurate analysis.

The total maximum daily load (TMDL) program is one of the primary frameworks for the
nation to maintain and achieve healthy waterbodies, implemented pursuant to section
303(d) of the Clean Water Act (CWA). More than 40,000 TMDLs have been developed
in the United States to determine the maximum pollutant loads allowable that would still
permit attainment of water quality standards. However, the majority of these analyses
have been conducted using assumptions of a stationary climate under which historical
data on flow and temperature can be assumed to be an adequate guide to future
conditions (Johnson et al. 2011). Research is needed to illuminate the ways in which
climate change considerations  could be incorporated into a TMDL, and how climate
change might influence restoration plans.

The U.S. Environmental Protection Agency (EPA) Region 10 and EPA's Office of
Research and Development (ORD) and Office of Water (OW) have launched a pilot
research project to consider how projected climate change impacts could be incorporated
into a TMDL and influence restoration plans. The pilot research project will use a
temperature TMDL being developed for the South Fork Nooksack River (SFNR), in
Washington, as the pilot TMDL for climate change analysis. An overarching  goal of the
pilot research project is to ensure that relevant findings and methodologies related to
climate change are incorporated into the SFNR Temperature TMDL in such a way that
the regulatory objectives and timelines of the TMDL are also met.

Because of the collaborative nature of this project, the project objectives have been
specified for EPA Region 10 and OW, and for EPA ORD. The pilot research  project
objectives are summarized below.

EPA Region  10 and OW Objectives
   1.  Support the implementation of EPA's National Water Program 2012 Strategy:
       Response to Climate Change.
   2.  Assess a range of outcomes from the Intergovernmental Panel on Climate Change
       (IPCC) Scenarios and Regionally Downscaled Global Climate Models (GCMs).
   3.  Explore the potential linkages between available climate change research and the
       TMDL process.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                                2


EPA ORD Objectives
    1.  Develop an EPA pilot research project and project report that documents the
       process and analysis to incorporate climate change considerations into a regional
       TMDL for the SFNR.

    2.  Assess the potential impacts of climate change on stream temperature and stream
       flow. Model the effects of riparian shading under climate change on Ecology's
       temperature criteria for salmonid designated uses.
    3.  Evaluate the effects of using inherently uncertain data from Regionally
       Downscaled GCMs to bracket a range of outcomes and create the boundary
       conditions for QUAL2Kw.
    4.  Integrate the objectives of the CWA 303(d) TMDL provisions to protect and
       restore designated uses, which support the recovery goals of the Endangered
       Species Act (ESA) Salmonid Recovery Plan.
    5.  Evaluate the prioritization of stream restoration actions in the SFNR.
    6.  Investigate the application of methods to identify coldwater refuges and evaluate
       the potential for protection/restoration actions under climate change.
    7.  Collaborate and incorporate the findings from the U.S. Geological Survey
       (USGS) Groundwater/Surface Water Study of the SFNR.

The pilot research project consists of three primary project phases: Phase 1 Research
Plan, March-September 2012; Phase 2 Research Analysis and Risk/Vulnerability
Assessment, October 2012-September 2013; and Phase 3 EPA Report, October 2013-
September2014.

This document constitutes the final deliverable of Phase 1 Research Plan. The research
plan identifies the goals and objectives of the pilot research project and outlines the
technical approach, major activities, subtasks, and schedule for completing the study.
Tasks 1 -4 as outlined in this research plan are associated with Phase 2; whereas Task 5 is
associated with Phase 3. The first task (Process  Roadmap) will develop an organizing
graphical framework that will serve to both illustrate the TMDL and climate change
assessment processes and to highlight potential linkages and integration points for further
study. The second task (Quantitative Assessment) will provide climate-altered boundary
conditions for the QUAL2Kw model.  The QUAL2Kw model will assist in the analysis of
potential climate change impacts on SFNR temperatures and TMDL allocations. Under
the third task (Qualitative Assessment), a comprehensive analysis of freshwater habitat
for ESA salmon restoration in the SFNR under climate change will be conducted, which
will result in a prioritized list of climate change  adaptation strategies to support salmon
restoration. The fourth task (Climate Change Considerations for TMDL Development in
the SFNR} will examine EPA TMDL regulatory requirements to identify potential areas
where climate change could be considered for inclusion in the SFNR temperature TMDL.
Each of project tasks one through four results in an interim deliverable. The fifth task,
production of the Phase 3, EPA final report, will integrate and synthesize the results from
the task reports into a coherent EPA final report, which  will serve as the final project
outcome.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
INTRODUCTION
Global climate change affects the fundamental drivers of the hydrological cycle.
Evidence is growing that climate change will have significant ramifications for the
nation's freshwater ecosystems, as deviations in atmospheric temperature and
precipitation patterns are more frequently recorded across the United States (Bates et al.
2008; Karl et al. 2009). For example, stream temperature is projected to increase in most
rivers under climate change scenarios due in part to increases in air temperature, which,
in turn, could adversely affect coldwater fish species such as salmon (Brekke et al. 2009).
It is critical that watershed management, planning, and regulatory approaches incorporate
climate change science and understanding to ensure holistic and accurate analysis.

The total maximum daily load (TMDL) program is one of the primary frameworks for the
nation to maintain and achieve healthy waterbodies, implemented pursuant to section
303(d) of the Clean Water Act (CWA). More than 40,000 TMDLs have been developed
in the United States to determine the maximum pollutant loads allowable that would still
permit attainment of water quality standards (WQS). However, the majority of these
analyses have been conducted using assumptions of a stationary climate under which
historical data on flow and temperature can be assumed to be an adequate guide to future
conditions (Johnson et al. 2011). Research is needed to illuminate the ways in which
climate change considerations could be incorporated into a TMDL, and how climate
change might influence restoration plans.

The U.S. Environmental Protection Agency (EPA) Region 10, Washington Department
of Ecology (Ecology), Nooksack Indian Tribe, and the Lummi Nation are collaborating
on a temperature TMDL for the South Fork Nooksack River (SFNR), in Washington.l In
addition to this regulatory objective, Region 10 has partnered with EPA's Office of
Research and Development (ORD) and Office of Water (OW), to initiate a pilot research
project to consider how projected climate change impacts for the SFNR could be
incorporated into the TMDL and influence restoration plans.  EPA is using a parallel
study strategy to concurrently accomplish the research objective (Longitudinal Analysis
(Start-To-Finish) Climate Change and Temperature TMDL) and regulatory objective
(SFNR Temperature TMDL). This allows EPA to learn by doing.

Using the SFNR as the pilot area for this research effort has several benefits,  specifically:
(1) the synchronized pairing of the research project with a real-world temperature TMDL
to ensure better understanding of the needs of water managers; (2) the pilot area
represents a typical landscape in the Pacific Northwest (PNW), which promotes broader
direct application of the project results; and (3) the pilot research project will be able to
leverage downscaled climate datasets and integrate ongoing research by other federal
agencies that is directly relevant to the project.

The SFNR is in northwest Washington and in an area considered typical of the
mountainous, remote, forested landscape in that region, with minor urban and agricultural
1 The project team for the regulatory project consists of EPA Region 10, Ecology, and the EPA consultant.
The Nooksack Indian Tribe and the Lummi Nation are cooperating partners.
 The project team for the pilot research project consists of EPA ORD, EPA Region 10, and the EPA
consultant. Ecology, the Nooksack Indian Tribe and the Lummi Nation are cooperating partners.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                                4


land uses. However, forest practices, including road building and timber harvest, are the
dominant land use practices in the SFNR watershed. The SFNR and its tributaries provide
migration routes, and spawning and rearing habitat for several salmon species throughout
the year. The SFNR has 14 segments, and 9 tributary segments are identified as being
impaired for temperature on Washington's 2008 303(d) list. These areas exceed the
temperature criteria established by Ecology to protect aquatic life use categories (salmon
versus warm-water species) and life-stage conditions (spawning and rearing). These
segments have data that indicate exceedances. Other segments without data might also be
experiencing exceedances. The temperature TMDL will identify the issues and outline
the solutions  needed to improve river temperatures.

Several relevant research efforts are ongoing to provide increased understanding of how
the SFNR temperature could change under climate scenarios, which will be leveraged for
the pilot research project:
    1.  The Climate Impacts Group (CIG) has developed hydroclimatic scenarios for the
       PNW, including for the pilot area (Mauger and Mantua 2011). The hydroclimatic
       scenarios have been developed for the A1B (moderate emissions scenario)3
       climate scenario using three downscaling approaches (hybrid delta, transient Bias
       Corrected Statistical Downscaling, and the delta method) and include three time
       steps (2020s, 2040s, and 2080s).
    2.  Dan Isaak, U.S. Forest Service (USFS), with support from the Great Northern
       Landscape Conservation Cooperative, is developing a regional stream
       temperature model, which includes the  SFNR. A potential application of this
       project will be to map river network temperatures to identify when and where
       WQS are being met and how that might change under climate change scenarios.
    3.  Tim Beechie, National Oceanic and Atmospheric Administration (NOAA), is
       exploring salmon vulnerability in Washington, including in the SFNR, by
       assessing salmon vulnerability from habitat and stock status stress, and from
       climate stress as determined through future temperature and future precipitation
       stress (Beechie et al. 2012).
    4.  Cristea and Burges, University of Washington, conducted an assessment of stream
       temperature and riparian shading for several streams in the Wenatchee River
       Basin to  evaluate the potential impact of climate change on stream temperature
       (Cristea and Burges 2010). We will use this study as a regional example of
       QUAL2Kw modeling and riparian shading under climate change.

