NOAA Technical Memorandum NMFS-NWFSC-97

Protocols for Monitoring

Habitat Restoration Projects

in the Lower Columbia River

and Estuary

February 2009

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
NOAA Technical Memorandum

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Reference throughout this document to trade names does 

not imply endorsement by the National Marine Fisheries 

Service, NOAA.

This document should be referenced as follows:

Roegner, G.C., H.L. Diefenderfer, A.B. Borde, R.M. Thom,

E.M. Dawley, A.H. Whiting, S.A. Zimmerman, and G.E. 

Johnson. 2009. Protocols for monitoring habitat restoration projects in the lower Columbia River and estuary. U.S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-97, 

63 p. 
NOAA Technical Memorandum NMFS-NWFSC-97

Protocols for Monitoring

Habitat Restoration Projects

in the Lower Columbia River

and Estuary

G. Curtis Roegner, Heida L. Diefenderfer,

1

Amy B. Borde,

1

 Ronald M. Thom,

1

Earl M. Dawley,

2

 Allan H. Whiting,

3

Shon A. Zimmerman,

1

 and Gary E. Johnson1

Northwest Fisheries Science Center

Fish Ecology Division

2725 Montlake Boulevard East

Seattle, Washington 98112

1 Pacific Northwest National Laboratory

Marine Sciences Laboratory

1529 West Sequim Bay Road

Sequim, Washington 98382

2 561 Grand Avenue

Astoria, Oregon 97103

3 Columbia River Estuary Study Taskforce

Present affiliation: P.C. Trask and Associates

322 Northwest 5th Avenue, Suite 315

Portland, Oegon 97209

February 2009

U.S. DEPARTMENT OF COMMERCE

National Oceanic and Atmospheric Administration

National Marine Fisheries Service
Most NOAA Technical Memorandums

NMFS-NWFSC are available online at the 

Northwest Fisheries Science Center

web site (http://www.nwfsc.noaa.gov)

Copies are also available from:

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phone orders (1-800-553-6847)

e-mail orders (orders@ntis.fedworld.gov)

ii
Table of Contents 

List of Figures.............................................................................................................................................vii 

List of Tables ...............................................................................................................................................ix 

Executive Summary .....................................................................................................................................xi 

Acknowledgments......................................................................................................................................xiii 

Abbreviations and Acronyms .....................................................................................................................xv 

1.0 Introduction............................................................................................................................................1 

1.1 Background .....................................................................................................................................1 

1.2 Restoration Strategies in the CRE...................................................................................................2 

1.3 Conceptual Model ...........................................................................................................................4 

1.4 Report Contents...............................................................................................................................5 

2.0 Core Monitored Metrics.........................................................................................................................6 

2.1 Metric Selection Criteria .................................................................................................................6 

2.2 Metrics.............................................................................................................................................7 

2.2.1 Hydrology ...............................................................................................................................7 

2.2.2 Water Quality..........................................................................................................................8 

2.2.3 Elevation .................................................................................................................................9 

2.2.4 Landscape Features.................................................................................................................9 

2.2.5 Plant Species Composition and Cover ....................................................................................9 

2.2.6 Vegetation Plantings ...............................................................................................................9 

2.2.7 Fish Community....................................................................................................................10 

3.0 Design Considerations.........................................................................................................................11 

3.1 Statistical Design...........................................................................................................................11 

3.1.1 Reference and Control Sites..................................................................................................11 

3.1.2 Before and After Sampling ...................................................................................................12 

3.1.3 Recommendations.................................................................................................................13 

3.2 Sampling Design ...........................................................................................................................13 

4.0 Monitoring Protocols...........................................................................................................................15 

4.1 Hydrology (Protocol 1)..................................................................................................................16 

4.1.1 Purpose..................................................................................................................................16 

iii
4.1.2 Goal.......................................................................................................................................16 

4.1.3 Design ...................................................................................................................................16 

4.1.4 Equipment .............................................................................................................................17

4.1.5 Site Selection.........................................................................................................................17 

4.1.6 Sampling Periodicity.............................................................................................................17 

4.1.7 Sampling Protocol.................................................................................................................17 

4.1.8 Calculations and Analysis.....................................................................................................19 

4.1.9 Site-specific Contingency Considerations ............................................................................20 

4.1.10 Additional Information.........................................................................................................20 

4.2 Water Quality (Protocol 2)............................................................................................................21 

4.2.1 Purpose..................................................................................................................................21 

4.2.2 Goal.......................................................................................................................................21 

4.2.3 Design ...................................................................................................................................21 

4.2.4 Equipment .............................................................................................................................21

4.2.5 Site Selection.........................................................................................................................21 

4.2.6 Sampling Periodicity.............................................................................................................22 

4.2.7 Sampling Protocol.................................................................................................................22 

4.2.8 Calculations and Analysis.....................................................................................................22 

4.2.9 Site-specific Contingency Considerations ............................................................................22 

4.3 Elevation (Protocol 3)....................................................................................................................23 

4.3.1 Purpose..................................................................................................................................23 

4.3.2 Goal.......................................................................................................................................23 

4.3.3 Design ...................................................................................................................................23 

4.3.4 Equipment .............................................................................................................................24

4.3.5 Site Selection.........................................................................................................................24 

4.3.6 Sampling Periodicity.............................................................................................................24 

4.3.7 Sampling Protocol.................................................................................................................25 

4.3.8 Calculations and Analysis.....................................................................................................27 

4.3.9 Additional Analysis Tools.....................................................................................................28 

4.3.10 Additional Information.........................................................................................................29 

4.4 Landscape Features (Protocol 4) ...................................................................................................29 

4.4.1 Purpose..................................................................................................................................29 

4.4.2 Goal.......................................................................................................................................29 

4.4.3 Design ...................................................................................................................................29 

4.4.4 Equipment .............................................................................................................................31

iv
4.4.5 Site Selection.........................................................................................................................31 

4.4.6 Sampling Periodicity.............................................................................................................31 

4.4.7 Sampling Protocol.................................................................................................................31 

4.4.8 Calculations and Analysis.....................................................................................................31 

4.4.9 Additional Analysis Tools.....................................................................................................32 

4.4.10 Additional Information.........................................................................................................32 

4.5 Plant Species Composition and Cover (Protocol 5) ......................................................................32 

4.5.1 Purpose..................................................................................................................................32 

4.5.2 Goal.......................................................................................................................................33 

4.5.3 Design ...................................................................................................................................33 

4.5.4 Equipment .............................................................................................................................33

4.5.5 Site Selection.........................................................................................................................34 

4.5.6 Sampling Periodicity.............................................................................................................37 

4.5.7 Sampling Protocol.................................................................................................................37 

4.5.8 Calculations and Analysis.....................................................................................................39 

4.5.9 Additional Information..........................................................................................................40 

4.6 Vegetation Plantings (Protocol 6) .................................................................................................41 

4.6.1 Purpose..................................................................................................................................41 

4.6.2 Goal.......................................................................................................................................42 

4.6.3 Design ...................................................................................................................................42 

4.6.4 Equipment .............................................................................................................................43

4.6.5 Site Selection.........................................................................................................................43 

4.6.6 Sampling Periodicity.............................................................................................................44 

4.6.7 Sampling Protocol.................................................................................................................44 

4.6.8 Calculations and Analysis.....................................................................................................47 

4.6.9 Additional Information..........................................................................................................47 

4.7 Fish Community (Protocol 7)........................................................................................................48 

4.7.1 Purpose..................................................................................................................................48 

4.7.2 Goal.......................................................................................................................................48 

4.7.3 Design ...................................................................................................................................49 

4.7.4 Equipment .............................................................................................................................49

4.7.5 Site Selection.........................................................................................................................49 

4.7.6 Sampling Periodicity.............................................................................................................50 

4.7.7 Sampling Protocol.................................................................................................................50 

4.7.8 Sample Processing ................................................................................................................53 

v
4.7.9 Additional Measurements .....................................................................................................53 

4.7.10 Calculations and Analysis....................................................................................................54 

4.7.11 Additional Information.........................................................................................................54 

5.0 References............................................................................................................................................57 

vi
vii

List of Figures 

Figure 1. Columbia River estuary conceptual model applied to estuary research, management, and 

evaluation action effectiveness research for tidal reconnection projects ......................................................5

Figure 2. Tide gates at Vera Slough before and after replacement with experimentally modified 

designs ........................................................................................................................................................15 

Figure 3. Tide gate at Kandoll Farm before and after culvert replacement ...............................................15 

Figure 4. Deployment options for data logging instruments: attached to a pile and attached to T-post 

and inserted in PVC pipe ............................................................................................................................18 

Figure 5. Water level variations surrounding a tide gate removal at Kandoll Farm, 2005 ........................19 

Figure 6. Exposure-elevation plot for prerestoration and postrestoration periods at Kandoll Farm 

restoration site, 2005...................................................................................................................................20 

Figure 7. Time series of mean daily temperature for reference and restoration sites surrounding tide 

gate removal, Grays River system, 2005 ....................................................................................................23 

Figure 8. A channel cross section surveyed within a dike breach at Kandoll Farm on the Grays River, 

2005–2007 ..................................................................................................................................................26 

Figure 9. Sediment accretion stakes leveled and measured in a pasture to collect baseline rates prior 

to hydrological reconnection with the mainstem river................................................................................27 

Figure 10. Example of baseline and transect sampling design in an herbaceous area...............................34 

Figure 11. Baseline tape and collapsible three-sided quadrat form a 1-m2

 herbaceous vegetation 

sampling plot...............................................................................................................................................35 

Figure 12. Example of sampling design in a forested wetland ..................................................................36 

Figure 13. Plot design for forested wetlands..............................................................................................36 

Figure 14. Elevation of dominant flora, Kandoll Farm, 2005....................................................................41 

Figure 15. Example of a woody vegetation planting site showing location of sample area, baseline, 

transects, and sample plots..........................................................................................................................42 

Figure 16. Replanting with native shrub and tree species at a Columbia River estuary restoration site ...48 

Figure 17. Beach seining near the Kandoll Farm culvert replacement at a forested wetland....................51 

Figure 18. Time series of relative CPUE for salmonids sampled at restoration and reference sites, 

Grays River system, 2006 and 2007 ...........................................................................................................54 

Figure 19. Size frequency of juvenile salmonids captured in restoration and reference sites, Grays 

River system, 2007......................................................................................................................................55
viii
List of Tables 

Table 1. Restoration strategies, examples of project types, and targeted ecosystem benefits for 

the CRE.........................................................................................................................................................3 

Table 2. Summary of core metrics for CRE restoration projects.................................................................8 

Table 3. The sequence of sampling events ................................................................................................14 

Table 4. Average percent cover of the dominant plant species at two sampling locations on a 

restoration site before and after a restoration action ...................................................................................39 

Table 5. Example of a weighted similarity index ......................................................................................40 

ix
x
Executive Summary 

This document describes a set of protocols developed by the National Marine Fisheries 

Service, the Pacific Northwest National Laboratory, and the Columbia River Estuary Study 

Taskforce, with the support of the U.S. Army Corps of Engineers. These protocols are designed 

for researchers and managers monitoring the effectiveness of actions to restore degraded wetland 

habitat in the lower Columbia River and estuary (CRE). The intent is to promote a standard set 

of monitoring protocols to assess and compare habitat restoration projects in the region. 

The goal of many restoration activities in the CRE is to repair the connectivity and 

function of wetland habitats and thereby allow juvenile salmon to regain benefit from these 

important rearing and refuge areas. To do this effectively, researchers and managers require the 

means to 1) evaluate the results of individual restoration activities, 2) compare results among 

projects, and 3) determine the long-term and cumulative effects of habitat restoration on the 

overall estuary ecosystem. 

To help achieve this, we have developed a standardized set of monitoring protocols. We 

limited the number of metrics to a proposed core set and selected measurement methods that are 

straightforward and economical to use. By “core,” we mean an optimum suite of metrics that 

can adequately detail the results of restoration, depending on the goals of the restoration action 

and financial and logistical limitations of comprehensively monitoring ecological change over 

extended temporal and spatial scales. We selected core metrics based on criteria that 1) 

correspond to commonly held restoration project goals; 2) are applicable to all sites; 3) 

characterize controlling factors, ecosystem structure, and ecosystem function; 4) are relevant to 

both present and future investigations; and 5) are practical in terms of level of effort. 

In this document, we summarize the types of restoration strategies being planned and 

implemented in the CRE. We then propose a set of metrics and statistical design for restoration 

monitoring activities based on commonly shared ecological goals. Finally, we provide seven 

specific protocols for this set of estuary monitoring metrics. Monitoring protocols are provided 

for 1) hydrology (water surface elevation), 2) water quality (temperature, salinity), 3) elevation 

(topography), 4) landscape features (remote sensing), 5) Plant species composition and cover 

(plant community), 6) vegetation plantings (success), and 7) fish community (species, temporal 

presence, size, and age structure). 

xi
xii
Acknowledgments 

This research was conducted under the auspices of the U.S. Army Corps of Engineers 

(USACE) Anadromous Fish Evaluation Program (study code EST-P-04-04), and funded by 

Congress through the Columbia River Fish Mitigation Project. The study was implemented and 

overseen by the USACE Portland District, with Blaine Ebberts and Doug Putman as the 

biological technical lead and program manager, respectively. The Pacific Northwest National 

Laboratory (PNNL, operated by Battelle for the U.S. Department of Energy), the National 

Marine Fisheries Service (NMFS), and the Columbia River Estuary Study Taskforce jointly 

conducted the study. 

The authors thank Ebberts and Putman for supporting the development of these protocols, 

beginning in 2004 with a process that included workshops, literature review, field-testing, and 

writing and releasing a first draft for review in 2006. During this process, many individuals with 

expertise on the Columbia River contributed their knowledge or reviewed the document, which 

could not have taken the present form without their assistance. The authors are particularly 

grateful to George Kral of Ash Creek Forest Management, Tigard, Oregon, for permitting the 

adaptation of his methods for monitoring revegetation. 

The authors invited a number of individuals to attend a meeting 23 June 2004 to involve 

restoration project managers in identifying minimum monitoring indicators and appropriate 

methods. The meeting was convened by the Lower Columbia River Estuary Partnership, 

USACE, PNNL, and NMFS at the offices of the estuary partnership in Portland, Oregon. 

Contributions of the following participants were invaluable foundations for this document: 

Michael Anderson, Taunja Berquam, Matt Burlin, Tim Counihan, Todd Cullison, Blaine 

Ebberts, Craig Haskell, Joe Hymer, Jason Karnezis, Scott McEwen, Michelle Michaud, Dave 

Sahagian, Ian Sinks, Kathryn Sobocinski, Janelle St. Pierre, Robert Warren, Jack Wiles, and 

Greg Williams. 

Following release of the 2006 working draft, we implemented the protocols at field-test 

sites and are grateful for cooperation by land owners and managers, the Columbia Land Trust, 

and the Port of Astoria. In addition to field-testing, we received valuable comments from others 

who implemented the draft protocols in the course of their work: Laura Brophy, Lori Lilly, Kate 

Norton, Micah Russell, Ian Sinks, and Melissa Rowe Soll. Many individuals assisted us in field 

testing, including Jimmie Cotton, Kate Hall, April Rouse, Micah Russell, and Kathryn 

Sobocinski. Following field-testing, we received additional feedback on the draft revised 

protocols at a meeting convened 8 February 2007 from: Rita Beaston, Laura Brophy, Matt 

Burlin, Suzi Cloutier, Robert Ellis, Kas Guillozet, Joe Krieter, Jill Leary, Lori Lilly, Margaret 

Magruder, Scott McEwen, Doug Putman, and Kathryn Sobocinski. We also received valuable 

review comments on the previous version of this document, a PNNL contract report to USACE 

(contract DE-AC05-76RL01830), from Krista Jones and Nikki Sather. 

xiii
xiv
Abbreviations and Acronyms 

APD average planting density 

BACI before-after control-impact 

BACIPS before-after control-impact paired series 

CPUE catch per unit of effort 

CRE lower Columbia River and estuary 

CRD Columbia River Datum 

CWT coded wire tag 

DO dissolved oxygen 

ESA Endangered Species Act of 1973 

ESU evolutionarily significant unit 

ETOH ethanol 

GIS geographic information system 

GPS global positioning system 

LiDAR light detection and ranging 

LWD large woody debris 

MLLW mean lower low water 

NAVD88 North American Vertical Datum 1988 

OPUS Online Positioning User Service 

PIT tag passive integrated transponder tag 

PNNL Pacific Northwest National Laboratory 

RTK real time kinematic 

USACE U.S. Army Corps of Engineers 

xv
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1.0 Introduction 

The recovery of salmonid stocks requires restoration of estuarine habitats supporting the 

diversity of life history patterns that historically mitigated for environmental variability (NOAA 

2004, Bottom et al. 2005). Research on salmon distribution patterns in the lower Columbia 

River and estuary (CRE), as well as other West Coast estuarine systems, indicates use of tidal 

freshwater and estuarine habitats by diverse stocks of subyearling and yearling salmonids (e.g., 

Reimers and Loeffel 1967, Healey 1980, Levy and Northrote 1982, Shreffler et al. 1990 and 

1992, Levings et al. 1991, Levings 1994, Sommer et al. 2001, Tanner et al. 2002, Roegner et al. 

