CHaMP protocol - Pacific Northwest Aquatic Monitoring Partnership

127 Pages·2011·2.99 MB·English

Scientific Protocol for Salmonid Habitat Surveys
within the
Columbia Habitat Monitoring Program

2011 Working Version 1.0

January 25, 2011

Prepared and funded by the
Bonneville Power Administration’s
Integrated Status and Effectiveness Monitoring Program

for
Bonneville Power Administration’s Columbia Habitat Monitoring Program
2011 Working Version Salmonid Habitat Protocol for CHaMP
This document was funded by Bonneville Power Administration‘s Integrated Status and
Effectiveness Monitoring Program (ISEMP; Project # 2003-017) for use with BPA‘s Columbia
Habitat Monitoring Program (CHaMP; Project #2011-006).

This document should be cited as:

Bouwes, N., J. Moberg, N. Weber, B. Bouwes, S. Bennett, C. Beasley, C.E. Jordan, P. Nelle, M.
Polino, S. Rentmeester, B. Semmens, C. Volk, M.B. Ward, and J. White. 2011.
Scientific protocol for salmonid habitat surveys within the Columbia Habitat Monitoring
Program. Prepared by the Integrated Status and Effectiveness Monitoring Program and
published by Terraqua, Inc., Wauconda, WA. 118 pages.

