U.S. Department of the Interior

U.S. Geological Survey

Techniques and Methods 2-A7 

Prepared in cooperation with the NORTH COAST AND CASCADES NETWORK, NATIONAL PARK SERVICE

Protocol for Monitoring Fish Assemblages in 

Pacific Northwest National Parks

Chapter 7 of

Section A, Biological Science

Book 2, Collection of Environmental Data
Cover: Photographs of diver counting fish in Olympic National Park. Photographs 

reprinted with permission from Tony Overmann (diver in North Fork Skokomish River), 

Javin Elliff (South Fork Hoh River, background), and Ernest Keeley (mountain whitefish 

and summer steelhead).
Protocol for Monitoring Fish Assemblages 

in Pacific Northwest National Parks

By Samuel J. Brenkman, National Park Service; and Patrick J. Connolly, 

U.S. Geological Survey

Chapter 7 of

Section A, Biological Science

Book 2, Collection of Environmental Data

Prepared in cooperation with the

North Coast and Cascades Network, National Park Service

Techniques and Methods 2–A7

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

DIRK KEMPTHORNE, Secretary

U.S. Geological Survey

Mark D. Myers, Director

U.S. Geological Survey, Reston, Virginia: 2008

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Suggested citation:

Brenkman, S.J., and Connolly, P.J., 2008, Protocol for monitoring fish assemblages in Pacific Northwest National 

Parks: U.S. Geological Survey Techniques and Methods 2–A7, 130 p.
iii

Contents

Narrative..........................................................................................................................................................1

Acknowledgments.........................................................................................................................................1

Executive Summary ......................................................................................................................................1

1. Introduction.................................................................................................................................................2

2. Sampling Design ........................................................................................................................................7

3. Methods of Sampling .............................................................................................................................20

4. Pre-Field Operations................................................................................................................................23

5. Field Operations ......................................................................................................................................25

6. Data Handling, Analysis, and Reporting .............................................................................................27

7. Revisions to Protocol ..............................................................................................................................52

8. References Cited .....................................................................................................................................54

SOP 1: Use of GPS and Data Downloading ............................................................................................59

SOP 2: Data Entry and Verification ..........................................................................................................71

SOP 3: Data Quality Review and Certification .......................................................................................75

Appendix A. Photographs of Fish Species Commonly Observed in NCCN Rivers ...........................87

Appendix B. Photographs and Locations of Reference Sites for the Eight Rivers in 

 Olympic National Park ........................................................................................................88

Appendix C. Power to Detect Regional Trends in Run Size Using the Maximum Count 

 After 5, 7, 10, and 15 Years of Multiple Annual Snorkel Survey in Each of 

 Five Rivers..............................................................................................................................96

Appendix D. Power to Detect Trends on Individual Rivers in Run Size Using the 

 Maximum Count After 5, 7, 10, and 15 Years of Multiple Annual Snorkel 

 Surveys in a Single River.....................................................................................................97

Appendix E. Example of Snorkel Data Form Used in River Surveys...................................................98

Appendix F. Example of Electrofishing Data Form Used in River and Stream Surveys..................99

Appendix G. Existing Section 10A1a Permit Issued by NOAA Fisheries for Sampling 

 in MORA That Is Valid through December 31, 2011 ......................................................100

Appendix H. Yearly Project Task List......................................................................................................101

Appendix I. Database Documentation .................................................................................................105
iv

Figures

Figure 1. Map showing location of eight reference sites for long-term monitoring of

fish assemblages in OLYM rivers ......................................................... 9

Figure 2. Graph showing regression analysis used to detect long-term trend in run

size of bull trout in the North Fork Skokomish River from 1994 to 2005 ............... 17

Figure 3. Graph showing regional run size regression analysis used to detect

long-term trends on multiple rivers ...................................................... 18

Figure 4. Schematic diagram that depicts two divers snorkeling downstream to count

fish species in the reference site in the North Fork Skokomish River, OLYM......... 21

Figure 5. Photograph of sampling methods for electrofishing in streams (Mink Lake

Creek, Sol Duc River, OLYM) ............................................................... 22

Figure 6. Photograph showing a large woody debris complex in the Sol Duc River that

would be potentially hazardous at flows higher than those depicted ............... 26