2005). Much of this historically abundant habitat has been isolated, degraded, or destroyed 

(Thomas 1983, Burke 2004). 

The goal of many restoration activities is to repair connectivity and function of habitats to 

allow fish to regain benefits from important rearing and refuge areas. However, researchers and 

managers require the means to 1) evaluate the effectiveness of individual restoration activities 

(Roni et al. 2002), 2) compare projects (Neckles et al. 2002, Williams and Orr 2002), and 3) 

determine the long-term and cumulative effects of habitat restoration on the overall ecosystem 

(Steyer et al. 2003, Diefenderfer et al. 2005b). This can best be achieved with a standardized set 

of research and monitoring metrics. The purpose of this document is to provide protocols for 

monitoring the effectiveness of habitat restoration projects in the CRE. 

A review of the literature uncovered many relevant examples of restoration monitoring, 

theory, and design (e.g., Simenstad et al. 1991, Callaway et al. 2001, Hillman 2004, Rice et al. 

2005), yet none concisely outlined procedures particular to the CRE (Diefenderfer et al. 2005b). 

The intent of this manual, therefore, is to provide the rationale and procedures for standardized 

metrics specific to the tidal waters of the Columbia River estuary. The ultimate goal for results 

using these methods—which may be fully realized decades from now—is to compile a 

compatible time-series database of physical and biological metrics collected from many 

individual restoration projects. This database will enable evaluation of the effectiveness of 

individual restoration projects, as well as the cumulative effects of many restoration projects, on 

improving salmon habitat in the CRE. Protocols for the metrics are provided herein. 

1.1 Background 

The CRE region has been highly modified by human activities that converted tidal 

wetlands into agricultural and commercial uses. Construction of dikes, docks, and roads; 

installation of tide gates; and alterations such as dredging and filling have destroyed habitat and 

disconnected large areas of emergent and forested wetlands from tidal inundation. This has 

resulted in the loss of 70–90% of the productive wetlands in the estuarine and tidal freshwater 

regions of the lower Columbia, including important spawning and rearing habitat (Thomas 1983, 

Simenstad et al. 1992, Weitkamp 1994, Kukulka and Jay 2003a and 2003b) for several 

evolutionarily significant units (ESUs) of salmonids (Waples 1991). 
The incentive for many restoration activities in the CRE involves increasing habitat for 

rearing and migrating juvenile salmonids listed as threatened or endangered under the 

Endangered Species Act (ESA). Salmon stocks most likely to directly benefit from restoration 

activities in the CRE are wild and hatchery-reared ocean-type Chinook salmon (Oncorhynchus 

tshawytscha), chum salmon (O. keta), and stream-type coho salmon (O. kisutch) from lower river 

tributaries (reviewed in Diefenderfer et al. 2005b). However, migrants from tributaries 

throughout the Snake, and upper- and mid-Columbia River systems are thought to have utilized 

estuarine habitat in the early 1900s prior to extensive dam construction and loss of shallow water 

and wetland habitat (Rich 1920, Weitkamp 1994, Lichatowich and Mobrand 1995, Burke 2004, 

Bottom et al. 2005). 

While most individuals from the surviving ESUs of upriver stocks currently migrate 

rapidly through the estuary to the ocean, some (usually the smallest and latest migrants) display a 

protracted migration to and through the estuary and presumably gain enhanced growth and 

survival prior to ocean entry (Dawley et al. 1986, Diefenderfer et al. 2005b). Thus while the 

greatest use of estuarine habitats is expected from fish originating in lower river tributaries, 

threatened and endangered salmon from upriver tributaries are also expected to benefit from 

increased habitat opportunity. 

There is growing momentum to reverse land use patterns and specifically to reconnect 

historical wetland areas to the influence of tidal inundation. The challenge faced is how to 

evaluate the effects of various restoration projects on wetland function, given that the goals, 

scales, resources, and managing partnerships of projects vary greatly. To this end, there has been 

a regional movement in the Pacific Northwest and elsewhere to standardize measurement metrics 

and techniques that will facilitate comparison between restoration studies over time (Callaway et 

al. 2001, Neckles et al. 2002, Hillman 2004, Rice et al. 2005, Johnson et al. 2008). Standardized 

metrics are required to provide the best possible input to managers making decisions regarding 

habitat restoration in the CRE. 

1.2 Restoration Strategies in the CRE 

Various types of restoration are occurring throughout the CRE region in an effort to 

recover lost habitats (see map online at http://www.lcrep.org/habitat_inventory.htm [accessed 27 

January 2009]). These activities fall under five broad strategies summarized in Table 1 (Johnson 

et al. 2003). The protocols herein are applicable to restoration,1

 enhancement, and creation 

activities, detailed as follows. 

• Restoration—Restoration activities are designed to return degraded habitat to a state 

closer to the historical ecological condition. The most common restoration approaches in 

the CRE are tidal reconnection through dike breaching, dike removal, culvert upgrades, 

or culvert installations. The selected monitoring metrics of this manual are specifically 

chosen to track ecosystem changes resulting from this type of restoration treatment. 

• Enhancement—Habitat enhancement is the improvement of a targeted ecological 

attribute or process or both. Enhancement projects in the CRE include tide gate or 

 

1

 Unless noted otherwise, the term “restoration” refers collectively to all strategies applied in the CRE. 

2
Table 1. Restoration strategies, examples of project types, and targeted ecosystem benefits for the CRE 

(adapted from Johnson et al. 2003). 

Strategy Project type Targeted ecosystem benefit 

Tide gate 

removal 

Restores partial or full hydrologic connection to slough habitat, 

improving water quality, access to lost habitat types and processes, 

and potential removal of invasive plant species. 

Dike breaching Provides similar benefits as tide gate removal; this application 

requires significant earth moving activities to allow tidal energy to 

influence historical slough signatures and can involve tidal channel 

excavation. 

Culvert upgrades 

and culvert 

installation 

Provides similar benefits to above restoration activities through 

improvement of water quality, access to lost habitat types and 

processes, and potential removal of invasive species. 

Restoration 

Elevation 

adjustment 

Restores elevation of site to level that will support appropriate 

wetland vegetation. 

Riparian 

plantings 

Promotes water temperature reduction, contaminant removal, 

connection of terrestrial habitat corridors, sediment reduction, and 

water storage; future source of LWD input. 

Tide gate and 

culvert 

replacement 

Promotes water temperature reduction, dissolved oxygen 

availability, and increased habitat access. 

Invasive species 

removal 

Increases opportunities for native species propagation. 

Bioengineered 

stream bank 

stabilization 

Reduces sediment load, diffuses hydrologic energy. 

Enhancement 

Riparian fencing Protects riparian zones from disturbances. 

Material 

placement 

Mimics habitat function and complexity through the placement of 

material at a given elevation. 

Creation 

Tidal channel 

modification 

Increases tidal flows, mimics tidal channel structure. 

Land 

conservation 

Limits land use impacts harmful to salmon habitat such as 

sediment, contaminants, and nutrient loading. 

Easements Benefits ecological features through legal protection of critical 

areas, potentially allowing for complimentary restoration strategies 

to take place. 

Riparian fencing Deters livestock from degrading stream side areas. 

Conservation 

Manure 

management 

Minimizes the inputs of nutrients and bacteria into stream corridor. 

Land acquisition Preserves existing intact ecological features, functions, and 

processes at site scale or enables the application of additional 

strategies without human land use constraints or both. 

Protection 

Land use 

regulations 

Limits or prohibits potentially harmful land use activities on or 

adjacent to the land surrounding the site, thereby protecting 

habitat-forming processes and features. 

3
culvert replacement, riparian plantings and fencing, invasive species removal, and stream 

bank stabilization. 

• Creation—Habitat creation involves constructing or placing habitat features where they 

did not previously exist to foster development of a functioning ecosystem. Examples 

include tidal channel excavation and the placement of dredge material intended to create 

marsh or other habitat. 

In addition, conservation and protection activities ongoing in the CRE include acquisition of land 

or development rights, regulations on land use such as zoning designations and protection 

ordinances, and financial incentives for landowners to manage land for conservation. Improved 

management techniques being encouraged through such means include riparian setbacks as well 

as agricultural practices such as manure management, the addition of riparian buffer strips, 

integrated pest management, and off-stream livestock watering techniques. 

1.3 Conceptual Model 

A conceptual model representing the existing ecological condition of a restoration project 

site and its landscape can be used to forecast alternative future conditions based on different 

restoration planning scenarios and environmental conditions (Fischenich 2008). Conceptual 

model development is also a useful tool for identifying which metrics to monitor. During 

restoration planning phases, conceptual models often serve to enhance communication between 

parties involved with the project. Five types of conceptual models commonly used in ecosystem 

restoration planning are described in Diefenderfer et al. (2005a): landscape, ecosystem, 

ecosystem performance, ecosystem services, and subsystem. 

Conceptual models should help identify features of the site that require study. For 

example, if a site is predicted to recover to a tidal marsh, elevation relative to water level is 

critical. In order to assure that elevation is correct, some elevation measurements are required in 

addition to collection of water level data proximal to the site. If elevation is too low or too high 

relative to the water level, the effectiveness of the restoration action toward satisfying the project 

goal will be poor. Further, monitoring water level relative to marsh development may help 

provide an explanation if the marsh is not developing as expected. 

It is important that each project document knowledge of ecosystem structures and 

processes at the site, relationships between the site and landscape, and expected changes 

following the implementation of restoration actions (Diefenderfer et al. 2003). An effective 

vehicle for this documentation is the conceptual model. Understanding such information is 

foundational to determining the relative success of a restoration project (Thom 1997, Thom 

2000). 

Simple conceptual models depict environmental factors or processes occurring in an 

ecosystem and represent the magnitude and direction of their relationships and interactions. 

Examples of factors and processes include 1) anthropogenic stressors, such as passage barriers; 

2) controlling factors, such as topography; 3) ecosystem structures, such as emergent marshes; 4) 

ecosystem processes, such as sediment trapping; and 5) ecosystem functions, such as providing 

salmonid rearing habitat. Key landscape factors that may influence system performance or be 

4
5

influenced by the restoration project include land use, roads, boats, air or waterborne 

contamination, domestic or wild animals, fishing, and water diversion. 

Examples of the Columbia River Estuary Conceptual Model adapted from Thom et al. 

(2004) and applied to both status and trends and action effectiveness monitoring in the estuary 

can be found in Johnson et al. (2008, Appendix B). A simple example of a conceptual model can 

be found in Diefenderfer et al. (2003). A general conceptual model for action effectiveness of a 

tidal reconnection project is shown in Figure 1. 

1.4 Report Contents 

In the following sections, we propose a set of metrics for restoration monitoring activities 

based on commonly shared ecological goals (Section 2), discuss design considerations (Section 

3), and provide specific protocols for this set of estuary monitoring metrics (Section 4), followed 

by the list of references (Section 5). 

Salmonid 

Performance

Primary and 

Secondary 

Production

Successional 

Development

Refugement

Food Web 

Interactions

Ecosystem 

Functions

Ecosystem 

Processes

Ecosystem 

Structures

Controlling 

Factors

Water Column

Mud/Sand Flat

Emergent 

Marsh

Scrub-Shrub

Hydrodynamics

Water Quality

Geology/ 

Sediments

Temperature

Bathymetry and 

Topography

Shallow Slope

Deep Channel

Sediment 

Supply and 

Trapping

Forested 

Wetland

Tidal Channel

Stressors

Passage/Flow 

Barriers

Regional 

Climate 

Change

Flow 

Regulation

Invasive 

Species

Dredging

Ocean 

Conditions Light

Watershed 

Conditions

Toxics

Figure 1. Columbia River estuary conceptual model applied to estuary research, management, and 

evaluation action effectiveness research for tidal reconnection projects (adapted from Johnson et 

al. 2008). The shaded boxes are relevant to restoration in the lower Columbia River and estuary. 
2.0 Core Monitored Metrics 

The CRE comprises a unique continuum of wetland ecosystems strongly influenced to 

varying degrees by river flow, tidal amplitude, and salinity. Unlike streams in nontidal upland 

regions, semidiurnal and spring neap tide variation in water level in the CRE impose a 

structuring force on both geophysical features and biota, especially as distance to the mouth of 

the river decreases. Water elevation fluctuations, keyed to site topography, directly determine 

periods of inundation and salinity intrusion (Kukulka and Jay 2003a, 2003b) and this in turn 

structures plant communities and fish habitat use (Thomas 1983, Fox et al. 1984, Small et al. 

1990). The tidal cycle controls the magnitude and duration of bidirectional current velocities 

that cause sedimentation and erosion and the evolution of geomorphological features such as 

tidal channels and levees (Hume and Bell 1993). Tidal currents additionally affect the spatiotemporal distribution of water quality parameters such as salinity and temperature, and the 

transport of organic and inorganic materials that affect organism abundance and growth 

(Roegner 1998). Many restoration projects in the CRE will be tidal reconnections. Our metrics 

reflect this and were specifically chosen to measure changes in hydrology due to restoration 

activities and physical and biological responses of the floodplain wetlands. 

2.1 Metric Selection Criteria 

The decision making process culminating in the suggested core monitoring metrics was 

based on several interrelated criteria. First, metrics need to be diagnostic of some relevant 

ecosystem function and also correspond to commonly held goals among the restoration projects 

in the CRE (Thom and Wellman 1996). Second, we followed NRC (1992) guidelines that at 

least three classes of monitoring attributes be tracked: one for controlling factors (e.g., tidal 

regimes), one for structural factors (e.g., vegetation growth), and one for functional factors (e.g., 

fish community structure). Third, metrics should be potentially applicable to all sites with 

measurements that result in comparable data sets relevant to both present and future 

investigations (Tegler et al. 2001). Finally, measurements and data analysis must be practical in 

terms of funding, personnel, and processing requirements (Callaway et al. 2001). 

This last factor necessitates limiting the number of metrics to a core2

 set and selecting 

measurement methods that are straightforward and economical to use. Ideally, all projects in the 

region would perform the core physical measurements, which we view as encompassing the 

fundamental forces on, and responses to, changes in the affected systems. However, we 

recognize that funding even these core metrics may not be feasible. In this case, an even smaller 

set of metrics may be usefully employed as part of a broader, extensive sampling effort (see 

Johnson et al. 2008 and Johnson and Diefenderfer 2008). Project goals for the biological 

variables (e.g., fish use or vegetation cover) may vary between studies. 

 

2

 By “core” we mean a suite of metrics that can adequately detail the effectiveness of restoration while 

acknowledging the financial and logistical limitations of comprehensively monitoring ecological change over an 

extended temporal and spatial scale. 

6
We also encourage researchers to make additional measurements, especially processrelated derivations of the core metrics (e.g., fish growth rate, primary productivity, and material 

flux). The relevance of various metrics such as these to the CRE is under investigation at this 

time, as described in the series of reports from this project: Diefenderfer et al. 2005b, 

Diefenderfer et al. 2006, Johnson 2007, and Johnson and Diefenderfer 2008. Structure and 

process oriented indicators of the effects of CRE wetland ecosystems range from materials flux 

to large woody debris (LWD) to sediment accretion rates. Those under review include salmonid 

growth, residence time, and prey; organic matter and nutrient fluxes; hydraulic geometry; swamp 

and marsh macrophyte productivity; species diversity and distribution; and hydrological and 

flood storage modeling. Research and monitoring on higher order metrics such as these will help 

reduce fundamental uncertainties in existing knowledge of the ecosystem of the lower Columbia 

and improve restoration project design and future monitoring. 