The present day condition of freshwater salmonid habitat in the SFNR is the result of
natural disturbances, land use (mostly forest and agricultural) and land use practices
(current and historical).  Current Best Management Practices (BMPs) and restoration
 The Al scenario family assumes very high economic growth, global population peaking mid-century and
then declining, and energy needs being met by a balance of fossil fuels and alternative technologies. A1B (a
subset of the Al family) lies near the high end of the spectrum for future greenhouse gas emissions,
particularly through mid-century. A1B projects a future where technology is shared between developed and
developing nations in order to reduce regional economic disparities. See CIG's website for more
information: http://cses.washington.edu/cig/fpt/climatemodels08.shtml.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
actions will take decades to restore watershed processes and historical habitat conditions
in the SFNR. The Habitat Conservation Plan (HCP) under the ESA are additional
measures for forest land use that go beyond the requirements of the Washington Forest
Practices Act (WFPA) to address current and historical impacts on freshwater salmonid
habitat in the SFNR .

Climate change adds an additional stressor to salmonid habitat in the SFNR. The
methodology outlined in this research plan uses downscaled GCMs, the Variable
Infiltration Capacity (VIC) and QUAL2Kw hydrologic models to assess the impacts of
climate change on salmonid habitat in the SFNR. The quantitative and qualitative
assessments in this Research Plan facilitate the integration of multiple stressors, current
and past land use practices, and restoration actions (ESA recovery and TMDL
implementation) to present an integrative analysis of future freshwater salmonid habitat
in the SFNR under Climate Change.

This research plan identifies the goals and objectives of the pilot research project and
outlines the technical approach,  major activities, subtasks, and schedule for completing
the study.
PROJECT OBJECTIVES
The following EPA objectives have been developed for this project:

1. EPA Regional (Region 10) and Program Office (OW) Objectives
   •   Support the implementation of EPA's National Water Program 2012 Strategy:
       Response to Climate Change - March 20124 to help achieve EPA's Vision
       Statement on Water Quality by promoting the management of sustainable surface
       water resources under changing climate conditions (USEPA 2012a).
   •   Assess a range of outcomes from the Intergovernmental Panel on Climate Change
       (IPCC) Scenarios and Regionally Downscaled Global Climate Models (GCMs),
       rather than a single prediction of climate change effects on stream temperature
       and the related WQS.
   •   Explore the potential linkages between  available climate change research and the
       TMDL process.

2. EPA Management Objectives
   •   Involve environmental practitioners and policy makers  (federal, tribal, state, local
       and nongovernmental organization) in developing a climate change risk
       assessment/management (vulnerability/adaptation) research pilot.
   •   Operate as one EPA (Region 10, OW, ORD) in the planning, execution and
       evaluation of this project.
4 Note that this document is currently available as a public review draft. The final draft has not yet been
released and may differ from the public review draft.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
   •   Encourage the consideration of EPA's National Tribal Science Priorities for
       Climate Change and Integration of Traditional Ecological Knowledge.

   •   Use a parallel study strategy to concurrently accomplish the research objective
       (Start-To-Finish Climate Change Temperature TMDL) and regulatory objective
       (SFNR Temperature TMDL).

3. EPA Research (ORD) Objectives

   •   Develop an EPA project and project report that documents the process and
       analysis used to incorporate climate change considerations into a regional
       temperature TMDL for the SFNR.

   •   Assess the potential impacts of climate change on stream temperature and stream
       flow from IPCC Emission Scenario A1B (moderate emissions scenario), based  on
       regionally downscaled GCMs  for the 2020s, 2040s and 2080s (Mauger and
       Mantua 2011). Model the effects of riparian shading under climate change on
       Ecology's temperature criteria for salmonid designated uses.

   •   Evaluate the effects of using inherently uncertain data from Regionally
       Downscaled GCMs by using the hybrid delta results under the A1B scenario for
       the GCM that is anticipated to produce model low (least warming) model medium
       (medium warming) and model high (highest warming) to bracket a range of
       outcomes and create the boundary conditions for QUAL2Kw.

   •   Integrate the objectives of the  CWA 303(d) TMDL provisions to protect and
       restore designated uses, which support the recovery goals of the Endangered
       Species Act (ESA) Salmonid Recovery Plan. Use the best available science from
       the Climate Science Programs under the United States Global Change Research
       Program (USGCRP).

   •   Evaluate the prioritization of stream restoration actions in the SFNR on the basis
       of the watershed processes or functions they attempt to restore and their ability  to
       ameliorate climate change effects on high stream flows, low stream flows, and
       high stream temperatures (Beechie et al. 2012).

   •   Investigate the application of methods to identify coldwater refuges and evaluate
       the potential for protection/restoration actions to increase the effective use of
       thermal refugia by coldwater fish under climate change (USEPA 2012b).

   •   Collaborate and incorporate the findings from the United States Geological
       Survey (USGS) Goundwater/Surface Water Study of the SFNR, WA (in progress
       and commissioned by the Nooksack Indian Tribe).
STAKEHOLDER ENGAGEMENT
This project is structured as a stakeholder-centric process. This project began with
extensive discussions involving EPA's Region 10, OW, and ORD about the scope and
purpose of the project. This conversation was expanded to include key stakeholders in the

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
SFNR including Washington's Department of Ecology (Ecology), Nooksack Indian
Tribe, and Lummi Nation, along with the University of Washington's CIG, USFS,
NOAA Fisheries and the USGS as research partners. Two stakeholder engagement
meetings have been held to date, and are further described below.

A workshop was held on June 25, 2012, at EPA Region 10 in Seattle to solicit input from
key stakeholders, scientists, environmental practitioners and policy makers (federal,
tribal, state, local and nongovernmental organization) and help develop the scope,
methods and study design for the EPA Region 10 Climate Change TMDL Pilot and
Temperature TMDL.

On October 4, 2012, a project scoping meeting was held with Washington's Water
Resources Inventory Area Number 1 (WRIA 1) Salmon Recovery Team. The purpose of
the meeting was to brief the team on the EPA Region 10 Climate Change and TMDL
Pilot and to solicit input on issues, concerns  and opportunities to improve the scope and
effectiveness of the project.  The WRIA 1 Salmon Recovery Team recommended
implementing Task 3 (Qualitative Assessment) as a rapid-prototype pilot.  Specifically,
these recommendations included: (1) developing an assessment methodology based on
Restoring Salmon Habitat For A Changing Climate, Beechie et al. 2012 and (2) leaving
open the possibility of another follow-on project to "refine the assessment methodology"
and/or "scale to a larger landscape", possibly for the entire Nooksack River Basin or
WRIA1.

The Nooksack Indian Tribe has identified two issues that are of substantial interest to the
tribe, and  we will accommodate those issues in the analyses to the extent we can within
the scope, resources, and capabilities available to this project: (1) upland watershed
processes  are fundamental biophysical mechanisms or systems that govern the
movement, delivery, or gain/loss of water, sediment, nitrogen and large woody debris to
aquatic ecosystems on the landscape, and (2) riparian buffer effectiveness  on regulating
stream temperature from forest practices. To the extent these issues are not readily
addressed in the analyses, we will identify possible future studies that can directly assess
the issue in more detail.

We will continue the stakeholder engagement during the research planning,
implementation and documentation phases of this project. The EPA Region 10 climate
change TMDL pilot is all about demonstrating how cutting-edge science can be applied
in a real-word problem-solving context with the participation of scientists, environmental
practitioners and stakeholders.
 Rapid prototyping is an engineering design method that is commonly used in the manufacturing and
software development sectors. The emphasis is on minimal planning and rapid development to allow the
accomplishment of a working model in a relatively short time frame. The chief advantage is the working
model is available for testing, evaluation and refinement in a much shorter time frame than would normally
be required. In addition, the working model creates an opportunity for adaptive management and learning
that is unavailable in a more traditional development cycle. In this case the Beechie et al. 2012 method is
the concept, the Task 3 Qualitative Assessment is the rapid prototype development of a working model in
the SFNR and the engineering design refinement and scaling is the follow-on project for the entire
Nooksack River Basin.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                               8


RESEARCH  APPROACH

Task 1 - Process Roadmap

Background and Problem
While the evaluation of potential climate change impacts has become increasingly
prevalent in water resources assessments, little research has been done on how to
incorporate climate change findings and data into the TMDL process. A comprehensive
review of the specific elements of a TMDL is needed to evaluate how to best integrate the
evolving understanding of climate change impacts into TMDL determinations and
implementation plans and to account for the inherent uncertainty underlying climate
change. Given the complexities of such an assessment, developing an organizing
graphical framework would serve to both illustrate the TMDL and climate change
assessment processes and to highlight potential linkages and integration points for further
study. This Project  provides an opportunity to explore the climate change implications of
stream temperature on the SFNR.

Approach and Methods
The process flowchart, referred to in this document as the process roadmap, will serve as
an organizing methodology for the  pilot research project and will specifically guide Task
4 of this research plan. The process roadmap will be continually updated through the life
of this project to illustrate the primary steps and decision points of the quantitative and
qualitative assessments and document climate change considerations as they relate to, and
inform the TMDL process. The three primary components of the process roadmap are
illustrated and described below.