Figure 7. Idealized flow schematic of the cyclical stages of project information

management, from pre-season preparation to season close-out ..................... 27

Figure 8. Recommended file structure for project workspace.................................... 28

Figure 9. Graph showing numbers of adult bull trout, cutthroat/rainbow trout, and

mountain whitefish in the reference site in the North Fork Skokomish River

based on snorkel surveys conducted from April to December 1996 .................. 35

Figure 10. Graph showing comparisons of mean monthly densities (fish/km) of

mountain whitefish in the East Fork Quinault (EFQR), North Fork Quinault

(NFQR), North Fork Skokomish (NFSR), and South Fork Hoh Rivers (SFHR),

Washington based on snorkel surveys in reference sites from June to

September 2005.............................................................................. 35

Figure 11. Graph showing mean monthly composition of adult bull trout, cutthroat/rainbow 

trout, and mountain whitefish in the South Fork Hoh River, Washington, based on 

11 snorkel surveys conducted in the reference site from June to September 2005...... 36

Figure 12. Graph showing trends in annual peak counts for adult bull trout and

mountain whitefish in the North Fork Skokomish River, OLYM from 1994 to 2006 ... 37

Figure 13. Graph showing comparisons of relative dates of peak counts for mountain

whitefish, bull trout, and cutthroat/rainbow trout among five rivers .................. 37

Figure 14. Graph showing mean monthly composition of adult bull trout,

cutthroat/rainbow trout, and mountain whitefish in the North Fork

Skokomish River, Washington based on 108 snorkel surveys conducted from

June to December, 1994 to 2006 ......................................................... 38

Figure 15. The estimated onset, peak, and end of migrations of adult bull trout (SACO)

and mountain whitefish (PRWI) in the North Fork Skokomish River using

snorkel data from 1994 to 2005 ............................................................ 39

Figure 16. Graph showing regression method for detecting abrupt change ..................... 41

Figure 17. Length-frequency histograms for rainbow trout in the middle and upper

Elwha River in June, July, August, and September 2004 and 2005 based on

backpack electrofishing .................................................................. 43
v

Tables

Table 1. Watershed characteristics of rivers that will be monitored for seasonal and

annual trends in fish assemblages in Olympic National Park ........................ 3

Table 2. Existing monitoring of Pacific salmonids that occur near reference sites of

the eight rivers in the Olympic National Park outlined in this protocol ............... 4

Table 3. Native and non-native fish species that inhabit watersheds that drain from

Olympic National Park with specific reference to river basins where species

have previously been observed............................................................ 10

Table 4. Fish species known to occur in Mount Rainier National Park and their

conservation status ........................................................................ 11

Table 5. Native and non-native fish species that inhabit watersheds that drain from

North Cascades National Park ............................................................ 12

Table 6. Specific locations of river reference sites in Olympic National Park and

Mount Rainier National Park based on Global Positioning System and pilot

fieldwork .................................................................................... 13

Table 7. Distribution of snorkel surveys in rivers in Olympic National Park and Mount

Rainier National Park during pilot field work, 2005–07 ................................. 14

Table 8. Characteristics of stream reference sites that will be monitored for

seasonal and annual trends in fish assemblages in Olympic National Park ......... 15

Table 9. Summary of response variables to detect seasonal and annual trends in fish

assemblages in rivers ..................................................................... 16

Table 10. Summary of response variables to detect seasonal and annual trends in fish

assemblages in wadeable streams ...................................................... 16

Table 11. Values of mean, variance, CV, auto-correlation, and number of rivers used in

the regional power analysis ............................................................... 19

Table 12. Proposed annual budget for implementation of the NCCN Fish Assemblages

Protocol in eight OLYM rivers and five OLYM wadeable streams ..................... 20

Table 13. Monthly schedule for hiring, training, field operations, data entry, and

reporting for monitoring of rivers and wadeable streams .............................. 23

Table 14. Functional comparison of the master project database and the working

database copy .............................................................................. 30

Table 15. Average run timing statistics for bull trout, mountain whitefish,

cutthroat/rainbow trout, and Chinook salmon in North Fork Skokomish River

based on snorkel counts in a 5 km reference site, 1994–2005 ........................ 38