The selection of relevant core metrics according to the above criteria was based on 1) a 

review of pertinent literature, 2) a meeting with local restoration managers (Diefenderfer et al. 

2005b, Appendix A), and 3) past iterations of this document based on our field results. We 

strove to keep the protocols useful not only to scientists but to staff and volunteers who 

potentially will be involved in restoration monitoring. Thus the format and level of detail in the 

protocols reflect the larger purpose of standardizing data collection on restoration projects in the 

CRE, that is, the development of a regional database consistent enough to permit estuary-wide 

analyses. 

As discussed above, we are concentrating on projects implementing tidal reconnection, a 

key ecological driver for a wide array of structural and functional attributes in the CRE. We 

found many relevant frameworks describing metrics important for monitoring restoration 

activities of potential salmonid habitat, although none were tailored specifically for the CRE. 

We relied extensively on papers by Simenstad et al. (1991), Simenstad and Cordell (2000), 

Zedler (2001), Johnson et al. (2004), Hillman (2004), and Rice et al. (2005) to derive an initial 

set of potential metrics. These were augmented and expanded during meetings with regional 

restoration managers and monitoring practitioners in June 2004 and February 2007. 

2.2 Metrics 

Table 2 outlines the set of core monitored metrics, their collection method, sampling 

frequency, and indicator category. We recommend a combination of data logging instruments, 

on-site survey and sampling methods, and remote sensing techniques. 

2.2.1 Hydrology 

Hydrology is a main controlling factor of wetland evolution in the CRE, and it influences 

habitat structure and processes as well as ecological functions (Sanderson et al. 2000, Rice et al. 

2005). Measuring water level variation is especially crucial for tidal reconnection restoration 

projects. Tidal forcing determines such processes as sedimentation and erosion, tidal channel 

development, inundation periods, and salinity intrusion. We advocate the use of automated data 

logging pressure sensors set to hourly frequency, which will record tidal, event scale, and 

seasonal water elevation variation. This method of data collection generates a time series of 

7
Table 2. Summary of core metrics for CRE restoration projects. 

Indicator category Monitored metric Collection method 

Sampling 

frequency 

Physical 

Hydrology Surface water elevation Data-logging instrument Hourly 

Water quality Temperature, salinity Data-logging instrument Hourly 

Habitat Landscape features Photography, GIS Annually 

Elevation Ground survey Annually 

Biological 

Species composition 

Percent cover 

Elevation 

Plants 

Planting success 

Ground survey Annually 

Species composition 

Size structure 

Fish 

Temporal presence 

Ground survey Monthlyseasonally 

measurements that can be compared between habitats and across seasons. Sensors can be stand 

alone or integrated into a water quality instrumentation package. 

2.2.2 Water Quality 

Water quality parameters such as temperature, salinity, dissolved oxygen (DO), pH, and 

turbidity play deterministic roles influencing species abundance and distribution in the CRE 

(OWEB 1999, Johnson et al. 2003). Most organisms have specific tolerances for water 

parameter ranges or rates of change (fluctuations). For example, temperature is a good predictor 

of juvenile salmon abundance and condition (OWEB 1999), and salinity is a main determinant of 

vegetation patterns (Thom et al. 2002). Oxygen concentration and pH can control the 

distribution of many organisms. Turbidity can limit the depth distribution of submerged aquatic 

vegetation. 

While all these parameters, and others such as specific dissolved constituents, are 

important and worthy of monitoring, we recommend temperature and salinity (in saline and 

brackish regions) as the core water quality metrics based on importance and methodological 

consistency. We advocate the use of automated data logging multiprobe instruments for 

measuring time-series of water quality parameters. Additional transect surveys with 

conductivity-temperature-depth probes can provide vertical and horizontal spatial scale 

perspectives useful for augmenting the spatially fixed time-series data (Callaway et al. 2001). 

8
2.2.3 Elevation 

Hydrologic reconnection usually results in substantial alteration of geomorphic features 

such as location and sinuosity of tidal creeks, changes in the extent and slope of intertidal 

regions, and substrate characteristics (Cornu and Sadro 2002, Williams and Orr 2002). These 

landscape changes in turn affect (and are affected by) the composition, distribution, and 

abundance of biota, which often have distinct habitat requirements in wetland areas (Sanderson 

et al. 2000). Establishing the time course of bathymetric and topographic change at a restoration 

site is crucial for evaluating the progress of the restoration effort. It is helpful if detailed 

topographic or bathymetric surveys are conducted by professional surveyors during the 

restoration planning phase. This information can be useful to predict restoration outcomes, plan 

invasive species management, identify areas appropriate for plantings, and identify areas that 

may require elevation increases or decreases to achieve desired species composition. Limited 

elevation surveys recommended in this manual include channel cross sections, vegetation plots, 

vegetation community boundaries, water level instruments, and sediment accretion stakes. These 

techniques have well-established methodologies and should be coordinated with biological 

surveys described below. 

2.2.4 Landscape Features 

Large-scale alterations of landforms and vegetation patterns often accompany wetland 

restoration activities (Tanner et al. 2002, Williams and Orr 2002). The measurement of spatial 

changes in biogeophysical features, such as evolution of tidal channel complexity, alteration in 

intertidal area, and succession of vegetation communities, is best accomplished by remote 

sensing using aerial imagery (e.g., Wright et al. 2000). Many technologies are available, 

including real color and near infrared aerial photography, hyperspectral imagery, digital aerial 

photography, high resolution satellite imagery, and Light Detection and Ranging (LiDAR). 

Ground truthing the imagery is necessary to ensure accurate analysis. Repeated measures over 

time are best analyzed using a geographic information system (GIS) to quantify the progress of 

restoration. 

2.2.5 Plant Species Composition and Cover 

Plant species composition and cover can change rapidly following reconnection to a tidal 

hydrologic regime (Cornu and Sadro 2002, Roman et al. 2002), especially if the reconnection 

fosters salinity intrusion (Thom et al. 2002). Vegetation patterns confer both structural elements 

and ecological processes to wetland ecosystems, and may increase ecosystem capacity for 

foraging salmonids (Sommer et al. 2001, Tanner et al. 2002). We recommend measurement of 

changes in vegetation community structure be accomplished at both landscape scale (described 

above) and through transect or ground survey techniques. 

2.2.6 Vegetation Plantings 

Some restoration projects include revegetation in riparian zones or across broader areas, 

which may be used to achieve a variety of objectives such as accelerating reestablishment of 

native plants, suppressing invasive plants, providing environmental conditions such as shade, or 

affecting the biota through, for example, salmonid prey production (Simenstad and Thom 1996, 

9
10

Naiman et al. 2005). The effectiveness of plantings can be assessed by tracking plant survival 

and growth. It is important to determine a criterion for success to ensure that project goals are 

being achieved, and this criterion will dictate specific monitored metrics. Typical metrics 

include a quantitative count (for density), height measurement (for growth), and qualitative 

estimation of condition (for survival) (Erwin 1990, Simenstad and Thom 1996). 

2.2.7 Fish Community 

The incentive for many restoration activities in the CRE involves increasing rearing and 

refuge habitat for juvenile salmonid ESUs listed as threatened or endangered under ESA (Thom 

et al. 2005). It is generally acknowledged that documenting “realized function” (Simenstad and 

Cordell 2000) is difficult because of the migratory nature of salmonids, while determining 

habitat capacity and opportunity are less problematic (Tanner et al. 2002). For minimum 

effectiveness monitoring, fish sampling should permit the evaluation of changes in community 

structure in restored locations compared with before-treatment and reference areas. 

Measurements of fish density (individuals per m2

) provide the most robust comparative value. 

We advocate conducting the most intense sampling effort logistically possible across sites, 

habitat types, and time. Additionally, it is highly desirable to determine higher order metrics 

(realized function attributes), such as residence time, growth, and survival, which necessitate 

measuring metrics such as prey availability, prey consumption, age assessment, genetic stock 

identification, parasite load, and mark-recovery data (e.g., Roegner et al. 2005). 
3.0 Design Considerations 

3.1 Statistical Design 

Monitoring data from individual restoration projects throughout the estuary is important 

for assessing project-specific outcomes and for analyzing changes in the broader estuary 

ecosystem. The roles of project monitoring data in the estuary-wide statistical design for 

ecosystem restoration in response to the biological opinion (NOAA 2007) are detailed in the 

document Research, Monitoring, and Evaluation for the Federal Columbia River Estuary 

Program (Johnson et al. 2008). The program incorporates both intensive monitoring of a small 

number of restoration projects and extensive monitoring of a smaller number of metrics at a 

larger number of projects (e.g., Trexler and Busch 2003). Through the efforts of the Lower 

Columbia River Estuary Partnership (Estuary Partnership) and the Bonneville Power 

Administration, a suite of reference sites is being established and monitored to allow comparison 

to restoration projects (see Borde et al. 2007); paired reference sites specific to a project are also 

recommended by Johnson et al. (2008). 

3.1.1 Reference and Control Sites 

The definitions of reference and control sites are used variously in the literature, so key 

elements distinguishing them are reiterated here, following Downes et al. (2002) and consistent 

with Johnson et al. (2008). Reference sites represent the state of an environment undisturbed by 

human activity, while control sites are as similar as possible in all respects to the impact location, 

except for the presence of the putative impact. One apparent source of confusion in the literature 

arises from the fact that the impact under consideration in ecological restoration is expected to be 

of a positive nature. Thus for example, in the case of hydrological reconnection of floodplain 

areas to the mainstem Columbia, a typical reference site would be a tidal wetland, while a typical 

control site would be a diked pasture. The best possible design is to monitor both reference and 

control sites relative to the restoration site; however, this will rarely be possible with limited 

monitoring funds. For most projects in the CRE, we therefore advocate concentrating on 

monitoring reference sites in conjunction with restoration sites. Conditions at restoration sites 

can be assessed in respect to the trajectory of their development against the target states 

represented by the reference sites (Johnson et al. 2008). 

The selected reference site should be spatially situated near the restoration site and 

subjected to similar large-scale climatic and environmental conditions, but be independent of 

activities affecting the restoration site to the extent possible. Ideally it represents a natural, 

minimally modified, or target condition and would be chosen to measure specific habitats or 

processes, such as tidal channels or marsh communities. It is widely recognized that choosing 

the reference site in regions that have been highly modified is challenging. The Estuary 

Partnership’s set of reference sites should be consulted. Within each hydrogeomorphic reach of 

the CRE, regional reference sites are being monitored to provide a range of target conditions for 

restoration activities. 

11
In general for projects in the CRE, the goal will be the return of the restored site to close 

approximation of its natural, undisturbed condition. Therefore, the key information needed to 

evaluate progress toward this goal is some measure of the similarity of the restored site to either 

predisturbance conditions or the conditions existing at nearby reference sites that are a 

reasonable approximation of predisturbance conditions. Because quantitative data on site 

conditions prior to disturbances are rarely available, reference sites are the only viable option. 

However, qualitative comparisons to information on predisturbance conditions using old 

photographs, land surveys, topographic surveys, etc., can be useful in concluding whether the 

site is actually returning to its former condition. 

3.1.2 Before and After Sampling 

The ability to detect ecological change due to restoration in a naturally varying 

environmental system is problematic (Osenberg et al. 1994). For restoration monitoring in the 

estuary, we considered two basic sampling designs, before-after control-impact (BACI, Green 

1979) and accident recovery (recovery, Skalski et al. 2001). BACI incorporates before and after 

sampling at control and restoration (impact) sites, while the recovery method incorporates afteronly sampling at reference and restoration sites. Because the original BACI design is susceptible 

to confounding project effects with other factors causing site-by-time interactions, the use of the 

modified before-after control-impact paired series (BACIPS) has recently been recommended for 

restoration monitoring (Osenberg et al. 2006). The essential difference between BACIPS and the 

recovery method is that BACIPS estimates the effect of the restoration based on the amount of 

effect, while recovery assesses the endpoint relative to target conditions. As Osenberg et al. 

(2006) suggest, “A combination of both approaches is likely ideal—we would like to know how 

much of an effect we have produced (effect-size-based outcomes) and if that change is sufficient 

(endpoint-based outcomes).” 

One measure of restoration success or performance is for values of the postrestoration 

parameters (the monitored attributes) to converge with those of the reference site (Kentula et al. 

1992, Simenstad and Thom 1996, Raposa 2002). The recovery model tests the parallelism 

hypothesis (Skalski et al. 2001): how a treatment site recovers in comparison to a relatively 

undisturbed reference site, as opposed to comparison to before conditions at a control site (cf 

Miller and Simenstad 1997, Skalski et al. 2001, Hood 2002, Thom et al. 2002, Steyer et al. 

2003). This analytical method is discussed in more detail and diagrammed in Johnson et al. 

(2008, their Figure 5). While the recovery model does not require multiple data collection times 

before implementation of restoration actions, before data is highly desirable for documenting the 

initial response of the system to the restoration process, as well as to assess interannual or 

seasonal variability in the reference and restoration sites (Skalski et al. 2001). See Hillman 

(2004) for further discussion of these types of statistical comparisons. 

Within either BACIPS or recovery sampling design, two primary data collection 

categories are likely to be employed in the CRE, depending on the parameter of interest: surveytype measurements and time series–type measurements. In contrast to the time-series measures 

described above, survey-type measurements are snap shots in the temporal frame and can include 

aerial photos, topographic surveys, vegetation surveys, and fish community sampling. Repeated 

measures over time are made to evaluate changes in metrics. 

12
3.1.3 Recommendations 

The choice of sampling design will depend on site-specific circumstances and the 

availability of funding for before- and after-project implementation periods. However, whatever 

the sampling design, it should be determined early in the restoration planning process. We 

recommend that in all cases the following occur during the project planning phase: 1) select a 

subset of reference sites from the existing suite, if reference sites comparable to target project 

conditions are being sampled; 2) establish a paired reference site, if possible, and secure access; 

and 3) determine whether monitoring will include a control and, if so, select the location and 

secure access. The recovery design is recommended for all restoration projects, using either a 

subset from the existing suite of restoration sites, a paired site, or both. If a control site is also 

selected, then use of the BACIPS design in addition to the recovery design is also recommended 

on a modular basis, that is, for those metrics to which such analysis is applicable. 

In general, we recommend a sequence of sampling events such as that listed in Table 3. 

Monitored parameters are sampled simultaneously at two or more locations (reference vs. 

restoration) before and after the restoration action (before vs. after). All sampling techniques and 

sampling periods should be identical between reference and restoration sites to the extent 

possible. These paired measurements are to be made before and after the restoration activity. 

The spatial and temporal replication of the measurements is dependent on the monitoring metric, 

the size of the restoration area, and logistics (Table 3). It should be emphasized that the 

ecological processes associated with a given restoration activity, such as breaching a dike, evolve 

for many years after implementation. A long-term monitoring commitment (5 to 10 years) is 

thus necessary for selected projects to adequately document the ecosystem response in relation to 

natural variation (Zedler 1988, Larsen et al. 2003, NOAA 2004). In forested wetlands, 

conditions may not converge for many decades. 

3.2 Sampling Design 

Generally, resources for restoration monitoring are too limited to permit random 

sampling of any parameter across an entire restoration site at a sufficient density to draw 

statistically defensible conclusions. Therefore, we recommend that most field sampling be 

concentrated on transects proximal to expected changes, for example, near a culvert replacement 

or a dike breach. This intensive monitoring at a small spatial scale can be complemented 

through mapping using an aerial photo and ground truthing methods (Erwin 1990) or other 

remotely sensed information such as LiDAR data to characterize aspects of the restoration site in 

its entirety. The use of georeferenced surveys wherever possible will permit the integration of 

hydrology, vegetation, fish, elevation, and other data at multiple scales. To maximize 

possibilities for integrating data, the following design is recommended (see Protocol 5, plant 

species composition and cover, subsection 4.5.3 Design). 