TMDL Process (Figure 1)
The TMDL process and elements are presented as Figure 1, an adaption from Guidelines
for Reviewing TMDLs under Existing Regulations issued in 1992 (USEPA 2002). EPA
identified  13 elements as part of the TMDL process; however two of those elements
(including a submittal letter and keeping  an administrative record) are not considered
germane to TMDL  development. Figure  1 thus includes only the 11 elements necessary
for developing the TMDL. Of the 11 elements, 7 are required by regulation (40 CFR
130.7), and 3 elements are recommended for inclusion by EPA guidance. The elements
have been conceptually grouped (and labeled TMDL Process in Figure 1) on the basis of
how TMDL practitioners typically address EPA requirements and recommendations in
the TMDL process.

Climate Change Assessment Process (Figure 2)
The primary elements generally associated with a climate change assessment are
illustrated in Figure 2, an adaptation from Scanning the Conservation Horizon, A Guide
to Climate Change  Vulnerability Assessment (Glick et al. 2011). While there is no set
formula for conducting a climate change assessment, as climate assessments vary by
sector focus, geographic and temporal scales, and by the resources available to conduct
the assessment, the elements in Figure 2 constitute primary considerations when
developing a climate change assessment.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
TMDL and Climate Change Assessment Process Linkages (Figure 3)
The conceptual linkages between the TMDL and climate change assessment processes
are presented as Figure 3. It is anticipated that the tasks conducted as part of the pilot
research plan will further refine the understanding of how these two processes can better
inform and reinforce each other. The process steps illustrated in Figure 3 will be further
categorized into sub-process steps, decision points, and causal relationships according to
research findings from the quantitative and qualitative assessments. Relevant findings
and lessons learned from other EPA climate change research will also  be incorporated as
appropriate.
            TMDL Process
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EPA Region 10 Climate Change and TMDL Pilot Research Plan
                           10
           Climate Change
         Assessment Process
Elements in a Climate
 Change Assessment
Participation
Publ
akeholder Involvemen
           Problem Understanding
           Identify Climate Trends
          Assess Vulnerability / Risk
             Identify Adaptation
             Options / Strategies
            Implementation and
                Monitoring
                                                  1.Determine element of concern
 2, Downscaling approach
 3. Emission scenario
 4. Time horizon
 5. Likelihood of event
 6,Consequence of event
 7. Reduce sensitivity
 8. Reduce exposure
 9, Increase adaptive capacity
 10. Set priorities
 11. Select targets
 12. Adaptive management
            Figure 2. Climate change assessment process and elements

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
                      11
               TMDL Process
   Climate Change
Assessment Process
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0
't->
fD
Q,
|y
'^
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Problem Understanding
TMDL Target
Identification
3
Source
Assessment
r
Linkage between Loading
and Waterbody Response
i
f
Allocation Analysis
i
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Implementation and
Monitoring Plan
i
f
TMDL Report and Submittal
                                                    Problem Understanding
                                                    Identify Climate Trends
                                                   Assess Vulnerability / Risk
                                                  Identify Adaptation Options
                                                         Strategies
                                                     Implementation and
                                                         Monitoring
    Figure 3. Process roadmap: Illustrative linkages, TMDL and climate change
                           assessment processes

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              12



Task 2 - Quantitative Assessment

Background and Problem
Segments of SFNR and some of its tributaries were included on Washington's 2008
303(d) list of impaired waterbodies for temperature violations of WQS. Ecology is
required under CWA section 303(d) to develop TMDLs for impaired waters of the state.
High water temperatures in the SFNR are detrimental to fish and other native species that
depend on cool, clean, well-oxygenated water. EPA, Ecology, the Nooksack Indian
Tribe, and the Lummi Nation are cooperating on developing a temperature TMDL for the
SFNR.

The study area includes all portions of the SFNR watershed, which is in Whatcom and
Skagit counties of Washington (see Figure 4). The river flows to the mainstem Nooksack
River, which empties into Bellingham Bay. The Nooksack River watershed, including the
SFNR, Middle Fork Nooksack River, North Fork Nooksack River, and associated
tributaries, provides migration spawning, incubation, rearing, and foraging habitats for all
native PNW salmon and trout species. These fish species are highly valued by the many
state residents that depend on them for cultural, recreational, or economic reasons.
Salmon in the Nooksack River watershed are a significant source of sustenance and are of
great ceremonial and cultural importance to the Lummi Nation and Nooksack Indian
Tribe. Yet abundances of many salmonid populations have diminished substantially from
historic levels. Local spring chinook, bull trout, and steelhead populations compose
components of the Puget Sound Chinook Evolutionarily Significant Unit (ESU), Puget
Sound Steelhead ESU, and Coastal-Puget Sound Distinct Population Segment (DPS), all
of which are listed as threatened under the ESA.

Improving water quality in the SFNR watersheds is necessary to support the recovery of
threatened coldwater fish species that spawn, rear, or live there. To protect these species,
Washington has established maximum temperature criteria for different portions of the
SFNR that range from 12 to  16 degrees Celsius (°C), expressed as the highest annual
running 7-day average of daily maximum temperatures. The criteria, along with the
impaired segments, are shown in Figure 4. Washington's water quality  standards
recognize that portions of many waterbodies cannot meet the assigned criteria due to
natural conditions. The estimated natural conditions of the  SFNR will be calculated as
part of the Regulatory TMDL. Washington water quality standards also recognize that
background conditions are sometimes cooler than the criteria; and in such cases, the
allowable rate of warming from human actions is restricted.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
13
  Legend

  I   I Watershed Boundary
     County Boundary
  ^^f Water

  	 Major Road
  ^^^~ Impaired Segment (Temperature, 2008)
  Aquatic Life Use Designations (Temp. Standard)
  	Core Summer Salmonid Habitat (16°C)

  	Char Spawning and Rearing (12°C)
  ^^^* Supplemental Spawning/Incubation (13°C)
 South Fork Nooksack River: Known Impaired Segments
 Figure 4. The SFNR and known temperature impairments (Kennedy and Butcher
                                       2012)
The Regulatory Project Team's TMDL study includes developing a predictive
temperature model that will be used to determine the river's capacity to assimilate
thermal loads and estimate the "system potential" temperature. The system potential is
the estimated water temperature if mature riparian vegetation and microclimate
conditions were present, along with any local groundwater and channel or streamflow
improvements planned for the future; and is an estimation of the natural condition of that
waterbody. The model will be used to determine the loading capacity that meets
temperature water quality criteria to protect designated uses and to evaluate potential
alternative pollutant allocation scenarios for point and nonpoint sources that meet the
loading capacity.

The modeling approach consists of a Shade model (Ecology 2003 a) linked to the
QUAL2Kw water quality model. QUAL2Kw (Chapra and Pelletier 2003; Ecology
2003b) serves as the model to perform in-stream temperature simulations. The steady-
state QUAL2Kw model is appropriate for evaluating impairments and determining
specific conditions during the summer low-flow period. The Shade model will simulate
shading factors on the basis of topography and riparian vegetation coverage, which will
feed into the QUAL2Kw in-stream  model.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                               14
QUAL2Kw is a quasi-steady state model and is Ecology's preferred tool for temperature
TMDLs (Kennedy and Butcher 2012). The model simulates daily temperature and heat
budget with hourly variations in input parameters and boundary conditions.
Meteorological conditions have strong influences on water temperature. Parameters
included in QUAL2Kw input that affect stream temperature are effective shade, solar
radiation, air temperature, cloud cover, relative humidity, headwater and tributary
temperature, and hyporheic flow. These parameters are calculated (e.g., effective shade
from Shade model), obtained from weather station information, or interpreted from other
sources.

QUAL2Kw will be applied to conduct focused analyses of critical conditions (e.g., late
summer low flow, clear sky, high air temperature conditions) that affect temperature
impairments from which TMDL targets can be determined directly. Model input for the
TMDL simulations will include flow, meteorological, and water temperature boundary
conditions developed from available data.

TMDL allocations and implementation plans developed in this way are contingent on
current climate, and might not be sufficient to support designated uses under potential
future climate regimes. The Pilot Research Project Team, therefore, intends to analyze
potential climate change impacts on SFNR temperatures and TMDL allocations. This will
be accomplished by reapplying the QUAL2Kw model using  climate-altered boundary
conditions. The purpose of the work described in this task is  to provide altered boundary
conditions for the QUAL2Kw modeling under the A1B climate scenario and for three
time horizons (2020s, 2040s, and 2080s). The actual QUAL2Kw modeling will be
accomplished as part of the Regulatory Project Team's SFNR Temperature TMDL.

Approach and Methods
After the QUAL2Kw TMDL model setup is completed and the model provides
acceptable predictions of current temperature conditions,  it will be applied to examine the
system potential temperature and the potential climate change impacts on SFNR
temperatures. This project will supply climate-altered boundary conditions to the
QUAL2Kw model. These boundary conditions will be derived from the work conducted
and served by CIG at the University of Washington (e.g., Mauger and Mantua 2011;
Hamlet etal. 2010).