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TABLE OF CONTENTS
TABLE OF CONTENTS ............................................................................................... III
LIST OF FIGURES ........................................................................................................ VI
LIST OF TABLES ....................................................................................................... VIII
SECTION 1: INTRODUCTION .....................................................................................1
1.1 The Genesis of CHaMP .......................................................................................1
1.2 CHaMP‘s Objective .............................................................................................3
1.3 Protocol Development Process ............................................................................3
1.4 Summary of the Habitat Survey Protocol ............................................................4
1.4.1 Channel units and topographic survey ..................................................4
1.4.2 Channel unit and site level attributes ....................................................7
1.5 Habitat Metrics and Indicators .............................................................................7
1.6 Inference Design ................................................................................................12
1.7 Potential Site Analyses and Indicator Development ..........................................13
1.7.1 Potential Applications .........................................................................14
1.7.2 The River Bathymetry Toolkit ............................................................16
SECTION 2: THEORETICAL BASIS FOR CHAMP ...............................................18
2.1 Physical Processes .............................................................................................19
2.2 Fish Habitat Requirements.................................................................................21
2.3 Juvenile Growth .................................................................................................22
2.4 Juvenile Survival................................................................................................23
2.5 Adult/Spawner Survival .....................................................................................23
2.6 Egg/Alevin Survival ..........................................................................................24
2.7 Scale and Landscape Setting..............................................................................25
2.8 Synthesis of Sampling Protocols .......................................................................28
2.9 Summary of Findings by Stream Habitat Category ...........................................29
2.10 Details on the Alternatives: Continuous Methods & GIS................................40
SECTION 3: SAMPLING DESIGN AND SITE SELECTION .................................43
3.1 Site Allocation ...................................................................................................44
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3.1.1 Spatial Design .....................................................................................44
3.2 Site Evaluation ...................................................................................................44
SECTION 4: SURVEY WORKFLOW ........................................................................46
SECTION 5: SITE LAYOUT ........................................................................................47
5.1 Locating the Site ................................................................................................47
5.2 Site Layout .........................................................................................................47
5.3 Channel Type .....................................................................................................51
SECTION 6: CHANNEL UNITS ..................................................................................53
6.1 Identify Channel Units .......................................................................................53
SECTION 7: CHANNEL TOPOGRAPHIC SURVEY ..............................................56
7.1 Setting up a Survey ............................................................................................56
7.2 Point Collection Methods ..................................................................................57
SECTION 8: CHANNEL UNIT LEVEL ATTRIBUTES ...........................................64
8.1 Channel Segment Number .................................................................................64
8.2 Fish Cover Elements ..........................................................................................65
8.3 Ocular Channel Unit Substrate Composition.....................................................65
8.4 Particle Size Distribution and Particle Embeddedness ......................................66
8.5 Large Woody Debris ..........................................................................................67
SECTION 9: SITE LEVEL ATTRIBUTES .................................................................69
9.1 Site Map .............................................................................................................69
9.2 Photos ...............................................................................................................70
9.3 Solar Input..........................................................................................................70
9.4 Riparian Structure ..............................................................................................71
9.5 Water Temperature ............................................................................................71
9.6 Stream Discharge ...............................................................................................74
9.7 Water Chemistry ................................................................................................76
9.8 Macroinvertebrate Drift .....................................................................................77
SECTION 10: DATA MANAGEMENT .......................................................................80
10.1 Pre-season documentation ...............................................................................81
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10.2 Field Data Capture and Field Quality Assurance ............................................82
10.3 Data Back Up and Submittal ...........................................................................83
10.4 Metric Generation and End of Season Quality Assurance Review .................83
SECTION 11: REFERENCES ......................................................................................84
SECTION 12: APPENDICES ........................................................................................94
Appendix A: Equipment Check List ........................................................................94
Appendix B: Revising the Protocol .........................................................................96
Protocol Revision History Log .....................................................................97
Appendix C: Fish Habitat Requirements Summary ................................................98
Appendix D: Monitoring Attribute Review ...........................................................102
Appendix E: Monitoring Design Review ..............................................................109
E.1 Spatial Designs ....................................................................................109
E.2 Response Design .................................................................................111
E.3 Inference Design ..................................................................................112
E.4 Overall Design Considerations ............................................................113
Appendix F: Glossary ............................................................................................115
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LIST OF FIGURES
Figure 1. (Top) Topographic survey of a 1 km long site in Bridge Creek. Red box is depicted in
1 B,C,D and blue box depicted in 2 A, B. (Bottom Left) A 0.25 m DEM and water
depths created with the topographic survey overlaid on an aerial photo taken from a
drone. (Bottom Middle) Aerial photos take from a blimp during base flow. (Bottom
Right) Aerial photos take from a drone survey during higher flows. ............................ 5
Figure 2. (Top Panel) Example of a TIN created using the CHaMP protocol overlaid on an aerial
photo taken from a drone. (Bottom Panel) Creation of the site planform and
delineation of channel units. .......................................................................................... 6
Figure 3. Predicted spatial variation in net rate energy intake, in a pool at two different flows
based on observed drift density (from Hayes et al. 2007). Also shown are the
centroids of foraging areas of trout (all≥0.5 m) observed over the flow range (open
circles). Centroids were equivalent to focal positions for the drift-feeding trout. ....... 15
Figure 4. Using a DEM of Difference (DoD) to quantifying spatial variations in change in
storage terms of a sediment budget. a) A DoD is created by subtracting the vertical
component of old DEM from the new DEM. b) DoD can be displayed to show where
erosion (shown in red) and deposition (shown in blue) occurred in the reach. c) A
distribution of changes (areas or volumes) can be depicted or summed to estimate a
gross reach sediment budget. ....................................................................................... 16
Figure 5. Example of cross-section analyses of a DEM that can be performed with the River
Bathymetry Toolkit. ..................................................................................................... 17
Figure 6. Example of longitudinal profile analyses of a DEM that can be performed with the
River Bathymetry Toolkit. ........................................................................................... 17
Figure 7. Examples of stream networks that can influence how sediment and water move from
headwaters to the outlet of a stream from Brierley and Fryirs (2005). ........................ 26
Figure 8. Location and function of reach types within a watershed and how they influence
sediment transport and storage (from Brierley and Fryirs 2005). ................................ 26
Figure 9. An example of the River Styles framework for prioritizing restoration actions and
implementing hierarchical monitoring programs from Brierley and Fryirs (2005). .... 27
Figure 10. The hierarchical channel unit classification used by CHaMP which is a modification
of the system developed by Hawkins et al. (1993) as reported in Bisson et al. (2006).
...................................................................................................................................... 33
Figure 11. The split panel design to be used by CHaMP in watersheds where status and trend
evaluations need to be balanced. .................................................................................. 44
Figure 12. Example of coding points to describe the perimeters of channel units and bars
showing which points require multiple codes. ............................................................. 58
Figure 13. Longitudinal view of the stream channel showing placement of thalweg survey points
that effectively capture the thalweg profile. ................................................................. 59
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Figure 14. Effective use of TOPO points in relation to other required topographic survey points
along a stream cross-section......................................................................................... 60
Figure 15. Example of streambank surfaces rendered a) without, and b) with breaklines surveyed
at the TOB and TOE of the bank. ................................................................................ 60
Figure 16. Cross-sectional view of a stream channel demonstrating the appropriate placement of
BF, TOB, and TOE breaklines. .................................................................................... 61
Figure 17. Example or a TOB breakline containing sufficient intermediate points to describe the
general shape of the bank feature. ................................................................................ 62
Figure 18. An example of a site map used to help characterize a site‘s unique and significant
features. ........................................................................................................................ 69
Figure 19. Cross-section of a streambed showing location of discharge measurements. ............ 74
Figure 20. View of active drift nets looking upstream. ............................................................... 78
Figure 21. Diagram showing the flow of data through the CHaMP data management plan. ...... 80
Figure 22. Relationship between fish consumption and total drift biomass in Bridge Creek. ... 105