• channel cross sections surveyed along vegetation sampling baselines 

• elevation data collected at vegetation plots 

• data logging sensors deployed year-round to acquire water level and temperature 

information near where the vegetation baseline crosses the restored channel 

• fish collection efforts located in the same channels 

13
14

Table 3. The sequence of sampling events. 

Steps before restoration activity 

1. Acquire and process available restoration and reference site data (Protocol 4). 

a. Locate elevation and tidal benchmarks from Web site (Protocol 3). 

b. Acquire digital aerial photograph of site (Protocol 4). 

c. Create and ground truth vegetation community map. 

d. Acquire LiDAR or topographic survey and local bathymetry (if available). 

2. Select field sampling areas. 

a. Choose reference and restoration sampling areas. 

b. Choose survey transect locations. 

3. Ground survey (at reference and restoration sites). 

a. Deploy and maintain water elevation and water quality data loggers at surveyed locations 

(Protocols 1, 2, and 3). 

b. Conduct cross-section and sediment-accretion surveys (Protocol 3). 

c. Conduct vegetation-elevation and fish community surveys (Protocols 3, 5, 6, and 7). 

4. Time series (before, if time permits). 

a. Maintain data loggers. 

b. Repeat steps 3b and 3c. 

Steps after restoration activity 

1. Repeat steps 1b, 1c, 3a, 3b, and 3c (above) to acquire the after data set. 

2. Evaluate change in hydrology and water quality (Protocols 1 and 2). 

3. Determine change in physical features (Protocols 3 and 4). 

4. Compute vegetation structure analysis (Protocol 5). 

5. Evaluate planting success, if applicable (Protocol 6). 

6. Compute fish community structure analysis (Protocol 7). 

7. Repeat steps 1–6 at designated frequencies. 

In summary, wherever possible, spatially link the location of data logging 

instrumentation, elevation and vegetation transects, and fish surveys so that changes in multiple 

metrics can be evaluated for a single site. This is especially important for documenting how 

changes in physical parameters such as tidal elevation and channel morphology affect biological 

metrics such as vegetation and fish communities. The specific elements of such sampling 

designs relevant to each metric are described in more detail in each of the following protocols. 
4.0 Monitoring Protocols 

Seven monitoring protocols are described in detail in this section: 1) hydrology, 2) water 

quality, 3) elevation, 4) landscape features, 5) plant species composition and cover, 6) vegetation 

plantings, and 7) fish community. For each protocol, we describe purpose, goal, design, 

equipment needed, site selection, sampling periodicity, sampling protocol, calculations and 

analysis, and site-specific contingency considerations, if any. Examples are provided from field 

research and monitoring at the Vera Slough (Figure 2) or Kandoll Farm (Figure 3) restoration 

sites. While selected literature or other additional information sources are provided with each 

 

Figure 2. Tide gates at Vera Slough before (left, open) and after (right, closed) replacement with 

experimentally modified designs. 

 

Figure 3. Tide gate at Kandoll Farm before (left) and after (right) culvert replacement. 

15
protocol, these represent only a small fraction of the available number of related protocols and 

the number of examples of published research using similar methods. Hillman (2004) and 

Brophy (2007) provide thorough explanations of monitoring approaches in Pacific Northwest 

freshwater and estuarine environments, respectively. Among the most recent references 

generally applicable to most of the protocols herein, we recommend Callaway et al. 2001, 

Neckles et al. 2002, and Rice et al. 2005. 

4.1 Hydrology (Protocol 1) 

4.1.1 Purpose 

Water level variation in wetlands is a function of river flow and tidal fluctuations. This 

variation largely drives wetland evolution in the CRE, with tidal fluctuations probably being the 

most deterministic for wetland restoration (Cornu and Sadro 2002). A key measure is change in 

tidal elevation within a restoration project due to tidal reconnection. The extent, period, and 

duration of tidal forcing will cause changes in aerial exposure, circulation patterns in tidal creeks 

(including the distribution of water quality parameters such as salinity, temperature, and DO), 

sedimentation and erosion patterns and tidal creek evolution, and the distribution of vegetation 

and fishes. In general, restoration sites on the Columbia Estuary are not close enough to existing 

NOAA water level stations for the data to reflect water levels at the site, thus field measurements 

will be necessary. 

Water level data should be properly georeferenced to local topographic data (Protocol 3, 

elevation) that is related to an established vertical elevation datum (e.g., North American Vertical 

Datum 1988 [NAVD88] or mean lower low water [MLLW] if applicable; see Additional 

Information subsection in Protocol 3). Water level information and topographic information 

combined can be used to determine inundation periods and vegetation response (Protocol 3, 

elevation, and Protocol 5, plant species composition and cover). In addition, tidal stage 

parameters for the site (i.e., MLLW) can be computed from each recording station. Elevation is 

thus a priority metric and is best measured with automated data logging pressure sensors. 

Current technology offers multiple parameter probes that combine measurements like depth with 

others such as temperature and salinity (see Protocol 2, water quality). Although we present 

separate protocols for hydrology and water quality, for most purposes a single instrument will 

perform both sets of measurements. 

4.1.2 Goal 

Measure the pattern of hydrology with respect to a known reference point to determine 

the timing, frequency, and duration of tidal inundation in reference and restored sites. 

4.1.3 Design 

Recovery or BACIPS time-series design or both should be used to evaluate changes in 

water elevation caused by the restoration activity. At a minimum, two instruments would be 

deployed, one at the reference and the other at the restoration site. Where logistically possible, 

prerestoration (baseline) measurements are desirable to evaluate natural variations in the system. 

Comparing ranges and fluctuations of the reference and restoration time series gives a measure 

16
of the effectiveness of the restoration project. In addition, if atmospheric pressure correction 

data is not locally available, an additional instrument will be needed that is exposed to air to 

collect this. Comparisons to conditions in the nearest river channel can also be informative if an 

additional instrument can be deployed there. 

4.1.4 Equipment 

Field: Continuous water level recorders (pressure transducer) or multiple parameter probe 

(see Protocol 2, water quality), laptop computer and data logger launching and downloading 

software (or waterproof shuttle), monumenting equipment (T-post, surveying equipment), a 

measuring device to determine heights sensor on post and water level at time of deployment, 

hammer, global positioning system (GPS), and extra batteries. 

Lab: Data logger software, and calibration and maintenance manual. 

4.1.5 Site Selection 

The primary site for data loggers in both restoration and reference sites is near the mouth 

of the tidal reconnection site (but within the hydrological constriction). These positions would 

ideally be located where other monitoring activities take place (i.e., channel cross section). 

Additional instruments, if available, should be placed upstream of the reconnection to evaluate 

the extent of hydrological reconnection, especially to gauge for lags in period and reductions in 

tidal amplitude. 

4.1.6 Sampling Periodicity 

The preferred sample frequency is 1 hour; try to initiate logging on the hour to simplify 

alignment with other time-series data. 

Download or change batteries at less than 6-month intervals during spring and autumn to 

limit data loss and maximize recovery opportunities due to seasonal variation in daylight and 

tidal amplitude. 

Note that while tidal parameters may be predicted after a 2- to 3-month period of field 

data, water level sensors record river flow events as well as tide; combined effects of extreme 

events (storms) may not be easily predictable, yet can have strong impacts on wetland 

development. 

4.1.7 Sampling Protocol 

Automated instruments require proper placement to ensure comparable monitoring. Data 

loggers should be secured subtidally with sensors positioned at least 25–50 cm below the 

anticipated lowest tide level and at least 10–20 cm above the substrate to prevent sedimentation 

or excessive abrasion in high-velocity areas. Remember that hydrologic reconnections that 

increase tidal amplitudes may convert subtidal areas to intertidal zones. 

Instruments can be attached directly to existing structures such as pilings, although it is 

prudent to encase the instruments in a protective plastic sleeve (e.g., PVC) to minimize metal-to17
metal contact that can cause corrosion. The sleeve can be simply the length of the sensor and 

attached by cable ties, or as shown in Figure 4 to allow for deployment and retrieval at higher 

water levels. If the length of PVC used for deployment is longer than the sensor, be sure to drill 

holes in the pipe to allow water to drain easily. 

For each deployment, the height of the sensors relative to a known elevation point must 

be determined to relate water level fluctuations to topography. To accomplish this, determine the 

vertical elevation of a surveyed point (usually the top of the post structure) (see Protocol 3, 

elevation). During deployment, measure the distance from the sensor to the top of the permanent 

attachment post. This will tie the sensor position to the actual elevation. Note: Add the length of 

the instrument body to the measurement if the measured distance is from the top of the 

instrument and the sensor is at the bottom. 

A measurement from the sensor to the water level at the time of deployment and retrieval 

provides a means of verifying the water level data during postprocessing. Additionally, record 

the location of the data logger with GPS and periodically visit data loggers as stipulated by the 

factory user’s manual to check for fouling or damage. When removing or redeploying the data 

logger, record the vertical position on the piling or post so that it can be replaced at the same 

position. Waterproof shuttles are available with the capability to download and relaunch water 

level loggers in the field, reducing time lapses in the data. Where necessary, calibrate sensors 

before each deployment. 

Water level data is affected by atmospheric pressure; therefore, data collected in the field 

needs to be corrected for atmospheric pressure. One method is to deploy an additional sensor at 

the site, above water. Generally, this will be required unless atmospheric pressure is available 

from another source (e.g., NOAA weather station) within a 10-mile radius of the site, per 

recommendations at www.onsetcomp.com [accessed 6 October 2008]. 

Figure 4. Deployment options for data logging instruments: attached to a pile (left) and attached to T-post 

and inserted in PVC pipe (right). 

18
4.1.8 Calculations and Analysis 

The primary output from data loggers is a time series of water levels. These relative 

heights should first be corrected for atmospheric pressure following guidelines specific to the 

data logger. Next, they should be converted into elevation relative to the standard topographic 

datum (NAVD88) using field surveyed elevation data; this references hydrology to site 

topography and also facilitates comparison between sites. Data storage requirements quickly 

increase with 1-hour interval data collection, and data management and archiving can require a 

substantial time investment. 

Data should be presented to contrast water level fluctuation at reference and restored sites 

prerestoration and postrestoration (Figure 5). 

Inundation period (percent of time inundated) can be calculated for any elevation within 

the site and used to generate an exposure-height curve, which relates percent inundation by 

vertical height (Figure 6). Be aware that calculated inundation periods vary according to 

seasonal changes in tidal amplitude and river flow, and results are affected by the time period 

used for the calculations. 

Percent inundation data can be integrated with topographic surveys to create percent 

inundation maps in GIS. 

2

4 Reference

Water Level (m)

0

2

4 Kandoll Inside

Reference 

Water level (m) 

Kandoll inside 

190 200 210 220 230 240 250 260 

Day of year 

Figure 5. Water level variations surrounding a tide gate removal at Kandoll Farm, 2005. Top, reference 

hydrograph; bottom, restoration hydrograph. The timing of the tide gate removal is indicated by 

the dashed vertical line. Tide gate removal resulted in reestablishment of the semidiurnal tidal 

pattern. 

19
Percent inundation

0 10 20 30 40 50 60 70 80 90 100

Height (m) 

0

1

2

3

4

Before breach

After breach

Figure 6. Exposure-elevation (hypsographic curve) plot for prerestoration and postrestoration periods 

at Kandoll Farm restoration site, 2005. 

4.1.9 Site-specific Contingency Considerations 

Observe bank conditions of the water body where equipment is deployed; assess its 

potential for slope failure that can place equipment at risk and affect data quality. 

Ensure probes’ metallic elements are not in close proximity to other metallic structures; 

this can cause electrolysis and instrument malfunction, especially in saline areas. 

Forecast tidal fluctuations and set up a maintenance schedule accordingly so that 

equipment can be deployed and retrieved safely. 

Review first sets of data carefully and use them to make inferences of unexpected site 

conditions. 

Data loggers should be from the same vendor when possible to facilitate data downloads 

and consistency with inherent variability of readings. 

4.1.10 Additional Information 

For planning purposes, real time and predicted water level data is online at 

http://tidesonline.nos.noaa.gov/ [accessed 6 October 2008]. In addition, tidal prediction software 

is available that provides more options for graphic and data outputs. 

Climate (atmospheric pressure) correction data is online at http://www.ncdc.noaa.gov/ 

oa/ncdc.html [accessed 6 October 2008]. 

20
4.2 Water Quality (Protocol 2) 

4.2.1 Purpose 

Organisms have varying tolerances to water quality parameters such as temperature, 

salinity, turbidity, pH, and DO (OWEB 1999). Measuring variations in prestoration and 

postrestoration water quality conditions are a direct measure of changes in habitat opportunity 

(Callaway et al. 2004), and are important for explaining floral and faunal changes that may 

accompany hydrologic reconnection. Increased circulation due to tidal reconnection may reduce 

excessive temperature and help maintain suitable DO levels. Increased salinity intrusion on a 

restored site can also determine the vegetation community structure. As with water elevation 

(Protocol 1, hydrology), we advocate the use of autonomous data logging equipment to measure 

water quality parameters. Some water level loggers also record temperature or salinity or both. 

While DO is an important metric, data collection is often problematic; therefore, the minimum 

recommended core metric is temperature in tidal freshwater regimes and temperature and salinity 

in estuarine habitats. 

4.2.2 Goal 

Measure time series of water quality parameters at reference and restoration sites and 

relate to biotic changes. 

4.2.3 Design 

The design follows Protocol 1, hydrology. A recovery or BACIPS time-series design or 

both should be used to evaluate changes in water quality caused by the restoration activity. At a 

minimum, two instruments would be deployed, one at the reference and the other at the 

restoration site. Position the latter in a reach near the site of the hydrological reconnection, 

which would ideally be located where other monitoring activities take place (i.e., fish 

abundance). Where logistically possible, prerestoration (baseline) measurements are desirable to 

evaluate natural variation in the system. Comparing ranges and fluctuations of the reference and 

restoration time series gives a measure of the effectiveness of the restoration project. 

4.2.4 Equipment 

Field: Data loggers, laptop computer, and data logger launching and downloading 

software, data logger attaching and anchoring equipment (stakes, cable ties), hammer, GPS, 

camera or field notebook for documenting data logger location, and extra batteries. 

Lab: Data logger calibration, maintenance manual, and data logger output software. 

4.2.5 Site Selection 

Install data loggers in both reference and restoration sites. Additional instruments, if 

available, should be placed upstream of the reconnection to evaluate the extent of hydrological 

reconnection. 

21
Choose locations that are representative of the overall reach with some assurance of 

repeatability under changing conditions from the restoration treatment (e.g., increased water 

level fluctuations and velocities). 

4.2.6 Sampling Periodicity 

The preferred sample frequency is 1 hour; try to initiate logging on the hour to simplify 

alignment with other time-series data. 

Download or change batteries at less than 6-month intervals during spring and autumn to 

limit data loss and maximize recovery opportunities. 

4.2.7 Sampling Protocol 

Attach monitoring the probe on secure structure at least 25–50 cm below the lowest 

anticipated water levels and 10–20 cm from channel bottom. If possible, install the data logger 

at a position relative to a known surveyed elevation (Protocol 1, hydrology) to ensure all data is 

collected at the same position in the water column. This will provide comparable data sets for 

the reference and restoration sites. Record the GPS location to aid in retrieval. Clean and 

maintain monitoring probe using factory recommendations and ensure equipment is placed in a 

consistent location in the water column after download or maintenance. 

4.2.8 Calculations and Analysis 

The primary output from data loggers is a time series of parameters which can be 

analyzed with methods such as spectral analysis to capture trends in the data. Data should be 

inspected for data outliers (±3 SD of the mean). Time series from reference and restoration site 

should be temporally aligned and graphed together. 

Comparisons between sites can be made with difference time-series plots (reference 

value/restoration value). Mean daily maximum values may be used to examine periods where 

temperatures exceed organism tolerances (Figure 7). 

4.2.9 Site-specific Contingency Considerations 

Observe bank conditions of the water body where equipment is deployed; assess its 

potential for slope failure that can place equipment at risk and affect data quality. 

Monitoring probes should be from the same vendor when possible to facilitate data 

downloads and consistency with inherent variability of readings. Ensure probes’ metallic 

elements are not in close proximity to other metallic structures, as this can cause electrolysis and 

instrument malfunction, especially in saline areas. 