CIG has taken output from GCMs and downscaled the meteorological output to a 1/16
degree scale for the PNW using quantile mapping on historical meteorological time series
(see Polebitski et al. 2007a). This has been done for 10 GCMs and multiple emission
scenarios for the period through 2099. Downscaling is also done in two different ways: a
composite delta method in which there is a single average change (delta) for each month
calculated from a time slice of the GCM for the region that is applied  to ever day in that
month, and a hybrid delta approach that uses statistical bias correction to maintain the
probability distribution. There is also a composite delta run that represents the central
tendency of the 10 hybrid delta GCMs for a given emission scenario.

CIG has also produced gridded estimates of surface runoff and baseflow at the 1/16
degree scale, using the Variable Infiltration Capacity or VTC model (Eisner et al. 2010).

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                                15


Seventy-nine climate scenario products are available from CIG covering the SFNR
watershed. Initial work for this project will focus on a limited subset of runs based on the
IPCC A1B emissions scenario because this is a robust available dataset. The A1B
scenario is considered a moderate emission scenario as compared to the other IPCC
emission scenarios. While there is uncertainty associated with any of the IPCC emission
scenarios, the A1B multi-model average is commonly considered to be "an informative
future climate scenario (i.e., it is closest to most model estimates and the weighting
scheme discounts extreme values)" (Beechie 2012). The A1B (moderate emission)
scenario has an ensemble mean that is 1° Celsius (C) lower in 2080 than the A2 (high
emission) scenario. The highest GCM model average for A1B projects a temperature
increase for 2080 that is 0.6 ° C lower than the A2 highest GCM model average.6

Three time horizons (2020s, 2040s, and 2080s) will be evaluated using the hybrid delta
results from GCMs under the A1B scenario for the South Fork Nooksack watershed, the
GCM that is anticipated to produce model low (least warming)  model  medium (medium
warming) and model high (highest warming), resulting in 3 climate products x 3 time
steps = 9 runs. This will achieve a project objective of evaluating the ensemble range of
outcomes from one IPCC scenario for the climate change risk assessment.

The following subtasks describe specific methods for converting CIG  climate products
into appropriate boundary conditions for the QUAL2Kw model of the SFNR.

Subtask Descriptions, Schedule, and Milestones
Subtask 2.1. Selection of Climate Scenarios
As noted above, the range of potential impacts will be evaluated at three time horizons
(2020s, 2040s, and 2080s) using the Scenario A1B hybrid delta results for GCMs under
the A1B scenario for the South Fork Nooksack watershed, the GCM that is anticipated to
produce model low (least warming) model medium (medium warming) and model high
(highest warming). The first subtask will be to review and select GCMs with the
appropriate characteristics from the available CIG products. This  will  be accomplished
through comparison of seasonal statistics on precipitation and temperature among the
different GCM outputs for the South Fork Nooksack watershed.
6 The Research Team is aware of current regional (Pacific Northwest) experimentation and model
comparison by the Climate Impacts Research Consortium (CIRC) of IPCC CMIP5 GCMs and
Representative Concentration Pathways (RCPs) that will be used in the upcoming Fifth IPCC Assessment
(AR5) in 2014. CIRC has compared current IPCC (CMIP3, IPCC AR4) SRES Scenarios with upcoming
(CMIP5, IPCC AR5) RCPs. Although this comparison is useful to put into context current studies (like this
one) that use IPCC (CMIP3, IPCC AR4) SRES Scenarios; however, the difference in methodologies
between these two IPCC Reports makes direct comparison or crosswalks between the two methods of
limited value.  The regional implementation of IPCC CMIP5 GCMs and RCPs will need additional testing
and implementation of a hydrological model, comparable to VIC, before it is useable in a similar
application for water quality/quantity or freshwater  salmonid habitat.

The Research  Team believes it is more important for this research project to embrace the concept of
"Iterative Risk Management" as defined by Yohe (NCADAC 2011). The iterative concept means that the
cycle of assessment and adaptive management is an unending process that refreshes itself as the cycle is
repeated. The  Team believes that the methodology and assessment offered in this Research Plan could be
refreshed using the new IPCC CMIP5 GCMs and RCPs (IPCC AR5) when they become available, with the
relative efficiency of a report update rather than a wholly new report.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                                16


Subtask2.1 Schedule - Nov. 2012-Dec. 2012
Milestone 2.1 Title: Excel spreadsheet that compares GCM outputs for the South Fork
Nooksack watershed and identifies selected GCMs.
Milestone 2.1 Completion Date: Dec. 2012

Subtask 2.2 Tributary andMainstem Flow Boundary Conditions
Subtask 2.2 Description: The QUAL2Kw core model (existing condition for TMDL) will
represent gaged or estimated flows or both in the mainstem and significant tributaries.
The TMDL application will scale the flow to a 7Q10 critical low-flow condition (or other
low-flow condition if a 7Q10 cannot be calculated).  The climate change application can
incorporate predicted changes in summer baseflow from assessments conducted by CIG.
CIG has paired climate scenarios with the VIC hydrologic model, operating at 1/16
degree resolution. For each grid cell, the VIC produces daily outputs of surface and
subsurface flow. During the critical low-flow periods for the TMDL, it is likely that all
flow will be baseflow.

The VTC model is a large-scale model that is not explicitly calibrated to the SFNR and
cannot be expected to exactly reproduce either current or future conditions for the
TMDL. Therefore, mapping/extrapolation of CIG estimates to the QUAL2Kw domain
will be necessary. Specifically, the CIG output will be applied using a change method in
which the TMDL 7Q10 flow at the model headwaters and for all tributary and diffuse
inflows is modified by the ratio of CIG estimates of  low flows of a similar return period
under current and future climate conditions.  The VTC model output for each grid cell
intersecting the South Fork Nooksack watershed will be analyzed to determine the
simulated low flow frequency (as depth of flow) for  current conditions and for future
climate scenarios. The ratios between future climate and current conditions for flows of
the critical duration and recurrence will be calculated for each VIC grid cell. For each
QUAL2Kw boundary inflow the ratio will be selected from the appropriate VIC grid cell
(or from an area-weighted average of multiple VTC grid cells if necessary for larger
tributaries) and applied to the boundary inflow to yield the climate-modified inflow
estimate for the critical condition.  The large-scale VTC model is not expected to provide
accurate estimates of flows from individual small streams in the South Fork Nooksack
drainage; however, the relative change predicted in unit area flows is believed to provide
a reasonable index of potential changes under future climate scenarios.

Subtask 2.2 Schedule - Oct.  2012 - Nov. 2012
Milestone 2.2 Title: Memorandum Documenting Tributary and Mainstem Flow
Conditions for Climate Scenarios
Milestone 2.2 Completion Date: Nov. 2012
 Note that output from the VIC model will not be used directly to drive the previously calibrated
QUAL2Kw model. Instead, VIC model output will be used to evaluate relative change under different
climate forcings. For example, the QUAL2Kw model will likely be applied to a critical low flow condition
in the TMDL. For future climate, VIC model output will be used to determine the potential ratio of such
low flows under future climate to the low flows used in the TMDL and the QUAL2Kw model input will be
adjusted by that ratio.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              17
Subtask 2.3 Tributary andMainstem Boundary Water Temperatures
Subtask 2.3 Description: The QUAL2Kw model application will encompass the
mainstem (only) of SFNR, beginning upstream of the first impaired segment. QUAL2Kw
provides a process-based simulation of temperature changes in the simulated reaches;
however, it requires specification of water temperatures for all influent boundary
conditions.

Boundary temperatures will be documented for critical conditions used in the TMDL
model. For the climate scenarios, these boundary temperatures will be altered using a
delta change method, in which an incremental change is imposed on the existing
temperature daily maximum and minimum.

The water temperature deltas will be assessed using a regression approach on the basis of
CIG output.  CIG provides daily minimum and maximum air temperature and daily
surface and subsurface flow. These will be used as independent variables (along with
other variables such as elevation and tributary shading) to develop two multiple
regression equations for available monitoring data on current climate tributary daily
minimum and maximum stream temperatures. The regression equations will then be
applied to future climate conditions, and the difference between future and current
condition predictions will be used as the delta on the temperature maximum and
minimum. Developing the regression relationships will be documented, including an
analysis of model fit uncertainty. Hourly temperatures will be distributed between the
minimum and maximum according to the diurnal pattern  in the TMDL model. Output of
this process will be a 24-hour time series for QUAL2Kw.

Subtask 2.3 Schedule - Oct  2012 - Dec. 2012
Milestone 2.3 Title:  Memorandum Documenting Boundary Temperatures for Future
Climate Scenarios
Milestone 2.3 Completion Date: Dec 2012

Subtask 2.4 Meteorological Forcing
Subtask 2.4 Description: Temperature simulation in the QUAL2Kw model requires
specification of a number of meteorological series, as described below.

Air temperature: Boundary air temperature is defined as a 24-hour time series in
QUAL2Kw. The QUAL2Kw core model will use meteorological data from a nearby
station for the existing air temperature on the simulation date. The TMDL application
will likely scale the air temperature to a critical condition such as the 90th percentile. The
climate change application can incorporate predicted changes in summer air temperature
from assessments conducted by the CIG. Mapping/extrapolation of CIG estimates to the
QUAL2Kw domain will be  handled using a delta change  method in which the existing
time series is modified by the predicted arithmetic change between current and future air
temperature conditions. Specifically, CIG output on daily minimum and daily maximum
temperatures will be used to establish deltas to predict future climate air temperature
minimum and maximum, and the hourly values will be distributed between the future
minimum and maximum according to the pattern contained in the TMDL model.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                               18
Cloud cover: The QUAL2Kw core model will use meteorological data from a nearby
station for the existing cloud cover on the simulation date. The TMDL application will
likely adjust the cloud cover to zero (clear sky) as a critical condition. No climate change
adjustment will be made for cloud cover because the critical condition will remain clear
sky.