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LIST OF TABLES
Table 1. The metrics and indicators used in the CHaMP protocol and the inference design
underlying each indicator. ............................................................................................. 9
Table 2. Metrics and indicators not included in the CHaMP protocol and the reasons why they
were omitted................................................................................................................ 12
Table 3. Critical stream habitat features and functions for salmonids at three different life stages.
..................................................................................................................................... 25
Table 4. Approaches used by Pacific Northwest salmonid monitoring programs to assess
channel unit-scale habitat. ........................................................................................... 30
Table 5. Comparison of channel unit classification schemes used by representative habitat
monitoring programs and those proposed by Hawkins et al. (1993). ......................... 33
Table 6. Types of indicators used to determine bankfull stage of a site (modified from Harrelson
et al. 1994). ................................................................................................................. 48
Table 7. Width category and site lengths according to the site average bankfull width determined
during site layout......................................................................................................... 49
Table 8. Montgomery and Buffington classification criteria. ...................................................... 52
Table 9. Criteria used to delineate Tier I channel units. .............................................................. 53
Table 10. Criteria used to delineate Tier II channel unit classification from Tier I fast-water
turbulent units. ............................................................................................................ 54
Table 11. Criteria used to delineate Tier II channel unit classification from Tier I slow-water
pool units. .................................................................................................................... 55
Table 12. Point description, point code, and code definition used in the topographic survey. ... 58
Table 13. Definitions of fish cover elements evaluated at each channel unit. ............................. 65
Table 14. Description of substrate composition types and size classes. ...................................... 65
Table 15. Size classes used to categorize large woody debris. .................................................... 68
Table 16. Timing of data management activities throughout the year. ....................................... 81
Table 17. Habitat attributes that directly and indirectly affects the growth of juvenile salmonids
in stream environments. .............................................................................................. 98
Table 18. Habitat attributes that directly and indirectly affects the mortality of juvenile
salmonids in stream environments. ............................................................................. 99
Table 19. Habitat attributes that directly and indirectly affects the survival to spawning for adult
salmonids in stream environments. ........................................................................... 100
Table 20. Habitat attributes that directly and indirectly affects salmonid egg to fry survival in
stream environments. ................................................................................................ 101
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Table 21. Ranges of precision and accuracy measures of various categories of stream habitat
attributes. ................................................................................................................... 102
Table 22. Summary of metric review for various attributes collected under fish habitat
monitoring protocols. ................................................................................................ 103
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SECTION 1: INTRODUCTION
This document is intended to explain the set of methods and associated metrics that will
be collected and analyzed by the Columbia Habitat Monitoring Program (CHaMP) to an
audience including salmon habitat scientists, data analysts, study designers, and monitoring
practitioners. The background and objectives of CHaMP and its habitat protocol are described in
Section 1. Section 2 describes the theoretical underpinning for this approach to salmonid habitat
monitoring and Section 3 summarizes the survey design and site allocation process. Sections 4
through 9 describe the data collection methods and metadata requirements in sufficient detail that
trained technicians can use this portion of the document as a field handbook. Section 10
describes how field data is processed into metrics that will be usable by natural resource
managers and decision makers. Finally, Section 11 and the several appendices provide
information that supports the protocol.
1.1 The Genesis of CHaMP
The 2008 Biological Opinion (BiOp) on the Federal Columbia River Power System
(FCRPS) identified offsite mitigation actions, largely in the form of habitat restoration, as a
means to offset mortality imposed by the FCRPS on anadromous salmonids. As such, the
Bonneville Power Administration (BPA) is working with the National Oceanic and Atmospheric
Administration (NOAA) and other regional fish management agencies to implement a tributary
habitat action effectiveness strategy across the Columbia River basin (FCRPS BiOp RPA 56.3)
which supports habitat restoration, rehabilitation, and conservation action performance
assessments and adaptive management requirements of the 2008 FCRPS BiOp. In 2010, BPA
began the development of CHaMP to meet FCRPS Action Agency (2010) programmatic
prescriptions for habitat monitoring.
CHaMP is designed as a Columbia River basin-wide habitat status and trends monitoring
program built around a single protocol with a programmatic approach to data collection and
management (RM&E Workgroup 2010). CHaMP will result in the collection and analysis of
systematic habitat status and trends information that will be used to assess basin-wide habitat
conditions. When coupled with biological response indicators, this status and trends information
will be used to evaluate habitat management strategies. This program will be integrated with
ongoing Pacific Northwest Aquatic Monitoring Program (PNAMP) recovery planning efforts
and will be part of the collaborative process across Columbia Basin fish management agencies
and tribes and other state and federal agencies that are monitoring anadromous salmonids and/or
their habitat. The implementation of CHaMP will characterize stream responses to watershed
restoration and/or management actions in at least one population within each steelhead and
spring Chinook Major Population Group (MPG) which have, or will have, ―fish-in‖ and ―fish-
out‖ monitoring (identified in RPA 50.6), thereby meeting the requirements of RPA 56.3, RPA
57, and RPA 3. CHaMP was designed to deliver trends in habitat indicators and requires that
monitoring occurs for three cycles of a sampling panel (see section 1.6), at least 9 years.
During the process of developing CHaMP, BPA has been advised by the Integrated
Status and Effectiveness Monitoring Program (ISEMP) which is a BPA-funded project
specifically tasked with assessing and developing standardized monitoring protocols for fish and
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