Forecast tidal fluctuations in advance and set up a maintenance schedule accordingly so 

that equipment can be deployed and retrieved safely. 

Review first sets of data carefully and use them to make inferences of unexpected site 

conditions. 

22
2005.50 2005.75

10

15

20

25

GR@Johnson

GR@Duffy's

2005.50 2005.75

C) Water Temperature (o

10

15

20

25

Water temperature (°C) 

Kandoll Channel

Kandoll Inside

Seal Slough Reference

July August September

Figure 7. Time series of mean daily temperature (±SD) for reference and restoration sites surrounding 

tide gate removal, Grays River system, 2005. Upper plot: time series from upstream and 

downstream monitoring stations illustrating strong temperature gradient. Lower plot: time series 

from stations at Seal Slough reference and within restoration site monitoring stations. The timing 

of the tide gate removal is indicated by the black vertical line. The 19°C temperature threshold is 

indicated by the dashed horizontal line. 

4.3 Elevation (Protocol 3) 

4.3.1 Purpose 

Wetland elevation is a factor in geomorphological evolution, vegetation succession, and 

fish habitat use (Rice et al. 2005). Dynamic alterations of channel morphology and vegetation 

patterns often accompany hydrologic reconnection of sloughs and backwaters with tidal forcing 

(Coats et al. 1995, Zedler 2001). Establishing the extent and rate of change of elevation at a 

restoration site is important for evaluating the progress of the restoration effort. 

4.3.2 Goal 

Quantify changes in elevation before and after restoration actions on portions of the site 

within the area influenced by tidal inundation; link data logging instruments to topography and 

biotic surveys. 

4.3.3 Design 

Accurately monitoring elevation changes in an intertidal area requires a precise elevation 

survey tied to a benchmark and linked to an established vertical datum (e.g., NAVD88 or 

MLLW; see Additional Information subsection below). Established survey benchmarks, 

however, may not be in close proximity to restoration sites and therefore may be of limited 

23
utility for determining elevations at a site. Often a site survey is conducted by a certified 

surveyor as part of the restoration project design. 

If elevation surveys are not conducted in combination with vegetation surveys or in other 

specific areas of interest such as tidal channels, they may not be useful for evaluating vegetation 

patterns or analyzing channel formation and change. At a minimum, surveys should establish a 

series of elevation benchmarks at the restoration site with line-of-sight to the portions of the site 

where elevation data is critical (e.g., at the location of vegetation transects, channel cross 

sections, and water depth sensors). An autolevel can then be used to survey elevation differences 

between the established benchmarks and the areas of interest. 

4.3.4 Equipment 

Field: Autolevel, tripod, stadia rod, meter tape, radio communications, GPS, PVC or 

rebar, and mallet or sledge hammer. 

4.3.5 Site Selection 

Sampling station locations may be generated from aerial photography. Elevation 

measurements should be constrained by the boundaries of expected change and should include 

the following locations: 

Fixed points 

• Along vegetation transects 

• Water level sensors 

• Cross section endpoints 

• Sediment accretion stakes 

Site features 

• Natural levees and channels 

• Created features that may be part of the restoration effort 

(e.g., added soils or excavated areas) 

• Boundaries between vegetation communities 

• Upper and lower elevation range of site 

In addition to taking elevation measurements, channel cross sections should be measured 

to determine channel volume and relative changes over time. Channel cross sections should be 

sited at the locations of water pressure sensors (proximal to restoration action) and near the 

expected boundary of postrestoration inundation. 

4.3.6 Sampling Periodicity 

Minimally, sampling should be conducted annually while the system is changing rapidly 

in years immediately following restoration. 

24
4.3.7 Sampling Protocol 

Elevations should be surveyed at 1) the location of data logging instruments (Protocol 1, 

hydrology, and Protocol 2, water quality), 2) at selected channel cross sections, 3) at the location 

of vegetation transects (Protocol 5, plant species composition and cover), and 4) at sediment 

accretion stakes. It is advantageous to use PVC or rebar to permanently mark transect endpoints 

as defined in Protocol 5 and the channel cross section endpoints. Elevations should be measured 

at the top of the stakes because the ground surface elevation can change over time. Additionally, 

a GPS should be used to determine the location of each stake. 

Water level sensors 

Water level sensor elevation is critical to linking the relative water level changes to a 

known elevation datum (Protocol 1, hydrology). This data can be used to predict inundation 

over areas of known elevations. The elevation of the sediment surrounding the post where the 

sensor is attached is likely to change over time due to accretion or erosion around the post. 

Therefore the elevation of the post should be measured by leveling the stadia rod on top of the 

post. Each time the sensor is deployed, the distance from the top of the post to the sensor must 

be measured. If the post is moved, the elevation must be reestablished. 

Channel cross sections 

Set transect end posts. The endpoints should be marked with a permanent marker (e.g., 

rebar or PVC) at a distance far enough from the bank to ensure they will not be washed out by 

erosive forces. Transect endpoint locations should also be recorded using a GPS, preferably with 

differential correction. If satellite coverage for the GPS is not available due to tree cover, points 

can be established in areas offset from the original location with measurements of distance, 

azimuth, and elevation difference. 

Attach measuring tape to fixed endpoints. Level the stadia rod at each predetermined 

interval and record the interval on the tape and the height measured with the autolevel. The 

interval can be greater (e.g., 1 to 2 m) in areas of low slope and smaller (0.5 m) in areas of 

steeper slope. Hand held radios are useful when distances make communication difficult. 

Repeat at each measurement interval. This procedure is useful for determining twodimensional change across an intertidal or tidal creek profile (Figure 8). 

Vegetation transects 

Elevation surveys at vegetation sampling areas are best conducted in a grid using 

transects along a baseline as outlined in Protocol 5, plant species composition and cover. If 

resources are limited, fewer points may be surveyed for elevation than for vegetation, for 

example, at the endpoints of the transects, borders between plant communities, or points 

representative of certain plant communities. To map elevations in the area of the vegetation 

transects, the elevations could be measured at three alternative times as follows: 

25
Horizontal Distance (m)

0 2 4 6 8 10 12 14

1.0

1.5

2.0

2.5

3.0

3.5

4.0

4.5

West East

Elevation (m NAVD88)

2005

2006

2007

Elevation (m NAVD88) 

Horizontal distance (m) 

Figure 8. A channel cross section surveyed within a dike breach at Kandoll Farm on the Grays River, 

2005–2007. 

Alternative 1: The elevation survey could be conducted at the same time as the vegetation 

survey by placing the stadia rod at the center of the quadrat before or after the vegetation 

percent cover is determined (see Protocol 5, plant species composition and cover) and 

measuring the elevation difference from the established benchmark with the autolevel. 

Alternative 2: The location of each quadrat location could be marked with flagging in the 

center of the quadrat and the elevation data can be recorded at a later time by positioning 

the stadia rod at the location of the flagging. The latter situation carries the risk of the 

flagging moving or being lost between the time of the vegetation survey and the elevation 

survey. 

Alternative 3: The meter tapes could be repositioned and the original locations of the 

quadrats remeasured. This alternative has the highest amount of potential error because it 

is highly unlikely that the exact position of the quadrats would be located. 

Sediment accretion stakes 

Sediment accretion stakes are an economical means for measuring the erosion or 

deposition of sediment, a typical result of hydrological reconnection projects. 

26
Sediment accretion stakes should be set prior to restoration in an area likely to be 

inundated and should be measured once before hydrological reconnection. Prerestoration 

measurements may be averaged or plotted for comparison to postrestoration measurements. 

Sediment accretion stakes can be made from 1-inch schedule 40 sunlight-resistant PVC 

conduit (gray). If possible, the stakes should be driven into the ground at least 1-m deep to 

ensure their stability against hydrological forces following restoration. Stakes are placed 1-m 

apart. The tops of the stakes must be leveled; this is accomplished by laying a construction level 

between them (Figure 9). 

To measure sediment accretion, a meter stick is set across the top of the sediment 

accretion stakes. A second meter stick is held vertically with the 0-end touching the sediment 

surface and is read to the lower edge of the resting meter stick. This is done at 10-cm intervals 

between the stakes. Measurements should be made to the nearest millimeter. 

It is useful but not necessary to measure the elevation of the top of one sediment stake by 

leveling the stadia rod on top of the post. 

4.3.8 Calculations and Analysis 

Data should be entered into a GIS and in a spreadsheet. 

Difference plots are derived by subtracting the before from the after elevations (or time 

series). Positive values indicate accretion and negative values indicate erosion. 

Figure 9. Sediment accretion stakes leveled and measured in a pasture to collect baseline rates 

prior to hydrological reconnection with the mainstem river. 

27
Elevations and vegetation can be plotted to show the means and ranges of elevation for 

species or communities. This information can be used prior to restoration to predict 

postrestoration vegetation colonization. 

Channel condition metrics calculated from above are: 

• Change in cross sectional area of tidal channel at selected transects. 

• Change in channel gradient (elevation change per unit of horizontal distance, dz/dx). 

• Wetted width: width of water surface perpendicular to flow (modeled from water 

elevation data). Water elevation analysis as described in Protocol 1, hydrology. 

4.3.9 Additional Analysis Tools 

For topographic surveys, we advocate use of a total station, which is a combination 

transit and electronic distance measuring device. Elevation and position data are logged 

internally and can easily be transferred to mapping software for analysis and display. Although 

simple transects measuring distance and elevation across areas of interest can be made using the 

total station, this system can also generate maps from regular or random grids of data points. 

Such maps can be digitized and overlain on aerial photography images to produce digital 

elevation maps, and change analysis can be used to measure changes to landforms over time. 

The total station system consists of an electronic instrument stabilized on a leveled tripod 

and a reflecting mirror affixed to the end of a graduated stadia rod. The instrument uses infrared 

light to measure the distance and angle from instrument to reflector, then calculates the relative 

position and elevation. Two benchmarks are required for a total station to provide accurate 

information. The instrument manual should be consulted for calibration and other procedures 

specific to the instrument employed. Similar to the autolevel method, the total station requires 

line of sight to points of interest and operation typically requires two people. 

In addition, real time kinematic (RTK) GPS technology is a useful means of establishing 

benchmarks and can be used for elevation surveys. Two GPS receivers are linked via a radio 

connection: the base unit is stationary and the mobile unit (rover) is used to make position and 

elevation measurements. This technique is advantageous in that measurements are made rapidly 

and only one individual is required. One drawback is that there may be satellite reception 

problems in areas of heavy tree or shrub cover. In addition, surveyed elevations using an RTK 

and NOAA’s Online Positioning User Service (OPUS) processing may differ from traditional 

field surveys using local benchmarks (see Additional Information subsection, below). NOAA’s 

height modernization program is designed to improve vertical control throughout the United 

States and, while there is no definite plan to update Columbia River region, efforts are underway 

in Oregon to implement the program. 

For bathymetry, surveys can be conducted in shallow water (<1 m) using the techniques 

described for topographic surveys. For deeper water areas, a GPS-referenced sonar will be 

required. 

28
4.3.10 Additional Information 

Two types of vertical datums relate elevations in the Columbia River estuary. Tidal 

datums, including MLLW, are based on data collected at tidal benchmarks over a 19-year period. 

Fixed geodetic datums, such as NAVD88, are based on a fixed set of constants and are generally 

used for terrestrial elevation surveys. The Columbia River Datum (CRD) is a fixed datum; 

however NOAA has linked the CRD to a tidal datum for eight locations on the river (Stolz et al. 

2005). The corrections between these datums are available at selected sites in the Columbia 

River, but interpolation of the corrections between sites should be done cautiously and is not 

recommended for locations away from the main channel of the river (e.g., up tributaries and 

sloughs). Tidal benchmarks information and datum correction information are online at 

http://tidesandcurrents.noaa.gov/ [accessed 6 October 2008]. 

Survey procedures are online at http://www.usace.army.mil/usace-docs/eng-manuals/ 

em1110-1-1005/toc.htm [accessed 6 October 2008].

Real Time Kinematic (RTK) GPS information is online at http://geodesy.noaa.gov/ 

OPUS/ [accessed 6 October 2008]. 

LiDAR information is online at http://pugetsoundlidar.ess.washington.edu/ [accessed 6 

October 2008]. 

4.4 Landscape Features (Protocol 4) 

4.4.1 Purpose 

Aerial photography and photo points are key tools for conducting quantitative 

measurements and qualitative assessments of landscape features at monitored sites. It is 

important to document the spatial changes in geomorphological features (such as tidal channel 

evolution or the intertidal area) and vegetation communities (e.g., agricultural meadow vs. 

emergent marsh) at a site scale to complement less extensive statistical sampling. Full color or 

near infrared aerial photographs are often publicly available through governmental agencies and 

provide a low cost alternative for evaluating environmental change without image analysis 

software and remote sensing expertise. If funds and expertise are available, hyperspectral or 

multispectral satellite imagery or digital aerial photography can provide additional information. 

4.4.2 Goal 

Quantify project-wide changes in landform and vegetation patterns accompanying 

restoration. 

4.4.3 Design 

Imagery 

Prior to restoration, aerial photos should be analyzed to identify hydrological barriers, to 

establish baseline vegetation conditions, and to make preliminary selections of sampling 

transects (Protocol 3, elevation, and Protocol 5, plant species composition and cover), locations 

29
for data logging instruments (Protocol 1, hydrology, and Protocol 2, water quality), and reference 

sites. Photos documenting historical conditions (i.e., prior to land use changes) are also useful 

for project design. After restoration actions are implemented, new aerial photographs must be 

acquired to assess changes in geomorphological features and vegetation communities. 

Specifications—The three sources of aerial imagery are 1) publicly available (free of 

charge), 2) commercially available (with a fee), or 3) data flown specifically for a site 

(individually contracted). Further, a variety of types of imagery useful to site-scale restoration 

project monitoring are available including 1) orthorectified black and white or color aerials, 2) 

stereo-paired aerials, 3) digital multispectral orthorectified aerials (including infrared), and 4) 

satellite imagery. Aerial imagery requires sufficient detail to identify features of interest (e.g., 

1-m resolution) and should be full color, near infrared to distinguish plant communities and 

vigor, or both. 

Tidal stage, time of day, and seasonality are also important factors to consider. For 

example, low water at spring tide can expose landforms and vegetation, while high water can 

document the extent of tidal inundation or channel development. Morning or afternoon increases 

light contrast. Late summer season maximizes vegetation growth and has a better chance of 

favorable weather in the Pacific Northwest. These conditions should be as similar as possible in 

all imagery, yet this may be difficult due to weather conditions and other factors. 

Recommendations depend on the main purpose of analyses. 

Interpretation—Interpretation of the acquired imagery can be conducted manually by 

digitizing polygons, lines, or points using a GIS platform. This method requires ground truth 

data to evaluate the photos and determine where features should be delineated. Key elements of 

ground truthing imagery include collection of GPS data with corresponding photos of the 

vegetation and geomorphological features at each point, line, or polygon. 

Analysis—GIS techniques may be employed to quantify changes in landforms and 

vegetation patterns. For example, polygons of vegetation classes can be developed from 

interpretation of the imagery and can be evaluated to determine the area of each classification 

and the change in area over time. Additionally, tidal channel delineations can be evaluated to 

assess the amount of marsh area that is accessible via the channels, channel order, and channel 

sinuosity. 

Photo point monitoring 

The essence of photo point monitoring is consistency. Photo point monitoring requires 

little more than a camera, compass, measuring and marking tools, and a map. Some important 

considerations include exact replication of the center point of the photograph, angle, and degree 

of zoom. A reference stake placed in the frame of the photo can provide scale and a consistent 

feature in all photos. In addition, bringing photos from prior years into the field makes it easier 

to replicate the exact frame. Photo points are best permanently marked with PVC or rebar. 

Using the same camera also increases consistency. 

30
4.4.4 Equipment 

If publicly available aerials are insufficient, overflights of target sites may be arranged 

through commercial vendors. Ideally, large areas of the CRE can be acquired during one flight, 

thus maximizing coverage and cost efficiencies. 

Desktop analysis requires GIS. 

Equipment includes camera, map, compass, stakes for marking and for reference in 

photo, and GPS. 