Relative humidity: CIG provides monthly summaries of relative humidity that will be
used to specify changes under future climates.

Wind: Conduction and convection heat exchange at the water surface depend on wind.
Wind stress will be kept constant at TMDL conditions for all climate change scenarios.
While wind is likely to change under future conditions, downscaled analysis of this
variable is not available from CIG.

Subtask 2.4 Schedule - Nov. 2012 - Dec. 2012
Milestone 2.4 Title: Memorandum Documenting Meteorological Boundary Conditions
Milestone 2.4 Completion Date: Dec 2012

Subtask 2.5 Other Boundary Conditions
Subtask 2.5 Description: Riparian Shade: The QUAL2Kw core model will use estimates
of existing shade on the mainstem river based on observations (e.g., Light Detection and
Ranging (LIDAR), field sampling) and the Shade model. The TMDL application will
likely include alternative shade conditions, including the natural condition of full
potential shade ("system potential" conditions). Even though there is a likelihood that
riparian vegetation composition (e.g., diversity and abundance) might change due to
climate change, we do not have the tools  to predict these changes and do not plan to
evaluate a climate change adjustment in riparian shade outside the range of conditions to
be evaluated for the TMDL.

Channel Structure: The channel structure will be set to existing conditions for all model
setups, including climate change scenarios.  If adequate information on historic channel
geometry or changes in channel geometry due to winter high-flow events (as a result of
climate change) are available,  channel geometry could be adjusted in QUAL2Kw.

Groundwater Inflow Temperatures: The QUAL2Kw TMDL model will use estimates of
existing groundwater inflow temperatures on the mainstem river. If existing data are
available, current conditions groundwater inflows are generally set at the average
groundwater temperature for the area. In the critical condition TMDL model,
groundwater may be set to the average of the maximum groundwater temperatures.  For,
the climate change scenarios, groundwater inflow temperatures will be modified on the
basis of the change in average annual air temperatures predicted by the CIG climate
scenarios.

Hyporheic Exchange: In rivers with coarse (sand, gravel, cobble) bed sediments, a
portion of the flow (hyporheic flow) occurs within the bed sediment. Heat flux between
the water and sediment during hyporheic flow can help stabilize stream water
temperatures and provide cooling during  summer months. Changes to flow and

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                               19


temperature under future climates could alter the effectiveness of hyporheic exchange in
maintaining stable water temperatures.

In QUAL2Kw, the heat flux from hyporheic exchange of water between the stream and
the hyporheic sediment zone is computed as
                                              •\   m  ;

where E^p . is the bulk hyporheic exchange flow in reach i (m3/day; user input), Asfi is the
surface area of the hyporheic zone in reach / (m2, calculated from stream segment length
and width), T^,/ is the temperature of the bottom sediment (°C, calculated), TU is the
temperature of the water (°C, calculated), andpCp is the density of the sediment (g/cm3)
times the specific heat of the sediment (cal/g-°C). The model estimates the product pCp as
Ks/as, where KS is the thermal conductivity (cal/s-cm-°C) and as is the thermal diffusivity
(cm2/s), both of which are input by the user based on the bed material. The overall heat
balance for the bottom sediment is then calculated as
                                       dt      PsCpsH2l

where H2j is the effective thickness of the sediment layer (cm, input by user).

The user inputs to QUAL2Kw that control the effect of hyporheic exchange on water
temperature are the thermal conductivity, thermal diffusivity, the effective thickness of
the sediment layer, and the bulk hyporheic exchange flow. The QUAL2Kw theory
manual recommends: "If hyporheic flow exchange is significant, then the effective
thickness of the hyporheic zone of rapid transient storage may typically range from about
20 to 300% of the stream depth (Harvey and Wagner, 2000; Gooseff et al, 2003), with
higher relative values in smaller streams." The exact value of effective thickness will not
be known for the South Fork Nooksack, although it can be partially constrained through
calibration of the TMDL model, but will be held constant for current condition and future
climate runs. The primary uncertainty for addressing climate impacts through hyporheic
flow in the QUAL2Kw model is that the bulk hyporheic exchange flow is a user-
specified input. The fraction of hyporheic flow adopted for the TMDL model will not be
altered for the future climate model runs, resulting in specification of a linear change in
hyporheic flow as total flow in the reach changes. Therefore, no additional changes to
boundary conditions will be needed to evaluate how the effects hyporheic exchange
might change under future climates.

Subtask 2.5 Schedule - Dec. 2012 - Dec. 2012
Milestone 2.5 Title: Memorandum Documenting Additional Boundary Condition
Assumptions for QUAL2Kw Model Applications to Future Climate Scenarios
Milestone 2.5 Completion Date: Dec. 2012

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
20
Subtask 2.6: Quantitative Assessment Report
Subtask 2.6 Description: At the conclusion of Subtask 2.5 a complete set of model
boundary conditions for future climate scenarios will be supplied to the Regulatory
Project Team. The quantitative assessment is the comparison of QUAL2Kw modeled
stream temperatures, including riparian shading, with and without Climate Change for the
2020s, 2040s, and 2080s.

It is assumed that Regulatory Project Team will run and analyze the future climate
scenarios using QUAL2Kw and provide the results back to the Pilot Research Project
Team. Under this subtask, a summary report on Task 2 will be prepared by the Research
Project Team.

Subtask 2.6 Schedule - Apr 2013 - June 2013
Milestone 2.6: Technical Memorandum on Quantitative Assessment of Temperature
Sensitivity of SFNR under Future Climate using QUAL2Kw
Mileston 2.6 Completion Date: June 2013
               Table 1. Quantitative assessment milestone schedule
Quantitative Assessment Milestone Schedule
Quantitative Assessment Subtask
Subtask 2.1. Selection of Climate Scenarios
Subtask 2.2 Tributary and Mainstem Flow
Boundary Conditions
Subtask 2. 3 Tributary and Mainstem Boundary
Water Temperatures
Subtask 2.4 Meteorological Forcing
Subtask 2.5 Other Boundary Conditions
Subtask 2.6 Quantitative Assessment Report
2012
Oct.






Nov.






Dec.
—




2013
Jan.






Feb.






March






April






May






June






July






Aug.






Task 3 - Qualitative Assessment

Background and Problem
The workshop that was held in EPA Region 10 on June 25, 2012, made clear the benefits
of separating the climate change risk assessment (see Figure 5) into two assessments
processes—one  quantitative and one qualitative.

The quantitative assessment is directly responsive to the CWA TMDL Numeric Cold-
Water Temperature WQS. The quantitative assessment is the comparison of QUAL2Kw
modeled stream temperatures, including riparian shading, with and without climate
change for the 2020s, 2040s and 2080s.

The qualitative assessment is a comprehensive analysis of freshwater habitat for ESA
salmon restoration in the SFNR under climate change. The output of this assessment is a
prioritized list of climate change adaptation strategies (stream restoration actions/TMDL
implementation) that supports salmon restoration in the SFNR under climate change.
Although quantitative methods are used in this assessment, there is no attempt to directly

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              21


attribute the quantitative contribution of these stream restoration actions on meeting the
CWA TMDL Numeric Cold-Water Temperature WQS.

Taken together, the quantitative and qualitative assessments represents the most robust
and comprehensive actions to protect the CWA designated uses (salmon habitat) and
ESA recovery goals under climate change.

Approach  and Methods
The foundational approach and method of this assessment is based on Restoring Salmon
Habitat For A Changing Climate (Beechie et al. 2012). In that paper, Beechie et al.
(Table III) grouped restoration actions on the basis of the watershed processes or
functions they attempt to restore and then classified them as either likely or not likely to
ameliorate a climate change effect on high stream flows, low stream flows, and stream
temperatures.

The risks of climate change will be evaluated for all three ESA listed (threatened) species
in the SFRN: 1 ) spring chinook (Oncorhynchus tshawytscha), 2) summer steelhead
(Oncorhynchus mykiss), and 3) bull trout (Salvelinus confluentus}. The Beechie  method
(Beechie et al. 2012) requires  a specific assessment of climate change risks for each fish
species/life history and the effectiveness of stream restoration actions to ameliorate those
risks.

In order to accomplish the output of the qualitative assessment, a prioritized list of
climate  change adaptation strategies (stream restoration actions/TMDL implementation)
that supports salmon restoration in the SFNR under climate change, integration of the
temporal,  spatial and limiting  factors requirements of all three ESA listed (threatened)
species is  needed. The lack of a specific ESA Recovery Plan for summer steelhead in the
SFNR will limit the testing of specific planned stream restoration actions to ameliorate
the risks of climate change. However, many  of the stream restoration actions in the ESA
Salmonid Recovery Plan for spring chinook  and bull trout will benefit summer steelhead
and a more general assessment of the risk and vulnerability of climate change to summer
steelhead in the SFNR is still possible.