Table 16. Summary of the number of fish observed by river and total number of

snorkel surveys from May through September 2005, based on pilot fieldwork ...... 40

Table 17. Means and coefficient of variations observed during replicate surveys of

the same river reach on the same day in 2005 for each of six rivers.................. 41

Table 18. Example of annual summary of the relative proportions of hatchery (marked)

and wild (unmarked) adult Chinook salmon, coho salmon, and steelhead

among reference sites in three coastal rivers .......................................... 42

Table 19. Example of a summary of the number of fish observed in a stream reference

site during electrofishing surveys in July and September of a given year ......... 42

Table 20. Example of a relational database application for storage of temperature

data collected using data loggers ......................................................... 44
vi

Conversion Factors

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

millimeter (mm) 0.03937 inch (in.)

kilometer (km) 0.6214 mile (mi)

meter (m) 3.281 foot (ft) 

Area

square meter (m2

) 10.76 square foot (ft2)

hectare (ha) 2.471 acre

square kilometer (km2

) 0.3861 square mile (mi2)

Mass

gram (g) 0.03527 ounce, avoirdupois (oz)

kilogram (kg) 2.205 pound, avoirdupois (lb)

Temperature in degrees Celsius (°C) may be converted to degrees Fahrenheit (°F) as follows:

°F=(1.8×°C)+32.

Temperature in degrees Fahrenheit (°F) may be converted to degrees Celsius (°C) as follows:

°C=(°F-32)/1.8.
Protocol for Monitoring Fish Assemblages in 

Pacific Northwest National Parks

By Samuel J. Brenkman, National Park Service, and Patrick J. Connolly, U.S. Geological Survey 

Narrative

Version 1.0

Revision History Log:

Revision Date Author Changes Made Reason for Change

Acknowledgments

Protocol development and pilot field work for this 

project were funded by the National Park Service (NPS) 

Inventory and Monitoring Program and the U.S. Geological 

Survey (USGS) Western Fisheries Research Center (WFRC), 

Seattle, Washington. The publication of this protocol was 

funded by USGS Western Fisheries Research Center, Seattle. 

We thank Phil Kennedy (NPS, OLYM), Andrea Woodward 

(USGS), Cat Hawkins Hoffman (NPS, OLYM), and James 

Peterson (USGS) for their support during the development 

of this protocol. Thanks to John Boetsch (NPS, OLYM) and 

Trent McDonald (WEST, Inc.) for their written contributions 

to the data management and statistical analyses sections, 

respectively. Thanks to Pat Crain (NPS, OLYM) and Katherine 

Beirne (NPS, OLYM) for their written contributions to the 

GPS section and for aerial photographs of reference sites. 

We thank Jennifer O’Neal (TetraTech Consulting), Christian 

Torgersen (USGS, University of Washington), one anonymous 

reviewer, and Marty Fitzpatrick (USGS, Forest and Rangeland 

Ecosystems Science Center) for their helpful comments to 

an earlier version of this protocol. We are grateful for the 

contributions of experienced field crew members: NPS-Phil 

Kennedy (crew leader for 3 years), Steve Corbett, Pat Crain, 

Chris Glenney, Matt Groce, Katy Hanna, Paul Olmsted, 

Carmen Welch, Ashley Rawhouser, Ben Wright, Heather 

Moran, and USGS biologists Brady Allen, Kyle Martens, 

Jodi Charrier, Jim Hatten, Ian Jezorek, Scott Sebring, Pete 

Kofoot, Jeff Duda, Steve Rubin, and Carrie Munz. We also 

thank Jeff Duda (USGS), Steven Fradkin (NPS), Jerry Freilich 

(NPS), George Pess (National Oceanic and Atmospheric 

Administration), and Reg Reisenbichler (USGS) for their 

valued input during development of this protocol. Ruth Jacobs 

(USGS) and Linda Rogers (USGS) provided technical edits 

and formatted the document for publication. We thank Jason 

Dunham, Javin Elliff, Philip RS Johnson, Ernest Keeley, and 

Tony Overmann for providing photographs that were used in 

this protocol.