4.4.5 Site Selection 

Imagery should include the restoration and reference sites in their entirety and be 

collected concurrently. Photo points should be located at vantage points offering views of 

expected areas of change. 

4.4.6 Sampling Periodicity 

The frequency of imagery acquisition is often a balance between sampling objectives and 

costs. For example, publicly available imagery is often flown at long intervals relative to 

restoration project development (e.g., once every 5 years). More frequent acquisition may be 

necessary to document periods with high rates of change, such as the time immediately following 

implementation of restoration actions. Photo point periodicity depends on sampling objectives, 

that is, comparing seasonal differences or annual variability. 

4.4.7 Sampling Protocol 

Step 1. Before: 

• Obtain aerial photos of reference and restoration sites. 

• Examine photos for hydrologic barrier locations. 

• Assess vegetation patterns and channel locations. 

• Plan location of random or stratified sampling grid. 

• Collect GPS coordinates and corresponding photographs to ground truth landform and 

vegetation patterns. 

Step 2. After: 

• Repeat Step 1 above. 

• Compare before and after images of reference and restoration sites for changes in 

landforms and vegetation using GIS. 

4.4.8 Calculations and Analysis 

GIS-based measurements include site area; width, sinuosity, density, and total edge of 

tidal channels; as well as area and configuration of landforms and broad vegetation communities. 

31
4.4.9 Additional Analysis Tools 

Digital imagery coupled with ground truthing may be analyzed using GIS to quantify the 

progress of restoration. With multispectral imagery and ground truth data, algorithms can be 

developed to identify pixel values in an image using image analysis software. The pixel values 

are then applied to the whole image to get a classified representation of the site. This kind of 

image classification provides a spatially explicit method of determining broad vegetation 

categories and the location of tidal channels that is not subjective and is repeatable in subsequent 

years. 

In addition, LiDAR information available for selected areas of the estuary can identify 

landscape features at a very high resolution. Examples of such features include topography, 

drainage signatures, and LWD. These data sets are important to correlate with monitoring 

attributes related to water elevation, passage barriers, and tidal channel edge. 

4.4.10 Additional Information 

Imagery 

Aerials from multiple years for Oregon, including most of the Columbia River estuary are 

online at http://www.oregon.gov/DAS/EISPD/GEO/data/doq.shtml [accessed 6 October 2008]. 

A source for aerial imagery (recent and historical) and satellite imagery is online at 

http://edcsns17.cr.usgs.gov/EarthExplorer/ [accessed 6 October 2008]. 

Aerials are available for purchase from the Washington Department of Natural 

Resources, online at http://www.dnr.wa.gov/BusinessPermits/Topics/Maps/Pages/ 

orthophotography.aspx [accessed 6 October 2008]. 

Photo points 

The Oregon Watershed Enhancement Board (OWEB) photo point monitoring protocol is 

online at http://www.oregon.gov/OWEB/docs/pubs/PhotoPoint_Monitoring_Doc_July2007.pdf 

[accessed 6 October 2008]. See also Hall 2002. 

4.5 Plant Species Composition and Cover (Protocol 5) 

4.5.1 Purpose 

Tidal reconnections can result in substantial changes in the species abundance and 

distribution of vegetation (Cornu and Sadro 2002, Roman et al. 2002, Thom et al. 2002). 

Vegetation is recognized as a key indicator of ecological conditions in a restored environment 

(Zedler et al. 2001, Rice et al. 2005), and floristic measurements can be used to document plant 

succession following the implementation of restoration actions. Native estuarine and tidal 

freshwater plant communities have both structural and functional effects on estuarine 

ecosystems, although we concentrate here only on structural elements. We encourage 

measurements of functional benefits (i.e., primary productivity); while equally important, these 

are often more labor intensive to measure. To measure vegetation changes, we advocate 

32
georeferenced surveys that can be integrated with Protocol 1, hydrology, Protocol 3, elevation, 

and Protocol 4, landscape-scale GIS data. 

4.5.2 Goal 

Measure changes in vegetation species composition and distribution to assess 

successional trajectories toward reference estuarine plant communities following reconnection to 

tidal influence. 

4.5.3 Design 

Vegetation monitoring at restoration sites in Pacific Northwest estuaries is typically 

designed to quantify changes in species percent cover (e.g., Frenkel and Morlan 1990 and 1991, 

Thom et al. 2002). Measurements are usually made along transects. We recommend sampling 

be concentrated on transects proximal to expected changes, for example, near a culvert 

replacement or dike breach. For comparability, vegetation sampling on reference sites is best 

conducted at portions of the site with similar hydrology, for example, at similar distances from 

channels. Information derived from measuring landscape features (Protocol 4) can complement 

this vegetation monitoring by mapping plant communities at the site scale. Sampling designs 

such as systematic sampling from a random start permit appropriate data analysis; transects are 

established at set intervals along an established baseline with plots spaced equally on each 

transect with a randomly selected starting point (Figure 10). 

A subset of plots may be fixed (i.e., sampled repeatedly) to track trends, while others are 

randomized anew for each sampling event to assess status. The location of the baseline is 

determined in part by site conditions, with the aim of stratifying major vegetation assemblages 

by elevation. Elevation gradients affect vegetation distribution at various distances from both the 

main channels and the riverine shore. While soil surveys and groundwater monitoring can 

provide additional information for stratification, these data sources may not be available. If a 

considerable elevation gradient is present at the site, multiple baselines may be required to 

encompass the different plant communities present at different elevations. 

Vegetation along transects is sampled in plots with plot size and shape depending on the 

type of dominant vegetation at the site: 1 m2

 plots are used for herbaceous plant communities 

(Thom et al. 2002), belt transects for shrubs (Havens et al. 2003), and large circular plots for 

forested wetlands. When multiple plant communities are present at a site, the sampling design 

selects smaller herbaceous plots from both within and outside of larger plots to represent a 

greater portion of the study area and improve precision. While the 10-m diameter tree plot size 

recommended here is smaller than some comparable methods (Havens et al. 2003), it 

approximates line-of-sight in Columbia River swamps and for this reason is highly efficient, 

enabling a greater number of plots to be sampled and increasing precision. 

4.5.4 Equipment 

Field: 1 m2

 quadrat, 100-m tapes, site map, rebar or PVC stakes, mallet or hammer, plant 

identification books, bags for unidentified plant collection, and GPS. Additional tools for 

forested wetland and shrub/scrub communities include diameter tape, calipers, increment borer, 

clinometer, 10-m tape, and meter stick. 

33
Figure 10. Example of baseline and transect sampling design in an herbaceous area. 

Lab: Aerial photos, GIS (if available). 

4.5.5 Site Selection 

General site selection considerations 

A sampling site is selected proximal to the proposed restoration action (e.g., dike breach). 

At the reference site, a sampling site similar to the restoration sampling site is selected, 

particularly with respect to proximity to the channel, channel size, and the width of the area 

sampled, allowing comparison between the two sites. If multiple plant communities are present 

(along elevation gradients), the sampling may need to be stratified by plant community. 

For herbaceous communities 

Step 1. A linear baseline is established that is oriented perpendicular to the elevation 

gradient and runs through the entire sampling site (Figure 10). This baseline transect should be 

representative of the vegetation community within an elevation gradient at the site and proximal 

34
to the proposed restoration action (e.g., dike breach). Multiple baselines can be chosen to 

systematically represent different vegetation communities. 

Step 2. Several transects are established at intervals perpendicular to the baseline. The 

position of the first transect is chosen at random from all possible points along the baseline 

(systematic sampling with a random start). The additional transects are equally spaced relative 

to the first transect (e.g., 5 transects at 20-m intervals along a 100-m baseline). 

Step 3. On each transect, monitoring plots (1 m2

) are established at equally spaced 

intervals depending on the size of the site (Figure 11). As with the positioning of transects along 

the baseline, the plots are spaced relative to the first plot, which is positioned at random along 

the transect and thus avoids a grid pattern. Typically 5 to 10 plots per transect are sufficient to 

adequately sample the cover of the vegetation. 

Forested wetland and shrub/scrub communities 

Step 1. The length of the focal channel to be sampled is determined (e.g., 300-m) and a 

random number between 0 and the length of the channel is chosen as the start point for 

placement of the first transect. Transects cross the channel encompassing the riparian area on 

both sides (e.g., 50 m on each side of the channel). Remaining transects are located parallel to 

the first and systematically spaced (e.g., 5 transects at 50-m intervals) (Figure 12). 

Step 2. Monitoring plots (10-m diameter circles) are then established at equally spaced 

intervals along each transect starting at the channel bank (Figure 13). In this example, a random 

Figure 11. Baseline tape and collapsible three-sided quadrat form a 1-m2 herbaceous 

vegetation sampling plot. 

35
36

 Figure 12. Example of sampling design in a forested wetland. 

 Figure 13. Plot design for forested wetlands. 
number between 5 and 50 would be used to locate the center of the first plot (numbers 4 or below 

would cause a portion of the channel to be included in the 10-m diameter plot). A very high 

number of plots may be required to achieve high precision in some of these communities (e.g., 

695 tree plots for alpha = 0.05 and precision = 0.05 in Sitka spruce [Picea sitchensis] swamps). 

Typically, such sampling is not economically feasible for restoration practitioners and a lower 

precision is accepted for reference purposes (e.g., 6 plots per transect on 5 transects yields 30 

plots). 

4.5.6 Sampling Periodicity 

If possible, sampling should occur at least once before restoration treatments and in the 

year following restoration. Subsequent sampling can be conducted at 1- to 3-year intervals for 5 

to 10 years to capture the major transition in vegetation communities. With limited resources, it 

is best to sample vegetation in midsummer to capture the period of greatest biomass and cover, 

although additional sampling in spring and late summer generally increases the number of 

species found on the site. 

4.5.7 Sampling Protocol 

Initial assessment 

The protocols for sampling are necessarily different for herbaceous, shrub/scrub, and 

forested wetland communities because of the horizontal and vertical scales appropriate for 

capturing variation within and between them. The boundaries between plant communities can be 

mapped using a GPS in the field or from aerial photography with ground truthing (Protocol 4, 

landscape features). This technique is being used in the Columbia Estuary Ecosystem 

Monitoring Program and is most effective when clear elevation gradients are present (Leary et al. 

2005). 

Step 1. Define the study area boundaries (Figure 10) based on the extent of expected 

inundation and proximal to the proposed restoration action. 

Step 2. Use aerial photos (Protocol 4, landscape features) to broadly characterize existing 

plant communities (e.g., herbaceous, shrub/scrub, forested). 

Step 3. Establish baselines based on broad plant communities and elevation strata. Mark 

baseline endpoints with permanent stakes (rebar or PVC) and record GPS positions.

Herbaceous-only vegetation communities 

Step 1. Establish transects at intervals along the baseline with a density of approximately 

5 transects per 100 m. 

Step 2. Select plots along each transect (5–10 plots per transect are often sufficient). The 

total number of plots depends on the size and homogeneity of the area. 

Step 3. In each 1 m2

 plot, visually estimate percent cover in 5% increments, using a 

“trace” category for species that cover less than 5% of the area within the quadrat (e.g., 25% 

37
Lyngbye’s sedge (Carex lyngbyei), 50% reed canary grass (Phalaris arundinacea), 20% 

broadleaf cattail (Typha latifolia), 5% water plantain (Alisma plantago-aquatica), and trace, 

threepetal bedstraw (Galium trifidum). 

Step 4. Using a random number generator, establish a subset of approximately one-third 

of the total number of plots to be permanent plots. These plots will be resampled each year. 

Mark two diagonal or all four corners of each permanent plot with 1.2–2.0 m, 1.9-mm (3/4-inch) 

PVC pipe driven to a depth of at least 1 m. Flag the pipe so that it can be easily identified from a 

distance and record GPS positions. 

Step 5. Repeat sampling using the same design at the reference site. 

Forested wetland and shrub/scrub communities 

The sampling methods for these community types are far less defined in the literature and 

are still under development by many organizations in the Pacific Northwest. The 

recommendations here are based on our investigations of Sitka spruce swamps in the vicinity of 

Grays Bay on the Columbia River. Tree, shrub, and herbaceous layers may be present in these 

communities and require sampling with different methods. Conditions in these systems are 

challenging at best, making many measurements difficult and time consuming relative to 

sampling precision objectives. The shrub belt transect method described here was efficient but 

did not capture as many species as a point-intercept method. Each situation needs to be 

considered individually for hazards, feasibility, and resources. 

Step 1. Establish transects as described in Site Selection above. 

Step 2. Place tree, shrub, and herb plots along each transect, systematically spaced from 

random starting points: 

• Starting at the channel bank, place 10-m circular tree plots along each transect; the 

number and spacing is dependent on the size and homogeneity of the area. In the Site 

Selection example from the Sitka spruce swamp research above, 30 plots or 3 plots on 

each side of the channel on five transects was sufficient to provide tree cover precision 

within 20% of the mean 80% of the time (i.e., 20-m spacing between 10-m plot centers). 

• Select a random subset of the tree plots in which to sample the shrub belt. The size of the 

subset depends on available resources; a randomly selected subset of 10 of the 30 tree 

plots was sufficient to provide shrub cover precision within 20% of the mean 80% of the 

time in some but not all of the Sitka spruce swamps that we sampled. 

• Place 1 m2

 herbaceous plots systematically spaced from a random start on each transect. 

The systematic spacing will place some herbaceous plots within and others outside of the 

tree plots and shrub belts. In the previous example, 50 plots may be sufficient to provide 

herbaceous cover precision within 20% of the mean 80% of the time. 

Step 3. Measure species cover for each plot using the following techniques: 

• For trees lay a 10-m tape perpendicular to the transect tape to delineate the 10-m diameter 

circular tree plot. Identify all trees in the plot to species, then measure diameter at breast 

38
height (dbh) with calipers or a dbh tape. Measurement of dbh is made at 1.4 m above the 

duff layer upslope of the tree, not including woody debris. 

• If the construction of site tables correlating age with height and dbh is desired, core these 

trees or a randomly selected subset of them with an increment borer and preserve the 

cores for later ring counts (drinking straws provide a convenient storage method), then 

measure the angle from the observer’s eye to the top of the tree with a clinometer, along 

with the distance from the observer to the tree for calculation of height. For more 

accurate dating or to analyze disturbance history, collect two cores from each tree and use 

cross-dating methods (Stokes and Smiley 1968, Kipfmueller and Swetnam 2001). 

• For shrubs lay a 10-m tape perpendicular to the transect tape to delineate a 1 m by 10 m 

belt across the tree plot. Identify all shrubs that are rooted within the belt to species and 

count number of stems at 1.4-m height and record by species. If level of effort permits, 

record stems by diameter class (at dbh) following Peet (1998): 0–1 cm, 1–2.5, 2.5–5, 

5–10, 10–15, 15–20, 20–25, 25–30, 30–35, and 35–40; stems greater than 40 cm should 

be measured. Following Peet (1998), individuals are defined as stems at 0.5 m: “Multiple 

stems arising from a common root system are recorded separately if they branch below 

0.5 m above ground level (stems branching above 0.5 m and below 1.4 m are measured at 

the narrowest point below the branch).” 

• For herbaceous vegetation, sample the percent cover of the herbaceous layer on 1 m2

plots as described above in herbaceous-only vegetation communities. 

Step 4. Repeat sampling using the same design at the reference site. 

4.5.8 Calculations and Analysis 

Data gathered from these protocols can then be used for the following: 

For herbs construct a table with a species list containing the mean with SD or 80% 

confidence limit for 1) cover of each species over the entire site, 2) cover of each species along 

each transect, and 3) total vegetation cover (±SD) for the entire site (Table 4). 

Table 4. Average percent cover of the dominant plant species at two sampling locations on a restoration 

site (SSE and SSW) before and after a restoration action. 

Scientific name Common name SSE 2005 SSE 2006 SSW 2005 SSW 2006 

Juncus effusus Soft rush 0.88 1.51 14.2 3.92 

Phalaris arundinacea Reed canary grass 27.1 57.0 33.1 56.3 

Ranunculus repens Creeping buttercup 21.5 13.7 6.78 1.85 

Rubus discolor Himalayan blackberry 0.00 0.00 16.8 3.42 

Trifolium pretense, 

T. repens, and

T. dubium 

Red clover, 

white clover, and 

small hopclover 

19.4 0.28 0.00 0.00 

n/a Mixed grass 49.7 22.5 4.19 3.13 

39
For shrubs construct a table with a species list containing 1) the number of stems of each 

species over the entire site along with the SD or 80% confidence limit, and 2) the stem density of 

each species (stems per hectare). 