The current restoration actions listed in the ESA Salmonid  Recovery Plan for the SFNR
will be evaluated and prioritized to optimize those actions that are most effective in their
ability to ameliorate a climate change effect  on high stream flows, low stream flows, and
stream temperatures.

Coldwater refuges will be identified and protection/restoration actions evaluated for their
potential to increase the effective use of thermal refugia by coldwater fish under climate
change (USEPA2012b).

The knowledge and experience of environmental practitioners, natural resource managers
and tribal  members in SFNS Washington will be used to the maximum extent possible.
Existing ESA salmonid recovery plans, data sets  and assessments by the Nooksack Indian
Tribe, Lummi Nation and other federal, state, local and nongovernmental organizations
on the SFNR will form the basis of this assessment.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
   22
Watershed process-based restoration has a long history of use and application in the
Puget Sound Basin. This body of evidence, methods and approaches will be incorporated
and used in this assessment (Montgomery et al. 2003; Pollock et al. 2009; Beechie et al.
2010).

We intend to collaborate and incorporate the findings from the USGS
Goundwater/Surface Water Study of the SFNR (in progress and commissioned by the
Nooksack Indian Tribe).
     Communication:
    Risk Assessor and
      Risk Manager
       (Planning)


Climate Change Ecological Risk Assessment
Problem Formulation






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                                    and Risk Manager (Results)

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                                    Climate Change Adaptation
                                       (Risk Management)

Note: Modified from USEPA 1992
                Figure 5. Climate change ecological risk assessment
Subtask Descriptions, Schedule and Milestones

Subtask 3.1 Title: Stakeholder Engagement and Project Scoping—Two-Day Meeting
Hosted by the Nooksack Indian Tribe—Restoring Salmon Habitat for a Changing
Climate in the South Fork Nooksack River,  Washington
Subtask 3.1 Description: The purpose of this  meeting is to (1) solicit input from
stakeholders on climate change and ESA salmon recovery, (2) review existing ESA
recovery plans, data sets and related studies, (3) discuss draft outline approach/method
for evaluating the  risk/vulnerability of climate change on ESA salmon recovery actions,

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              23
and (4) gain a better understanding of the setting (biophysical) and current/past
restoration of freshwater habitat on the SFNR.

The first day is devoted to a series of presentations and panel discussions to understand
how landscape watershed processes and climate change will impact ESA Salmonid
Recovery Planning.

The second day is focused on a review of the existing ESA Salmonid Recovery Plan, data
sets and related studies to support the development of the step-by-step methodology for
the qualitative assessment in the SFNR.

Subtask 3.1 Schedule
Start Date: 1/22/13
End Date:  1/23/13
Milestone 3.1 Title:  Stakeholder Engagement and Project Scoping Meeting Report
Milestone 3.1 Completion Date: 1/31/13

Subtask 3.2 Title: Develop a Method for Evaluating the Risk/Vulnerability of Climate
Change on ESA Salmon Recovery Actions
Subtask 3.2 Description: This is the step-by-step methodology based on Restoring
Salmon Habitat For A Changing Climate, Beechie et al. 2012.

Subtask 3.2 Schedule
Start Date: 2/01/13
End Date:  4/30/13
Milestone 3.2 Title: Report; Methods for evaluating the Risk/Vulnerability of Climate
Change on ESA Salmon Recovery Actions
Milestone 3.2 Completion Date: 4/30/13

Subtask 3.3 Title: Conducting the Qualitative Assessment of Risk/Vulnerability of
Climate Change on ESA Salmon Recovery Actions
Subtask 3.3 Description: This subtask accomplishes the qualitative assessment and
provides the prioritized list of climate change adaption  strategies (stream restoration
actions/TMDL implementation) to support ESA salmon restoration in the SFNR  under
climate change.

Subtask 3.3 Schedule
Start Date: 5/01/13
End Date:  10/31/13
Milestone 3.3 Title: Draft Report; Risk/Vulnerability of Climate Change on ESA Salmon
Recovery Actions in the SFNR.
Milestone 3.3 Completion Date: 10/31/13

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
24
Subtask 3.4 Title: Stakeholder Engagement; Communication between Risk Assessors
& Risk Managers—One-Day Meeting Hosted by the Nooksack Indian Tribe—
Restoring Salmon Habitat for a Changing Climate in the South Fork Nooksack River,
Washington
Subtask 3.4 Description: The results of the draft report; qualitative assessment of
risk/vulnerability of climate change on ESA salmon recovery actions will be presented
and discussed. The goal of this meeting is to gain consensus among the Risk Managers on
the prioritized list of climate change adaption strategies (stream restoration
actions/TMDL implementation) to support ESA salmon recovery in the SFNR under
climate change.

Subtask 3.4 Schedule
Start Date: 11/15/13
End Date: 11/15/13

Subtask 3.5 Title: Develop Final Report; Risk/Vulnerability of Climate Change on
ESA Salmon Recovery Actions in the South Fork Nooksack River, Washington, based
on Stakeholder Engagement.
Subtask 3.5 Description: Develop final report; risk/vulnerability of climate change on
ESA salmon recovery actions in the SFNR based on stakeholder engagement.

Subtask 3.5 Schedule:
Start Date: 11/16/13
End Date: 2/15/14
Milestone 3.5 Title: Final Report; Risk/Vulnerability of Climate Change on ESA Salmon
Recovery Actions in the SFNR
Milestone 3.5 Completion Date: 2/15/14
               Table 2. Qualitative assessment milestone schedule
Qualitative Assessment Milestone Schedule
Qualitative Assessment Subtask
Su bias k 3.1 Stakeholder Engagement for Project
Scoping
Subtask 3. 2 Climate Change MethodologyforESA
Salmon Recovery Actions
Subtask 3. 3 Conducting the Qualitative Assessment
Subtask 3. 4 Stakeholder Engagement for Risk
Assessment
Subtask 3. 5 Develop Final Report
2013
Jan.
-



Feb.





March





April





May





June





July





Aug





Sept.





Oct.





Nov.





2014
Jan.





Feb.





March





Task 4 - Climate Change Considerations for TMDL Development
in the SFNR
Background and Problem
While more than 40,000 TMDLs have been developed in the United States, very few of
these analyses have considered the potential implications that climate change could have

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
                                                                               25
on the key parameters influencing water quality, such as flow and water temperature. The
potential impact of climate change on water resources has been widely acknowledged in
the scientific community; however, the various layers of uncertainty that surround
climate change has created confusion among water resource managers and made
evaluation of climate change impacts and adaptation options difficult. The importance of
using an adaptive management framework, where additional data and findings are able to
be incorporated in an evolving context, is an important management tool when dealing
with climate change (refer to Figure 6).
                                                          Define the Problem
                                                          Determine Objectives
Recognizing these challenges, EPA identified
climate change as a top priority in its FY 2011-
2015 Strategic Plan (USEPA 2010) and has
included Strategic Action 35 in EPA's Draft
National Water Program Guidance, which,
"encourage[s] that development of future
TMDLs include evaluation of projected climate
impacts and uncertainty and incorporate this
information into the TMDL, as appropriate"
(USEPA 2012a).

As a supportive action, EPA Region 10 has
identified the SFNR Temperature TMDL as a
pilot by which to explore the potential linkages
between the TMDL process and climate change
considerations.

Approach and Methods
The EPA Region 10 climate change and TMDL pilot research concept was developed on
the basis of a unique parallel study strategy. The strategy uses a real-world regulatory
action, the SFNR temperature TMDL, as a pilot by which to evaluate various
methodologies and approaches to incorporate climate change considerations. It is
intended that the synchronized pairing of the research project with an on-the-ground
temperature TMDL will assist the project team in better understanding the needs of water
managers, including consideration of schedule and budgetary constraints, along with
typical approaches used by water managers to meet the TMDL regulatory requirements.

Task 4 is specifically designed to leverage this parallel study strategy. In this task, the
EPA TMDL regulatory requirements will be examined to identify potential areas where
climate change could be considered for inclusion in the SFNR temperature TMDL. A
systematic methodology will be proposed and used to evaluate climate change
considerations to identify those that could be incorporated in the SFNR temperature
TMDL, as illustrated in Figure 7, within the constraints of the uncertainty of climate
change impacts, schedule, budget, and need for additional input.
                                                Figure 6. Adaptive Management
                                                          Framework

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
                                                              26
   tl A  How do we incorporate
   W ^ systems thinking in the
   Climate Change TMDL Pilot?
           What are the components
           of a Climate Change
   Vulnerability/Risk Assessment?
           What are the Climate Change
           Considerations to include in
   the Development of a TMDL?
           What are the methods
           and technical approaches
   for including Climate Change
   Considerations in the development of a
   Temperature TMDL in the SFNR?
          Use a
 start-to-finish Process Model;
   TMDL Process Roadmap
        (Figure 1)
         Adopt
      a best practice
  method for Climate Change
Vulnerability/Risk Assessment;
 Climate Change Assessment
     Process (Figure2)
    EPA TMDL Guidance
     cross-walked with
Climate Change Considerations
          SFNR
 Climate Change TMDL Pilot;
  Quantitative (Task 2) and
    qualitative (Task 3)
       Assessments
   What additional Input would
    be useful for Improving the
Incorporation of climate science into
          TMDLs?
                                                                                       I
                                                                               Define the Problem
                                                                              Determine Objectives
                                                          Regions
                                                          States•
                                                             Tribes
                                                                  Water
                                                               Managers
  Figure 7. Illustrative decision-tree for evaluating climate change considerations in
                                          the SFNR TMDL.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              27


The following elements of a TMDL submittal will be used as an organizing research
framework (see USEPA 2002).8
    1.  Identification of Waterbody, Pollutant of Concern, Pollutant Sources, and Priority
       Ranking
    2.  Description of the Applicable WQS and Numeric Water Quality Target
    3.  Loading Capacity—Linking Water Quality and Pollutant Sources
    4.  Load Allocations (LAs)
    5.  Wasteload Allocations (WLAs)
    6.  Margin of Safety (MOS)
    7.  Seasonal Variation
    8.  Reasonable Assurances
    9.  Monitoring Plan to Track TMDL Effectiveness
    10. Implementation
    11. Public Participation

Subtask 4.1 Title: Broad Review of TMDL and Climate Change Issues

Subtask 4.1 Description: Conduct a broad review of issues involved in incorporating
climate change into TMDLs. This includes the following steps: 1) review EPA regulatory
guidance and technical direction, using the TMDL elements as an organizing framework;
2) identify and review TMDLs that incorporate climate change issues to identify any
lessons learned and best practices;  and 3) identify the state of the practice for
incorporating climate change science in TMDLs.