Executive Summary 

Rivers and streams that drain from Olympic, Mount 

Rainier, and North Cascades National Parks are among the 

most protected corridors in the lower 48 States, and represent 

some of the largest tracts of contiguous, undisturbed habitat 

throughout the range of several key fish species of the Pacific 

Northwest. These watersheds are of high regional importance 

as freshwater habitat sanctuaries for native fish, where habitat 

conditions are characterized as having little to no disturbance 

from development, channelization, impervious surfaces, roads, 

diversions, or hydroelectric projects. Fishery resources are of 

high ecological and cultural importance in Pacific Northwest 

National Parks, and significantly contribute to economically 

important recreational, commercial, and tribal fisheries. 

This protocol describes procedures to monitor trends in 

fish assemblages, fish abundance, and water temperature in 

eight rivers and five wadeable streams in Olympic National 

Park during summer months, and is based on 4 years of 

field testing. Fish assemblages link freshwater, marine, and 

terrestrial ecosystems. They also serve as focal resources 

of national parks and are excellent indicators of ecological 
2 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

conditions of rivers and streams. Despite the vital importance 

of native anadromous and resident fish populations, there is no 

existing monitoring program for fish assemblages in the North 

Coast and Cascades Network. 

Specific monitoring objectives of this protocol are to 

determine seasonal and annual trends in: (1) fish species 

composition, (2) timing of migration of adult fish, (3) relative 

abundance, (4) age and size structure, (5) extent of nonnative and hatchery fish, and (6) water temperature. To detect 

seasonal and annual trends in fish assemblages in reference 

sites, we rely on repeated and consistent annual sampling at 

each monitoring site. The general rationale for the repeated 

sampling of reference sites is to ensure that we account for the 

high interannual variability in fish movements and abundances 

in rivers. One underlying assumption is that the monitoring 

program is designed in perpetuity, and consequently our 

capability to detect trends substantially increases with time. 

The protocol describes sampling designs, methods, 

training procedures, safety considerations, data management, 

data analysis, and reporting. The allocation of sampling effort 

represents a balance between ecological considerations, a 

sound monitoring approach, and practical limitations caused 

by logistical constraints and a limited annual budget of 

$55,000. The widespread declines of native fish species in 

western North America highlights the importance and urgency 

of understanding trends in fish assemblages from undisturbed 

habitats. Seasonal and annual trends in fish assemblages will 

provide insights at the individual, population, and assemblage 

level. 

This protocol will allow managers to detect increases 

and decreases in abundance of priority management species, 

and occurrence of non-native, hatchery, and federally 

listed fish. The detection of trends in fish assemblages will 

allow for specific management actions that may include: 

implementation of more appropriate fishing regulations, 

evaluation of existing hatchery releases, control of non-native 

fish species, and prioritization of habitat restoration projects. 

Dissemination and communication of scientific findings on 

North Coast and Cascades Network fish assemblages will be a 

core product of this protocol, which will have much relevance 

to decision makers, park visitors, researchers, and educators.

1. Introduction

A. Background

This protocol outlines the rationale, sampling design, 

and methods for monitoring fish assemblages, fish abundance, 

and water temperature in rivers in the North Coast and 

Cascades Monitoring Network (NCCN) during summer 

months. The protocol also outlines the sampling design and 

methods for monitoring juvenile fish assemblages in streams 

that are co-located with river monitoring sites. The protocol 

format and content is in accordance with Oakley and others 

(2003). The NCCN is 1 of 32 networks of parks in the 

National Park System that comprises 7 national park units in 

the Pacific Northwest. The NCCN includes Mount Rainier 

[MORA], Olympic [OLYM], and North Cascades National 

Parks [NOCA]) and 4 small historic-cultural parks including 

Ebey’s Landing National Historical Reserve, Lewis and Clark 

National Historical Park, Fort Vancouver National Historical 

Park, and San Juan Island National Historical Park. 

This protocol was designed for rivers in the NCCN 

that have high water visibility and are conducive to snorkel 

methods from June through September each year. Although 

this protocol was specifically designed for use in Pacific 

Northwest National Parks, it should be helpful in the 

development of protocols in other National Park Service units 

and other areas of the Pacific Northwest. The sampling of 

NCCN rivers is challenging because of high costs, arduous 

logistics, and safety concerns. The sampling design in this 

protocol addresses many of the challenges inherent in working 

in remote, roadless wilderness parks, and it is considered 

to be logistically feasible based on pilot studies conducted 

from 2004 to 2007. The protocol was extensively tested and 

evaluated in 10 OLYM rivers, 3 MORA rivers, and 3 OLYM 

streams. 