For trees create a table with the basal area of each species, percent frequency, density, 

basal area per hectare (dominance), relative frequency, relative density, and relative dominance. 

Construct a species time x-y plot showing the mean cover of one to three selected species 

vs. sampling period at the restored site. 

Create a bar graph showing the mean cover with SD or 80% confidence limit bars of the 

selected species at both the restored and reference sites. 

Calculate the similarity of species composition at the restored site vs. the species 

composition at the reference site and between years using the formula presented in Thom et al. 

2002 (Table 5). 

Correlate dominant plant community with elevations, if elevation data are collected 

(Figure 14, see also Leary et al. 2005). 

4.5.9 Additional Information 

See Frenkel and Morlan 1990 and 1991, Cornu and Sadro 2002, Thom et al. 2002, 

Havens et al. 2003, and Leary et al. 2005. 

Useful plant identification books include Hitchcock and Cronquist 1973, Pojar and 

MacKinnon 1994, Cooke 1997, and Washington Department of Ecology 2001. 

Table 5. Example of a weighted similarity index. This assesses the similarity of the vegetation cover 

between baseline conditions in 2005 and postrestoration conditions in 2006 at two restoration 

sites (SSE and SSW), and compares baseline and postrestoration conditions at each site with a 

reference site (KR). 

SSE 2005 SSW 2005 SSE 2006 SSW 2006 KR 

SSE 2005 72.6 92.8 – 23.4 

SSW 2005 – 94.0 30.6 

SSE 2006 86.3 23.4 

SSW 2006 53.2 

40
0.00

1.00

2.00

3.00

4.00

5.00

6.00

7.00

8.00

Carex obnupta

Phalaris arundinacea

Juncus effusus

Galium trifidum var. pacificum

Lysimachia nummularia L.

Ranunculus repens

Impatiens noli-tangere

Mixed Grass

Lysichiton americanum

Polygonum hydropiper

Plantago lanceolata var. lanceolata

Carex stipata

Lotus corniculatus

Glecoma hederacea

Alnus rubra

Trifolium repens

Trifolium dubium

Cirsium arvense var. horridum

Trifolium pratense

Hypochaeris radicata

Prunella vulgaris

Rubus discolor

Polystichum munitum

Sambucus racemosa

Parentucellia viscosa

Rubus laciniatus

Heracleum lanatum

Tellima grandiflora

Rubus ursinus

Species

Elevation (feet above NAVD88)

Figure 14. Elevation of dominant flora, Kandoll Farm, 2005. 

4.6 Vegetation Plantings (Protocol 6) 

4.6.1 Purpose 

Vegetation planting3

 can increase the rate at which desired species become established at 

a restoration site. Planting native vegetation can reduce erosion, increase cover and shade, and 

often reduce nonnative invasive species (e.g., reed canary grass). To date, native vegetation 

plantings in the Columbia River estuary have been primarily trees and shrubs (woody species); 

however, this protocol outlines methods for monitoring woody species and herbaceous species 

(e.g., emergent wetland vegetation) to meet potential needs as restoration efforts increase in 

scope and diversity. The effectiveness of habitat vegetation plantings can be determined by 

assessing survival, overall health, and growth of the plantings over time. Often, invasive species 

management is a critical component to ensure the success of native species. It is important to 

determine a criterion for success when monitoring vegetation plantings to ensure that the project 

goals are being achieved and, if not, adaptive management corrections should be implemented. 

Examples of success criteria are 1) percentage of tree or shrub survival (stems per unit area) of 

 

3

 Substantial elements of this protocol have been drawn directly from previously released methods developed and 

written by George Kral of Ash Creek Forest Management in Tigard, Oregon. While we have not field-tested this 

method, it is currently in use by others monitoring revegetation planting success in the lower Columbia River and 

estuary. 

41
initial planting stock, 2) amount of area covered by vegetation plantings, or 3) similarity to 

reference system within an established time period. 

4.6.2 Goal 

Measure percent cover and density of vegetation prestoration and postrestoration to 

determine whether a site is meeting success criteria and identify any needed corrective actions. 

4.6.3 Design 

The aim of the monitoring design is to capture the range of plantings that may occur in 

the Columbia River estuary, including herbaceous and woody vegetation. The sampling design 

is very similar to that described in Protocol 5, plant species composition and cover. Systematic 

sampling with a random start is recommended to achieve results that are representative of the 

conditions at the site. Transects are established at equal intervals from a random point along an 

established baseline; likewise plots are spaced at equal intervals from a random point on each 

transect (Figure 15). A subset of plots may be fixed (i.e., sampled repeatedly) to track trends, 

while others are randomized anew for each sampling event to assess status. The baseline 

remains the same each year. Photo points are also recommended to capture qualitative changes 

on the site over time (see Protocol 4, landscape features). 

Figure 15. Example of a woody vegetation planting site showing location of sample area, baseline, 

transects, and sample plots (note: example only, not an actual planting site). 

42
4.6.4 Equipment 

Field: Field notebook, meter tapes (100 m for baseline and transects, 10 m for tree and 

shrub plots), densiometer (a small, hand-held curved mirror grid used for canopy cover 

measurements; see Additional Information subsection below), rebar or PVC stakes, GPS, 

camera, and 1 m2

 quadrats. 

Lab: Aerial photos, GIS to assess GPS coordinates and create maps. 

4.6.5 Site Selection 

General site selection considerations 

Using aerial photos or other site information, stratify sites by vegetation community or 

potential planting areas. If the area has already been planted, identify the planted areas. If 

possible, a reference site with desired species composition also should be identified. The 

reference site can be monitored using the methods outlined in Protocol 5, plant species 

composition and cover, or an existing reference site can be used (e.g., Lower Columbia River 

Estuary Partnership Reference Site Study or City of Portland, Bureau of Environmental Services, 

Watershed Revegetation Program Reference Sites). 

Determine location of baseline, transects, and sample plots. 

The location of the sample plots can be determined in the office, based on the aerial 

photos or site maps as follows. 

For each area to be monitored (e.g., potential or existing planting site), determine the 

dimensions and area of the site. The recommended number of sample plots per site is: 

Size Woody plots Herbaceous plots

<0.1 ha (1,000 m2) 3 10 

0.1–1.0 ha 10 20 

1–5 ha 10 per ha 20 per ha 

For sites greater than 5 ha, a portion of the site that is representative of the whole area should be 

sampled, with a maximum of 50 woody plots and 100 herbaceous plots. 

The size of the area will determine how many sample plots are needed, while the 

dimensions will influence the length of the baseline, number and length of transects, and 

placement of the plots. For the following discussion, assume the area of a site is 3 ha (300 m by 

100 m) and therefore requires 30 woody plots or 60 herbaceous plots. 

Determine the length and width of the site and establish a baseline along the longest part 

of the planted area. In our example, the baseline would be 300 m. 

Transects should encompass the width of the planted area (e.g., 100 m) and should be 

spaced to cover the entire monitoring site. The spacing between transects and sample plots does 

not need to be equal and can be closer within transects than between transects. The main factor 

43
to consider is the distribution throughout the site. At an irregularly shaped site, the length of 

transects will need to be adjusted to stay within the site boundaries; it is acceptable for transects 

on irregular portions of the site to have different lengths. In the above example, 6 transects 

would be spaced 50 m apart along the baseline. 

To determine the location of transects, choose a random number between zero and the 

length of the baseline and place a cross transect perpendicular to the baseline at the location of 

the random number. Remaining cross transects are located parallel to the first and systematically 

spaced. In the example above, if the baseline random number were 77 then cross transects would 

be set at 27, 77, 127, 177, 227, and 277 meters. In excessively narrow sites, such as some 

riparian plantings, other methods may be used to select plot locations provided that they are 

random and unbiased. 

Sample plots (8-m diameter circles for woody species and 1 m2

 quadrats for herbaceous 

species) are located at equally spaced intervals along each transect, with the start point chosen 

randomly for each cross transect. In the example above, 5 plots per transect on 6 transects yields 

30 plots with the plots spaced 20 m apart. For herbaceous vegetation monitoring, 10 plots per 

transect at 10-m spacing would be needed to yield 60 plots. 

4.6.6 Sampling Periodicity 

A prerestoration assessment is recommended to determine existing stems per area, 

canopy cover, and herbaceous cover. Sites will also be stratified into vegetation communities at 

this time. 

Comprehensive monitoring for woody species will occur the first year after planting, then 

every 5 years (at least years 1, 5, and 10), and for herbaceous wetland species every 2 years (at 

least years 1, 3, and 5) until the project can be evaluated for relative success. 

Rapid monitoring of vegetation planting success is also recommended to ensure potential 

failure is identified, so that contingency management can be implemented if needed. Rapid 

monitoring would be conducted every year for the duration of the project, including 

comprehensive monitoring years. 

Monitoring should be conducted at the end of the growing season before leaves begin to 

fall to capture maximum growth for the season. 

4.6.7 Sampling Protocol 

Prerestoration assessment 

The prerestoration assessment should happen as soon as the site is accessible and cleared 

of any restrictive vegetation (e.g., dense blackberries). 

Step 1. Define the study area boundaries (see example above) based on extent of 

expected restoration. 

44
Step 2. Use aerial photos (Protocol 4, landscape features) to broadly characterize existing 

plant communities (e.g., herbaceous, shrub/scrub, forested). 

Step 3. Assess sites in the field prior to restoration to verify existing vegetation 

communities, size, soil characteristics, and topography. 

Step 4. Establish baselines based on broad plant communities and elevation strata. Mark 

baseline endpoints with permanent stakes (e.g., rebar or PVC) and record GPS positions. 

During this assessment, at least two sample plots (8-m diameter) should be sampled per 

existing vegetation strata, with plots located to best represent the strata. A list of common 

species for each strata can be developed from the sampling and observations at the site. 

Recommended measurements in the plots are 1) tree and shrub density, 2) canopy cover (using a 

densiometer), and 3) an estimate of herbaceous cover by species. The herbaceous and canopy 

cover data can be collected using cover classes such as outlined in Daubenmire (1959) as 

follows: 

Class Cover (%)

1 

2 

3 

4 

5 

6 

0–5 

6–25 

26–50 

51–75 

76–95 

96–100 

The information collected during this assessment is useful for determining a treatment 

plan, if necessary, and the planting scheme. 

Comprehensive monitoring 

For woody plants, the steps are: 

Step 1. Establish overall size of the planting area and mark boundaries with GPS (all 

four corners of site and more points if the shape is irregular). 

Step 2. Select sample plots throughout the site as described in Site Selection above, 

record each with GPS, and establish an 8-m diameter circular plot by laying an 8-m tape 

perpendicular to the transect tape to delineate each 8-m diameter tree plot with crosshairs. 

Step 3. To monitor trends at the site, choose a randomly selected subset of approximately 

one-third of the total number of plots to be permanent plots. These plots will be resampled each 

year. Mark the center of the plot with rebar or a PVC stake and record the GPS position. (Note: 

If a subset is chosen as permanent plots, then the number of sample plots will increase in future 

years in order to include new randomly selected plots and existing permanent plots.) 

Step 4. Identify and count all woody plants in all plots by species and record the 

following: 

• Live or dead 

45
• Natural or planted 

• Plant vigor as defined in three categories. 

Category Description

High Plants exhibiting remarkable growth and vigor 

Medium Plants exhibiting moderate growth and vigor and expected 

to live beyond the immediate growing season 

Low Plants expected to die within the year 

This measurement yields plant density as discussed in the Calculations and Analysis 

subsection below. 

Step 5. For sites 5 or 10 years old, record dbh for the stem closest to the center of the 

plot (must be at least 2-m tall). 

Step 6. Take four densiometer readings, using the Daubenmire Cover Classes described 

above at 1.4 m above the ground and 2 m from the plot center, facing north, east, south, and 

west. Record average measurement. 

Step 7. Estimate herbaceous cover by estimating the percentage of plot occupied by all 

species using Daubenmire Cover Classes. (Note: This is the herbaceous cover within an area 

planted with woody species, not to be confused with the section below describing monitoring 

methods for herbaceous plantings.) The information gathered in this step is important in 

identifying potentially competing vegetation. 

Step 8. Record observations on causes of plant mortality, animal activity, and other 

significant natural or anthropogenic occurrences. 

Step 9. Establish permanent photo points of the area planted as described in Protocol 4, 

landscape features. 

For herbaceous plants, the steps are: 

Step 1. Establish overall size of planting area or seeded area and mark the boundaries 

with GPS (all four corners of the site and more points if the shape is irregular). 

Step 2. Select sample plots throughout the site as described in Site Selection above, 

record each with GPS, and center 1 m2

 quadrat on cross transect meter tape so that the tape acts 

to divide the quadrat in two halves (this aids in estimating cover classes). 

Step 3. Estimate herbaceous cover by percentage of plot occupied by all species using 

Daubenmire Cover Classes. 

Rapid monitoring 

At each site, establish the location of sample plots as described in the Site Selection 

section above using the previously established baseline. The sample plots should be established 

using a new random start point along the baseline and new random start points on each transect. 

46
Identify and list native and nonnative species at the site. 

If woody species were planted, count the number of stems per plot as outlined above, but 

not by species. Calculate average number of trees and shrubs per acre (see below). 

Estimate percentage cover within the plot of nonnative weedy species. 

Recommend maintenance treatments such as removal of invasive species, additional 

planting, seeding, and animal damage control. 

4.6.8 Calculations and Analysis 

Obtain the number of plants installed per hectare (i) from the planting contractor. Sum 

the total number of live, installed plants (T) observed on all plots. Divide the total number of 

live, installed plants (T) by the number of plots sampled (n) to obtain the average number of live, 

installed plants per plot (Tp). 

Tp = T/n (1) 

Multiply the average number of live, installed plants per plot (Tp) by 200 to obtain the total 

number of live, installed plants per hectare (Th). Note: A 4-m radius plot equals 1/200th of a 

hectare. 

Th = Tp × 200 (2) 

Divide the total number of live, installed plants per hectare (Th) by the number of plants installed 

per hectare (i) to obtain the survival rate of installed plants. 

Survival rate = Th/i (3) 

Multiply the survival rate by 100 to assess percent survival against the performance goal for 

survival of initial planting stock (Figure 16). Use Th to compare total number of live plants to a 

reference site. 

4.6.9 Additional Information 

A densitometer is a small hand-held curved mirror grid. The canopy cover can be 

predicted by estimating the percent of the grid that is covered by the image of the canopy. 

47
Figure 16. Replanting with native shrub and tree species at a Columbia River estuary restoration site. 

4.7 Fish Community (Protocol 7) 

4.7.1 Purpose 

The incentive for many restoration activities in the CRE is to increase habitat available 

for rearing and migrating juvenile salmonid ESUs listed as threatened or endangered under ESA. 

One measure of success in effectiveness evaluations is a demonstration of increased habitat use 

by salmonids at restored locations relative to reference habitat. The minimum protocols for fish 

monitoring include abundance and size measurements of species at each site. From these basic 

data, species composition and size-frequency histograms can be produced. However, we 

advocate higher order measurements for quantitative assessment of habitat utilization by 

different salmon stocks and life history types, which require analysis of, for instance, genetics, 

marks and tags, and prey availability and consumption (see Additional Measurements 

subsection, below). Ultimately, relation of fish habitat use to physical conditions such as water 

quality (Protocol 1, hydrology, and Protocol 2, water quality) will be important for evaluating 

and predicting restoration success in the CRE. 

4.7.2 Goal 

Evaluate species composition (lowest practical taxon), temporal abundance patterns 

(catch per unit effort [CPUE] by date), and fish size (fork length or total length) in prerestoration 

habitat, postrestoration habitat, and reference sites. 