Subtask 4.1  Schedule:
Start Date: Oct. 1,2012
End Date: Dec. 30,2012
Milestone 4.1 Title: Issues for TMDL and Assessment Report
Milestone 4.1 Completion Date: Dec.  30, 2012

Subtask 4.2 Title: Assessment of SFNR TMDL

Subtask 4.2 Description: Best practices and lessons learned from Task 4.1 will be
evaluated with respect to the SFNR TMDL and climate science issues and potential
research approaches will be identified. The process roadmap will be used to organize  the
research, which will be considered in the following order:

    •   Problem Understanding and TMDL Target/Source Assessment (Dec. 1, 2012-Jan.
       31,2013)

    •   Loading Capacity and Allocation Analysis (Feb. 1, 2013-April. 30, 2013)
8 The Process Roadmap described in Task 1 of this Research Plan includes EPA's eleven critical elements
and will also be used to conceptually guide the research process.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
28
   •   Wasteload Allocation Issues (Feb. 1, 2013-April. 30, 2013)
   •   Margin of Safety Issues (Feb. 1, 2013-April. 30, 2013)

Subtask 4.2 Schedule:
Start Date: Dec. 1,2012
End Date: April. 30, 2013
Milestone 4.2 Title: SFNR TMDL Climate Change Assessment: Recommendations and
Areas for Additional Study
Milestone 4.2 Completion Date: April. 30, 2013

Subtask 4.3 Title: Implementation and Monitoring Plan Assessment

Subtask 4.3 Description: Document and analyze potential approaches that could inform
incorporation of updated downscaled climate change scenario information into
implementation and monitoring plans.

Identify issues and research areas considered outside the scope of the SFNR TMDL, and
recommend approaches.

Subtask 4.3 Schedule:
Start Date: May. 1,2013
End Date: June 3 0,2013
Milestone 4.3 Title: 4.2 Implementation and Monitoring Plan Assessment Report
Milestone 4.3 Completion: Date: June 30, 2013

Subtask 4.4 Title: Final Report

Subtask 4.4 Description: Draft and complete SFNR Temperature TMDL Climate
Change Assessment Report - Final Report.

Subtask 4.5 Schedule:
Start Date: July. 1,2013
End Date: Aug. 31,2013
Milestone 4.5 Title: SFNR Temperature TMDL Climate Change Assessment Report -
Final Report
Milestone 4.5 Completion: Date: Aug 31, 2013
    Table 3. Climate change considerations for TMDL development in the SFNR
                               milestone schedule
Evaluation of SFNR TMDL Climate Change Considerations Milestone Schedule

Program Assessment Subtask
Subtask 4.1 Broad Review of Programmatic Issues
Subtask 4.2 Assessment of SFNR TMDL
Subtask 4.3 Implementation and Monitoring Plan
Analysis
Subtask 4.4 Final Report
2012
Oct.




Nov.




Dec.




2013
Jan.




Feb.




March




April




May




June




July




Aug.





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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              29


Task 5 - EPA Final Report

Background and Problem
The EPA Region 10 climate change TMDL pilot is a complex project with both research
and development and demonstration components. The project has been divided into tasks
to facilitate the operational implementation of the research. Ultimately, we will have to
integrate and synthesize the results from the task reports into a coherent EPA final report.

The output of this task is the EPA final report, which documents the process and analysis
used to develop the climate change temperature TMDL for the SFNR.

Approach and Methods
The task reports are the building blocks for the EPA final report. The EPA final report
will be written by the task leads with the assistance of a technical writer and editor. The
EPA final report will be peer reviewed and cleared by EPA's ORD in conformance with
ORD's Policies and Procedures Manual (USEPA 2009).

Subtask Descriptions, Schedule and Milestones

Subtask 5.1 Title: Develop the Draft Outline for the EPA Final Report
Subtask 5.1 Description:  A draft outline will be developed for the EPA final report.
Figures and tables from the task reports will be assembled as an electronic library to
facilitate their use in the EPA final report. EndNote reference libraries from the task
reports will be consolidated in a master reference library to facilitate its use in the EPA
final report.

Subtask 5.1 Schedule
Start Date: 8/15/13
End Date: 9/30/13
Milestone 5.1 Title: Draft Outline for the EPA Final Report with Figures/Tables and
Endnote Library.
Milestone 5.1 Completion Date: 9/30/13

Subtask 5.2 Title: Write the Draft EPA Final Report
Subtask 5.2 Description:  A draft of the EPA final report will be written by the task leads
with the assistance of a technical writer and editor.

Subtask 5.2 Schedule
Start Date: 10/01/13
End Date: 2/28/14
Milestone 5.2 Title: Draft EPA Final Report
Milestone 5.2 Completion Date: 2/28/14

Subtask 5.3 Title: Peer Review and Reconciliation of Draft EPA Final Report.
Subtask 5.3 Description:  A peer review and reconciliation will be conducted for the draft
EPA final report.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
30
Subtask 5.3 Schedule
Start Date: 3/01/14
End Date: 5/30/14
Milestone 5.3Title: Peer Reviewed and Reconciled Draft EPA Final Report.
Milestone 5.3 Completion Date: 5/30/14

Subtask 5.4 Title: EPA Final Report Review and Clearance
Subtask 5.4 Description: The EPA final report will be reviewed and cleared through
ORD.

Subtask 5.4 Schedule
Start Date: 6/01/14
End Date: 7/31/14
Milestone 5.4 Title: EPA Final Report.
Milestone 5.4 Completion Date: 7/31/14
                  Table 4. EPA final report milestone schedule
EPA Final Report Milestone Schedule
EPA Final Report Subtask
Subtask 5.1 Draft Outline
Subtask 5.2 Draft Report
Subtask 5.3 Peer Review and
Reconciliation
Subtask 5.4 ORD Review and
Clearance
2013
Aug.




Sept.




Oct.




Nov.




Dec.




2014
Jan.




Feb.




March




April




May




June




July




RELEVANCY TO EPA DECISION MAKING
The primary objective of this project is to demonstrate a process to evaluate EPA's
decision-making needs for climate change adaptation under the CWA section 303(d)
TMDL program.

This project supports the implementation of EPA's National Water Program 2012
Strategy: Response to Climate Change - March 2012 to help achieve EPA's Vision
Statement on Water Quality by promoting the management of sustainable surface water
resources under changing climate conditions (USEPA 2012a).

This project also provides the opportunity to explore the potential linkages between the
TMDL process and climate change considerations.

The risk assessment approach used in this project provides decision makers with a robust
context and temporal sensitivity for including climate change adaption in their decision
making. A Climate Change TMDL can be thought of as an embedded climate change risk
assessment within a CWA section 303(d) TMDL.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              31
EPA's final report that documents the process and analysis used in this pilot
demonstration (climate change temperature TMDL for the SFNR) will assist other EPA
regions and states to include climate change adaption in their CWA 303(d) temperature
TMDL programs.
SCHEDULE AND OUTCOMES
The pilot research project consists of three primary project phases: Phase 1 Research
Plan, March-September 2012; Phase 2 Research Analysis and Risk/Vulnerability
Assessment, October 2012-September 2013; and Phase 3 EPA Report, October 2013-
September2014.

Tasks 1 -4 as outlined in this research plan are associated with Phase 2, and Task 5 is
associated with Phase 3. The schedule for each of the phases, tasks, and subtasks of the
Research Pilot Project are illustrated in Figure 8.

Each of the project tasks result in interim deliverables. The EPA final report will
integrate and synthesize the results from the task reports into a coherent EPA final report,
which will serve as the final project outcome.