The protocol will be implemented in eight rivers and 

five wadeable streams in OLYM based on the importance 

and high priority of fishery resources in that park (table 1). 

The protocol will not be implemented in MORA or NOCA 

due to other higher monitoring priorities in those parks and 

because of funding constraints. In this protocol, we do provide 

information on watersheds and fish assemblages for all three 

large wilderness parks in the NCCN. The inclusion of other 

NCCN rivers for sampling purposes (for example, NOCA: 

Baker, Chilliwack, North Fork Cascade, Skagit, Stehekin 

Rivers; MORA: Ohanapecosh) would require additional funds, 

field testing, and perhaps the inclusion of alternate sampling 

methods to accommodate local conditions.

The NCCN rivers support numerous fish species and 

unique populations of Pacific salmon, trout, and char. OLYM 

is the only national park in the lower 48 States that contains 

significant numbers of wild Pacific salmonids with at least 

70 populations in park rivers (Houston and Contor, 1984). 

These salmonids are critical to ecosystem function, and 

link freshwater, marine, and terrestrial ecosystems. Pacific 

salmonids provide food for more than 130 species of aquatic 

and terrestrial wildlife species (Cederholm and others, 2001), 

and studies have shown that 20–40 percent of the phosphorus, 

nitrogen, and carbon in freshwater systems may be marinederived through carcasses of spawned salmon (Kline and 

others, 1990, 1994; Bilby and others, 1996).
1. Introduction 

3

Table 1. Watershed characteristics of rivers that will be monitored for seasonal and annual trends in fish assemblages in Olympic National Park.[Abbreviations: ha, hectare; km, kilometer; m, meter; m3/s, cubic meter per second; ft3/s, cubic foot per second; <, less than; WDOE, Washington Department of Ecology]

River

Watershed 

area 

(ha)

Percentage of 

watershed 

area in park

Elevation (m) River length (km) River 

gradients 

(percent)

Mean summer flow Maximum flows safe to snorkel

Anadromous 

fish present

Hatchery 

present

Drains into which 

water body Park 

boundary

Headwater Total Total in park m3/s ft3/s m3/s ft3/s River gage

Bogachiel 32,849 64 103 1,288 75.3 42.1 <1 15.5 1193 42.5 1,500 Calawah Yes Yes Quillayute River

Dosewallips 30,091 63 326 1,872 45.8 25.9 Upper 2–4 

Lower 4–8

NA 11.3 400 North Fork 

Skokomish River at Staircase

No No Hood Canal

East Fork Quinault 23,278 100 117 2,245 21.4 21.4 <1 NA 42.5 1,500 Quinalt 

River

Yes Yes Quinault River

North Fork Quinault 20,837 100 115 1,238 30.8 30.8 <1 NA 39.6 1,400 Quinalt 

River

Yes Yes Quinault River

North Fork 

Skokomish

31,081 48 225 1,622 251.8 22.7 Upper 2–4 

Lower <1

8.7 306 10.6 375 North Fork 

Skokomish River at Staircase

No Yes Lake Cushman

South Fork Hoh 11,338 79 244 1,318 31 24.3 <1 18.1 1287 42.5 1,500 Hoh River Yes No Hoh River

Sol Duc 19,442 29 318 1,440 105.6 25.9 1-2 13.8 1134 34.0 1,200 Sol Duc, 

WDOE

Yes Yes Quillayute River

North Fork Sol Duc 7,965 100 329 1,520 24.3 24.3 Upper 1–2 

Lower 2–4 

12.6 191 28.3 1,000 Sol Duc, 

WDOE

Yes Yes Sol Duc River

1Lieb and Thomas (2005).2Includes reservoirs.
4 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

In NCCN rivers, fishery resources are of high ecological 

and cultural importance, and contribute significantly 

to recreational, commercial, and tribal fisheries. Fish 

communities were ranked third among all potential vital 

signs to monitor in the NCCN. Fish assemblages that inhabit 

these rivers and streams serve as important benchmarks that 

define natural limits of variation and monitoring will identify 

rivers where management actions are necessary (Jenkins and 

others, 2003). The decline in native fish species in western 

North America highlights the importance of understanding 

patterns observed in least-disturbed habitats within the park 

boundaries.