48
4.7.3 Design 

The BACIPS/recovery survey design with prerestoration measurements should be 

utilized whenever possible to establish baseline community structure (see 3.1 Statistical Design 

subsection, above). However, fish presence or absence in restored vs. reference sites is the 

minimal metric for comparing habitat use. Repeated sampling allows a time series of abundance 

to be generated, information that is used to calculate migration timing and overall habitat use for 

juvenile salmonids. Fish lengths are used to construct size-frequency histograms that help 

determine which life history stages are utilizing the various habitats (e.g., fry, smolt-sized 

subyearling, or yearling salmon). Standard indexes of community structure (catch, number of 

species, diversity) provide an assessment of the recovery trajectory of restoration relative to 

reference sites. Fish community metrics can be correlated with physical (Protocol 1, hydrology, 

and Protocol 2, water quality) and biological (Protocol 4, landscape features, and Protocol 5, 

plant species composition and cover) features to characterize habitat opportunity and capacity. 

4.7.4 Equipment 

There are a variety of gear types used for sampling juvenile salmon and other fish in the 

CRE, including seines, fyke (trap) nets, barrier nets, and pit traps, discussed in detail below. 

Particular gear choices depend largely on the physical conditions and constraints at the sites. 

Terrain, bottom contour, hydrography, and debris load will influence the gear type as well as the 

sampling location at a given site. For comparative purposes, it is highly desirable to utilize the 

same gear type throughout the monitoring program; however, the varied topography of wetland 

habitats may render this impossible, and often more than one gear type will be required to 

sample all sites of interest. 

Ancillary hardware and materials: Plastic buckets or garbage cans for holding containers 

(with 3/16-inch holes drilled in side for water overflow), battery powered aerators, plastic dish 

pan for anesthetic bath, buffered anesthetic solution (MS 222 solution at a concentration of about 

50 mg/liter), dip nets, measuring boards, portable scale for weights, and standardized waterproof 

data forms. 

Permits: Annually, a state fish sampling permit must be obtained from the Oregon 

Department of Fish and Wildlife or the Washington Department of Fish and Wildlife to conduct 

sampling in the Columbia River and its tributaries. An Endangered Species Act permit from 

NOAA Fisheries Service must also be obtained because of the likelihood that threatened or 

endangered Chinook, coho, and chum salmon and steelhead (Oncorhynchus mykiss) will be 

captured. 

4.7.5 Site Selection 

Sampling site selection depends on the physical conditions necessary for the available 

sampling gear. Sites should be selected in each habitat type of the restoration area. Sites within 

the reference area should be as similar as possible to those of the restoration area. Fixed or 

random stations can be established. Fixed sites offer the benefit of generating time-series 

measurements at locations where other monitoring metrics are being collected (e.g., data logging 

49
instruments or vegetation plots). Randomizing sampling sites allows measurement of sample 

variability across habitats. 

4.7.6 Sampling Periodicity 

The minimum sampling frequency is 1 day per month at each selected site during the 

March through October timeframe that encompasses the time period most salmonids are residing 

in or passing through the lower river and estuary. To the degree possible, the tide cycle and time 

of day for all samples should be standardized. 

4.7.7 Sampling Protocol 

Seines and nets of various shapes, sizes, and methods of deployment are used to sample 

fish community structure. Net type and size are dependent on the width, breadth, and depth of 

the water body. Ideally, catch measurements should be standardized to density (fish per m2

), 

although accurate determination of area swept may not be possible due to variability between 

sets. Abundances expressed as CPUE are therefore often reported, and it is important to be 

cognizant that CPUE values are not strictly comparable between different gear types. Below we 

discuss protocols for commonly used net types. 

Beach seines 

Beach seines (Figure 17) require a shoreline area with sloping beach for ease of 

collection. The length of the seine depends on the area to be sampled. General dimensions are: 

10–30 m long by 2 m deep using 1–2 cm (stretch measure) webbing and 0.6-cm mesh bunt in the 

middle. Two methods can be used to fish a beach seine: pull-to-shore and semicircular hauls. 

Use pull-to-shore haul for smaller tidal channels. 

Step 1. Deploy the seine on the bank parallel to the channel and situate personnel on 

opposite shore. 

Step 2. Retrieve net by pulling the two wings simultaneously to shore, being careful to 

maintain the leadline at the bottom. Crowd fish into the center bunt for capture, and transfer fish 

with a dip net to holding containers for measurement. 

Step 3. Area sampled is net length multiplied by channel width, A = L × W. Density = 

CPUE/A. 

Use semicircular haul for larger channels or unenclosed habitats. 

Step 1. Anchor one end of seine at the beach, and deploy net either in a pile or stretched 

along shore. 

Step 2. Using skiff, tow net in semicircular pattern back to shore. Haul net in from the 

free end to anchor end, forcing fish into the bunt for capture. Use a dip net to transfer fish to 

holding containers for measurement. 

50
Figure 17. Beach seining near the Kandoll Farm culvert replacement at a forested wetland. 

Step 3. Area sampled is a half circle with radius equal to the net length, A = 0.25 πr

2

. 

Density = CPUE/A. 

Pole seines 

Pole seines are usually smaller nets that can be fished in areas of topographic complexity 

that would foul larger nets. General dimensions are: up to 10-m length (but often smaller) and 

1.5-m depth (1–2 cm stretch measure with 0.6-cm mesh bunt in the middle). The fishing 

procedure is similar to seine nets. These versatile nets are easily adjustable for size of area, and 

can be utilized in many locations. However, CPUE may be correspondingly small. 

Fyke trap nets 

Fyke trap nets provide a method for sampling shallow, low velocity tidal channels. This 

gear type works best in blind tidal channels, but can also be used in conjunction with barrier nets 

(described in the following section) in open-ended tidal systems. The general trap design 

consists of a cylindrical trap tunnel ending in a sanctuary area, which is positioned in the main 

section of the tidal channel. For fish retrieval, it is convenient to have the cod end of the fyke 

constructed into a live floating box. Net wings stretch from either side of the trap mouth to the 

shoreline. As the tide ebbs, water and fish are funneled into the trap, where they are periodically 

recovered and measured. This gear is dependent on volitional entry and water current for 

entrapment, and works best in sections of tidal channel that drain completely, thus providing 

good estimates of fish utilization upstream of the trap. Sufficient depth for sanctuary of captive 

51
fish during low water periods is necessary. This method is useful for time-series measures of 

fish habitat use. 

Step 1. Set net tunnels (2 by 2 by 2 m long, 0.6-cm nylon mesh, with an attached fyke 

tunnel) at high slack tide at a point above which the marsh channel system completely dewaters 

on a sampling tide. 

Step 2. Attach upstream facing net wings of appropriate length with 0.6-cm mesh to act 

as a barrier net to deflect fish into the fyke tunnel during ebb current. 

Step 3. Periodically empty the trap and process catch. After the tidal channel has 

drained, continue sampling in the remaining upstream pools, if any, with pole seines and dip 

nets. 

Step 4. Density of fish is a function of wetted surface area, which is dependent on tidal 

amplitude. Area is best estimated by linking the water level (Protocol 1, hydrology) to marsh 

elevation (Protocol 3, elevation). Fish density = CPUE/area. 

Barrier nets or screened panels 

These nets are used in conjunction with traps and nets to close off all or portions of a 

sampling area to acquire greater precision of fish density calculations. Nets and panels are 

constructed of 1–2 cm webbing (of sufficient length and depth for the site) bordered with 

corkline and leadline or solid framework of any desired construction materials. Use in 

conjunction with seines and fyke trap nets for sampling short reaches. 

Step 1. Deploy panels to completely enclose upstream and downstream ends of channel. 

Measure area of channel enclosed. A = L × W. 

Step 2. Fish are collected within the blocked section with pole, pull-seines or beach 

seines. Continue seining until the catch approaches zero (depletion sampling). Catches should 

show an exponential decay pattern with increasing sweep number. 

Step 3. This technique provides a direct measure of fish density in discrete areas: Density 

(fish/m2

) = CPUE/area of channel. 

Pit traps 

Pit traps can be employed in shallow water marsh areas where small fish may reside but 

are not accessible by boats and are too shallow for seines. Brown plastic dish pans make an 

appropriate pit trap. The concept is to deploy the trap flush with the substrate during low tide. 

The trap samples over the next high water period and is recovered on the ensuing ebb tide. Fish 

are stranded or seek refuge in the water filled plastic dish pan. The disadvantage with this 

technique is that it is behaviorally based and not quantitative; but it may provide qualitative data 

on small juvenile fish underrepresented by other methods. Natural impoundments may be 

analogously sampled. 

Step 1. Bury traps flush with marsh surface at low water. 

52
Step 2. Allow tide to rise and fall; fish are passively collected during ebb tides from pit 

traps. 

4.7.8 Sample Processing 

After collection of fish by the gear types described above, use a dip net to transfer the 

catch into a darkened and covered holding container (to diminish stress). Ensure that the water 

quality (especially temperature and DO) of the holding container is maintained near river 

conditions during processing. Portable air bubblers are useful. If the numbers of fish are too 

large and must be subsampled (>100 salmon; >30 other species), ensure a random and unbiased 

subsample by crowding the fish together to limit stratification of different sizes and species. 

It is crucial to anesthetize active and energetic fish (such as salmon) to minimize stress or 

physical damage during measurements. Place a few fish at a time into anesthetic solution (e.g., 

MS 222) until fish become lethargic and loose equilibrium. Identify species and individually 

measure fork length of salmonids (tip of snout to center of fork in caudal fin) and fork length or 

total length (tip of snout to end of caudal fin) of other fish. After measurement, let the fish 

recover in a container of fresh river water, and maintain water quality prior to reintroducing the 

fish back to the river. For depletion sampling and trap nets, remember to release fish outside of 

area being sampled. 

4.7.9 Additional Measurements 

For restoration projects with extensive resources, increased sampling efforts and 

assessment protocols will provide estimates of enhanced fish production such as growth, 

residence time, feeding rate, and food resources. Some additional measurements commonly 

made during fish sampling surveys are presented below. 

All marks and tags should be recorded. External marks include fin clips (especially 

adipose fin), latex beads, freeze branding, and variously colored paint marks. Internal tags 

require detection equipment and include coded wire tags (CWT) and passive integrated 

transponder (PIT) tags. CWT data requires sacrificing the fish to collect the tag; data from PIT 

tags can be deciphered in the field with the appropriate instrument. 

Collection of genetic data: Small fin clips can be taken from anesthetized fish for 

subsequent analysis of stock identification. Clip tissue samples from a pelvic fin and preserve in 

separate plastic vials with 70% ethanol (ETOH), labeled with date, time, location, species, and 

size. 

Nonlethal collection of stomach contents by gastric lavage: This technique entails 

flushing a fish’s stomach with a stream of water and collecting and preserving the contents for 

laboratory analysis. Gut contents should be preserved in the field using ETOH and stored in 

individual vials labeled with species and site-specific data. 

Capture efficiencies can be determined by mark and recapture techniques. This requires 

releasing a known number of marked fish above a trap net or within a blocked barrier net section, 

and calculating the percent recaptured. 

53
4.7.10 Calculations and Analysis 

Absence or presence of catch is a minimum metric. Plot CPUE by time for a time series 

of abundance. To highlight timing of migration between sites or years, standardize CPUE by 

annual total (Figure 18). Wherever possible, report catch as density (fish/m2

) as described above 

in the subsection on barrier nets or screened panels. 

Size-frequency histograms are used to evaluate salmon life history categorization. Plot 

the length in 5-mm increments. Columbia River stocks vary in their size-at-age characteristics. 

In general, salmon are categorized as fry at less than 60-mm fork length and fingerlings between 

60 and 130 mm. Yearling salmon range in size from 90 to greater than 130 mm (Figure 19). 

Compute time series of mean size and SDs by species for each date sampled. This data 

may be indicative of residence time and growth. 

Compute standard measures of fish community structure. 

• Number of fish, N 

• Number of species, S 

• Shannon-Weiner diversity index, H’ = -Σpi ln(pi), where pi is the proportion of species i. 

4.7.11 Additional Information 

Fish identification sources are McConnell and Snyder 1972, Scott and Crossman 1973, Carl 

et al. 1977, and B.C. Ministry of Environment, Lands, and Parks 1997. For two-sweep depletion 

method, see Seber and LeCren 1967. 

J FMAMJ J A

0

20

40

60

80

100

J FMAMJ J A

0

20

40

60

80

100

J FMAMJ J A

0

20

40

60

80

100

2006

2007

Chinook Chum Coho

Restoration 

Reletive CPUE (%)

Reference

J FMAMJ J A

0

20

40

60

80

100

J FMAMJ J A

0

20

40

60

80

100

J FMAMJ J A

0

20

40

60

80

100

Month

Chinook Chum Coho 

) %( Relative CPUE 

Month

Figure 18. Time series of relative CPUE for salmonids sampled at restoration and reference sites, Grays 

River system, 2006 and 2007. This plot emphasizes migration timing. Upper row, restoration 

trap net samples; lower row, reference beach seine samples. 

54
0

10

20

30

40

50

0

20

40

60

0

10

20

30

40

50

Chinook Chum Coho

N=15 N=68 N=50

Percent occurance

25 50 75 100 125 150

0

10

20

30

40

50

25 50 75 100 125 150

0

20

40

60

25 50 75 100 125 150

0

10

20

30

40

50

N=15 N=15 N=26

Fork length (mm)

Restoration

Reference

Percent of occurrence 

Figure 19. Size frequency of juvenile salmonids captured in restoration and reference sites, Grays River 

system, 2007. Upper row, restoration trap net samples; lower row, reference beach seine 

samples. 

55
56
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Recent NOAA Technical Memorandums

published by the

Northwest Fisheries Science Center

NOAA Technical Memorandum NMFS-NWFSC96 Currens, K.P., R.R. Fuerstenberg, W.H. Graeber, K. Rawson, M.H. Ruckelshaus, N.J. Sands, and J.B. 

Scott. 2009. Identification of an independent population of sockeye salmon in Lake Ozette, Washington. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-96, 18 p. NTIS number PB2009-108060. 

95 Harms, J.H., J.A. Benante, and R.M. Barnhart. 2008. The 2004–2007 hook and line survey of shelf 

rockfish in the Southern California Bight: Estimates of distribution, abundance, and length composition. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-95, 110 p. NTIS number PB2009-106740.

94 Fleischer,G.W., K.D. Cooke, P.H. Ressler, R.E. Thomas, S.K. de Blois, and L.C. Hufnagle. 2008. The 

2005 integrated acoustic and trawl survey of Pacific hake, Merluccius productus, in U.S. and Canadian 

waters off the Pacific coast. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-94, 41 p. NTIS 

number PB2009-104774.

93 Keller, A.A., B.H. Horness, E.L. Fruh, V.H. Simon, V.J. Tuttle, K.L. Bosley, J.C. Buchanan, D.J.

 Kamikawa, and J.R. Wallace. 2008. The 2005 U.S. West Coast bottom trawl survey of groundfish resources off Washington, Oregon, and California: Estimates of distribution, abundance, and length composition. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-93, 136 p. NTIS number PB2008-113766.

92 Levin, P.S., M.J. Fogarty, G.C. Matlock, and M. Ernst. 2008. Integrated ecosystem assessments. U.S. 

Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-92, 20 p. NTIS number PB2008-113765.

91 Wainwright, T.C., M.W. Chilcote, P.W. Lawson, T.E. Nickelson, C.W. Huntington, J.S. Mills, K.M.S. 

Moore, G.H. Reeves, H.A. Stout, and L.A. Weitkamp. 2008. Biological recovery criteria for the Oregon 

Coast coho salmon evolutionarily significant unit. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-

 NWFSC-91, 199 p. NTIS number PB2008-113764.

90 Ward, L., P. Crain, B. Freymond, M. McHenry, D. Morrill, G. Pess, R. Peters, J.A. Shaffer, B. Winter, and 

B. Wunderlich. 2008. Elwha River Fish Restoration Plan–Developed pursuant to the Elwha River Ecosystem and Fisheries Restoration Act, Public Law 102-495. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-90, 168 p. NTIS number PB2008-111689.

89 Holt, M. 2008. Sound exposure and Southern Resident killer whales (Orcinus orca): A review of current 

knowledge and data gaps. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-89, 59 p. NTIS

 number PB2008-111688.

Most NOAA Technical Memorandums NMFS-NWFSC are available online at the

Northwest Fisheries Science Center web site (http://www.nwfsc.noaa.gov).