Figure 9 highlights the inter-relationships between the pilot research project and the
regulatory project.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
32
ID

1


4
5
6
7
8


11
12

14


17

19
20

22

24
25

Taik Hame

Phase 1: Research Plan
Phase 2: Research Analysis and
Risk/Vulnerability Assessment

Subtask 1 Selection of Climate Scenarios
Subtask 2 Tributary and Mainstem Flow
Boundary Conditions
Subtask 3 Tributary and Mainstem
Boundary Water Temperatures
Subtask 4 Meteorological Forcing
Sublask 5 Other Boundary Conditions
Subtask 6 Quantitative Assessment Report

Subtask 1 Stakeholder Engagement for
Project Scoping
Subtask 2 Climate Change Methodology
for ESA Salmon Recovery Actions
Assessment
Subtask 4 Stakeholder Engagement for
Risk Assessment
Subtask 5 Develop Final Report
Considerations
Subtask 1 Broad Review of TMDL and
Climate Change Issues

Subtask 3 Implementation and Monitoring
Plan Assessment
Subtask 4 Final Report
Phase 3: EPA Final Report
Subtask 1 Draft Outline

Subtask 3 Peer Review and Reconciliation
Subtask 4 ORD Review and Clearance

2012
Jan Mar Mav Jul Seo Nov



^^^^^^^^
'

1 '



















2013 2014
Jan Mar Mav Jul Sec Nov Jan Mar Mav 1










*


•




^^^^^^™
j» Deliverable



^^^^^^^^^^^™
^^^^™


•1 | Ssp | Nov


























                       Figure 8. EPA Region 10 climate change TMDL pilot schedule and deliverables

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EPA Region 10 Climate Change and TMDL Pilot Research Plan
                                                                                                  33
                           EPA Region 10 Climate Change TMDL Pilot and Temperature TMDL - Parallel Study Strategy
                              Research Plan
                                                                                         Research Analysis and Risk/Vulnerability Assessment
    I
ja
O

|
a
          Project
          Kick-off
                                                                 Evaluation of SFNR TMDL Climate Change Considerations
                                                                 Quantitative Assessment
                                                                Develop boundary conditions for future
                                                                      climate scenarios
                                                                 Qualitative Assessment
                                                                Develop risk/vulnerability r
                                                            Meeting
                                                            hosted by
                                                          Nooksaik Indian
                                                             Tribe
  Meeting
  hosted by
Nooksack Indian
   Tribe
                                                 August   Septemb
   Meeting
'  hosted by
 Nooksack Indian
    Tribe
                                                                                                                                          August  September
               Figure 9. EPA Region 10 climate change TMDL pilot and temperature TMDL—parallel study strategy

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              34
MANAGEMENT PLAN AND QUALITY ASSURANCE

Management Plan
The management plan for this project is based on tiered and interactive decision making
and responsibility between the project team (project leader, task leaders and
collaborators). This project is structured as a stakeholder-centric process and as such the
stakeholders have an ongoing role. Within the current ORD research structure of National
Programs, the project leader described here would be the Task Leader for ORD Air
Climate and Energy (ACE) Task 204. The task leaders described here would be
cooperating scientists from EPA ORD or EPA Region 10.

The project leader is responsible for the overall planning, management, and
accountability of the project.

The task leaders are responsible for the planning, management and accountability of their
respective task.

Collaborators (scientists and environmental practitioners) are responsible for guiding and
participating in the technical planning, execution, and documentation of this project.

Stakeholders (decision makers, policy makers, tribal members and concerned citizens)
are responsible for making their issues, concerns and needs known to the project team
and actively participating in this project.

Quality Assurance
In conformance with ORD's Policies and Procedures Manual, Chapter 13 - Quality
Assurance (Draft June 12, 2012), this Project Research Plan is classified as QA Category
2 and the EPA Final Report will be reviewed and published as an Influential Scientific
Information (ISI) document.

The overall quality assurance of this project will be guided by a Quality Assurance
Project Plan (QAPP). ORD will complete this QAPP by April 30, 2013.

The plan will briefly describe the overall project (referencing this Project Plan for
details), and consist primarily of a description of quality assurance activities relating to
Tasks 3 - Qualitative Assessment and Task 4 - Climate Change Considerations for
TMDL Development in the SFNR. Task 3 is the comprehensive assessment of freshwater
habitat for ESA salmon recovery in the SFNR under climate change. Task 4 will examine
EPA TMDL regulatory requirements to identify potential areas where climate change
could be considered for inclusion in the SFNR temperature TMDL, and will develop a
systematic methodology by which to evaluate climate change considerations to identify
those that could be incorporated in the SFNR temperature TMDL.

Quality Assurance for Task 2 - Quantitative Assessment, is addressed in a separate
QAPP completed by Ecology, EPA Region 10 and Tetra Tech (a contractor to EPA
Region 10) ((Kennedy and Butcher 2012)).  The quantitative assessment is the

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                               35
comparison of QUAL2Kw modeled stream temperatures, including riparian shading,
with and without climate change for the 2020s, 2040s, and 2080s. An addendum to the
SFNR Regulatory QAPP will be developed to address quality considerations for the
regression relationships described in subtask 2.3.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                             36
LITERATURE CITED
Bates, B.C., Z.W. Kundzewicz, S. Wu and J.P. Palutikof, eds. 2008. Climate Change and
       Water. Technical Paper of the Intergovernmental Panel on Climate Change,
       Geneva, Switzerland.

Beechie, T.J., D.A. Sear, J.D. Olden, G.R. Pess, J.M. Buffington, H. Moir, P. Roni, and
       M.M. Pollock. 2010. Process-based Principles for Restoring River Ecosystems.
       BioScience 60:209-222.

Beechie, T., H. Imaki, J. Greene, A. Wade, H. Wu, G Pess, P. Roni, J. Kimball,
       J.  Stanford, P. Kiffney, and N. Mantua. 2012. Restoring salmon habitat for a
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Brekke, L.D., I.E. Kiang, J.R Olsen, RS. Pulwarty, D.A. Raff, D.P. Turmpseed, RS.
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CBPO  (Chesapeake Bay Program Office). 2010. Chesapeake Bay Executive Order
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       Chesapeake-Launches-Major-Initiatives-and-Holds-Government-Accountable-
       for-Progress.aspx.

Chapra, S.C., and GJ. Pelletier. 2003. QUAL2K: A Modeling Framework for Simulating
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Cristea, Nicoleta, and Stephen Burges. 2010. An assessment of the current and future
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Ecology (Washington Department of Ecology). 2011. Snoqualmie TMDL.
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Ecology (Washington Department of Ecology). 2003a. Shade.xls -A Tool for Estimating
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       Olympia, WA. www.ecv.wa.gov/programs/eap/models.html

Ecology (Washington Department of Ecology). 2003b. QUAL2Kw.xls - A Diurnal Model
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Ecology (Washington Department of Ecology). 2012. Draft South Fork Nooksack River
       Temperature TMDL, Water Quality Study Design (Quality Assurance Project
       Plan). Washington Department of Ecology, Olympia, WA.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                              37
Eisner, M.M., L. Cuo, N. Voisin, J.S. Deems, A.F. Hamlet, J. Vano, K.E.B. Mickelson,
       S.Y. Lee, andD.P. Lettenmaier. 2010. Implications of 21st Century Climate
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Glick, P., B.A. Stein, and N.A. Edelson, eds. 2011. Scanning the Conservation Horizon,
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Gooseff, MN, SM Wondzell, R Haggerty, and J Anderson. 2003. Comparing transient
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Hamlet, A.F., P. Carrasco, J. Deems, M.M. Eisner, T. Kamstra, C. Lee, S.-Y. Lee, G.S.
       Mauger, E. P. Salathe, I. Tohver,  and L.W. Binder. 2010. Final Report for the
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Harvey JW, and BJ Wagner. 2000. Quantifying hydrologic interactions between streams
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Johnson, T.E., J.B. Butcher, A. Parker, and C.P. Weaver. 2011 (in press). Investigating
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Karl, T.R, Melillo, J.M. and T.C. Peterson, eds. 2009. Global Climate Change Impacts
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Kehrl, B. 2010. Cape Cod Nitrogen Law suits May Set Precedents, But Consequences Are
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Kennedy, J.T. and J. Butcher. 2012. South Fork Nooksack River Temperature Total
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Mauger, G.S., and N. Mantua. 2011. Climate Change Projections for USFS Lands in
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Montgomery, D.R, S. Bolton, D.B. Booth, and L. Wall. 2003. Restoration ofPuget
       Sound Rivers. University  of Washington Press, Seattle, WA.

Pollock, M. M., T. J. Beechie, M. Liermann, andR. E. Bigley. 2009. Stream Temperature
       Relationships To Forest Harvest In Western Washington. JAWRA 45:141-156.

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EPA Region 10 Climate Change and TMDL Pilot Research Plan                             38
Polebitski, A., L. Traynham, andR.N. Palmer. 2007a. Technical Memorandum #4:
      Approach for Developing Climate Impacted Meteorological Data and its Quality
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Polebitski, A., L. Traynham, andR.N. Palmer. 2007b. Technical Memorandum #5:
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      Assessment, EPA/630/R-92/0001, February 1992.

USEPA (Environmental Protection Agency).  2002. Guidelines for Reviewing TMDLs
      under Existing Regulations issued in 1992.
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USEPA (Environmental Protection Agency) Office of Research and Development. 2009.
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USEPA (Environmental Protection Agency).  2010. FY 2011-2015 Strategic Plan:
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USEPA (Environmental Protection Agency),  RegionlO. 2012b. Primer for Identifying
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Yohe, Gary. 2011. Incorporating (Iterative) Risk Management into the National Climate
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