Rivers and streams that drain from OLYM, MORA, 

and NOCA also have many key fish species other than 

Pacific salmon. There are several fish species in the NCCN 

that are non-commercially viable yet are ecologically and 

recreationally important. For instance, mountain whitefish 

have received little attention despite being one of the most 

abundant fish species in many river systems (Northcote and 

Ennis, 1994). Additionally, cutthroat trout are an important 

species targeted by recreational anglers. There are no existing 

monitoring programs for non-commercial fish species in 

watersheds that drain from OLYM (table 2).

Despite the vital importance of native anadromous and 

resident fish populations (Jenkins and others, 2003), there 

is no integrated monitoring program for fish assemblages in 

the NCCN. Historically, the monitoring of fish assemblages 

in rivers and streams has been extremely limited, and there 

are no published studies that describe the monitoring of fish 

assemblages in the any of the NCCN rivers. Perhaps this is 

not surprising due to the physical challenges (for example, 

visibility, high riverflows, and poor access) associated with 

sampling rivers in those national parks. Additionally, there has 

been an absence of fisheries scientists in the NCCN until the 

late 1980s. 

Generally, the fisheries studies that have occurred 

in NCCN rivers were limited in duration, limited to the 

summer sample season, or focused on a single species and 

not the entire fish assemblage (table 2). Recently, formal 

fish inventories were conducted in selected river basins in 

the NCCN (Brenkman and others, 2004, 2007a; Zyskowski, 

2007), and annual monitoring now occurs for several salmonid 

stocks in OLYM rivers where trend data dates back to 1989. 

There also have been species-specific studies published from 

rivers in OLYM (Brenkman and others, 2001; Brenkman and 

Corbett, 2005; Brenkman and others, 2007b, 2008a, 2008b; 

Connolly and Brenkman, 2008). Lastly, OLYM, Washington 

Department of Fish and Wildlife, and coastal tribes monitor 

escapements of selected stocks in portions of OLYM rivers as 

related to harvest management (table 2).

Table 2. Existing monitoring of Pacific salmonids that occur near reference sites of the eight rivers in the Olympic National Park 

outlined in this protocol. 

[No monitoring programs exist for non-salmonid fish species and all other monitoring programs are single-species focused. Information for surveys 

conducted by Quinault Indian Nation and Washington Department of Fish and Wildlife was based on personal communications with Larry Gilbertson and 

Roger Mosely, respectively. Abbreviations: rkm, river kilometer; OLYM, Olympic National Park; WDFW, Washington Department of Fish and Wildlife; 

N/A, not applicable]

River Fish 

species

Survey source: 

Agency/Tribe

Type of 

survey

Duration of 

monitoring

General location 

of monitoring 

sites (rkm)

Bogachiel Winter steelhead WDFW/OLYM Redds–Helicopter April–June 36.5–54.8

Dosewallips None None None None None

East Fork Quinault Winter steelhead Quinault Indian Nation Redds-Walking April–June 75.8–77.8

Spring Chinook Quinault Indian Nation Redds-Walking August–September 75.8–85.2

Fall Chinook Quinault Indian Nation Redds-Walking October–November 75.8–77.8

Fall coho Quinault Indian Nation Redds-Walking November–January 75.8–77.8

North Fork Quinault Winter steelhead Quinault Indian Nation Redds-Helicopter May 12.1–0

Spring Chinook Quinault Indian Nation Redds-Helicopter September 12.1–0

Fall Chinook Quinault Indian Nation Redds-Helicopter N/A 12.1–0

North Fork Skokomish Bull trout OLYM Snorkel October to December 48.1–45.5

South Fork Hoh Winter steelhead Hoh Tribe Redds-Walking March–June 0–2.6; 9.9–13.4

Spring Chinook WDFW Redds-Walking September–October 0–2.6; 9.9–13.4

Fall Chinook WDFW Redds-Walking October–December 0–2.6; 10.5–14.9

Fall coho WDFW Redds-Walking October–January 10.5–14.9

Sol Duc Summer coho OLYM Redds-Walking October–December 97.2–104.3

Winter steelhead OLYM/WDFW Redds-Walking April–June 98.9–104.7

North Fork Sol Duc Winter steelhead OLYM Redds-Walking April–June 3.6–6.8
1. Introduction 5

There have been widespread declines or extirpations of 

native fish populations in the Pacific Northwest rivers that 

have led to increased numbers of threatened or endangered 

species (Williams and others,1989; Nehlsen and others, 1991). 

Native fish in the NCCN face several potential threats that 

include overharvest, deleterious effects from hatchery fish, and 

non-native fish invasions. The decline of Pacific salmonids 

on the West Coast has been attributed to overharvest, 

displacement by non-native fish, influence of hatchery fish 

on wild fish, and habitat degradation (Bottom, 1995; Emmett 

and Schiewe, 1997; Francis, 1997). Of the 41 salmonid 

stocks on the Washington coast and Puget Sound, 26 were 

categorized as being at high risk of extinction, 8 at moderate 

risk, and 7 of special concern (Nehlsen and others, 1991). 

In the NCCN, a total of five fish species are listed as 

threatened under the Endangered Species Act including 

Puget Sound Chinook salmon, Puget Sound steelhead, Puget 

Sound/Coastal bull trout, Hood Canal summer chum salmon, 

and Lake Ozette sockeye salmon. MORA and NOCA each 

contain three federally threatened fish species. There are 

five fish species that are federally threatened in OLYM that 

occur in rivers that drain into the Hood Canal, Strait of Juan 

de Fuca, and the Washington coast. The rivers along the 

Washington coast that drain from OLYM contain some of the 

last remaining areas on the West Coast without a federally 

threatened salmon or steelhead ESU.

In OLYM rivers, migratory salmonids are especially 

vulnerable to harvest because they migrate outside the park 

for most of their life cycle, or require multiple watersheds 

throughout their life history (Brenkman and others, 2007b). 

Pacific salmon and steelhead are subjected to intensive 

recreational and commercial gill-net fisheries that operate 

most weeks of the year in coastal rivers of the NCCN. 

Recreational fishing is allowed within OLYM, MORA 

and NOCA, and is a $850 million industry each year in 

Washington State. Ultimately, commercial and recreational 

fishery’s greatly influence the number of adult salmonids that 

return to National Park waters. 

Past and present State and Tribal hatchery practices 

also pose threats to wild salmonids in the NCCN. Hatcheryproduced fish are used to supplement recreational and 

commercial fisheries with limited regard to their influence on 

park resources. The establishment of hatchery-origin fish in 

National Park rivers and streams is of particular concern based 

on the deleterious genetic effects of hatchery fish on wild 

populations. Hatchery fish, through interbreeding with wild 

fish, genetically alter wild populations, reduce fitness, and 

reduce genetic differentiation among stocks (Reisenbichler 

and McIntyre, 1977; Chilcote and others, 1986; Araki and 

others, 2007).

Invasions of non-native fish species also pose imminent 

threats to native fish fauna in NCCN rivers, and they are 

cited as a primary factor negatively influencing native fish 

assemblages throughout western North America (Fausch and 

others, 2006). Potentially significant threats to native fish in 

OLYM may be the invasion of Atlantic salmon (Salmo salar). 

Atlantic salmon are commercially raised in marine net pens 

in Washington State and British Columbia. Annual escapes 

of Atlantic salmon from pens are difficult to quantify but may 

approach 500,000 fish annually in British Columbia where 

Atlantic salmon have been documented ascending at least 78 

coastal rivers (www.biology.ualberta.ca/faculty/john_volpe). 

In Washington, catastrophic events resulted in the escape of 

107,000; 369,000; and 115,000 Atlantic salmon in 1996, 1997, 

and 1999, respectively (Amos and Appleby, 1999). Atlantic 

salmon have been observed in Olympic Peninsula rivers 

including the Elwha and Quillayute Rivers, both of which 

drain from the park. 

Non-native brook trout (Salvelinus fontinalis) also 

occur throughout MORA, NOCA, and OLYM, and became 

established from historic introductions in those parks. Brook 

trout pose particular threats to federally threatened bull 

trout (Markle, 1992; Rieman and McIntyre, 1993) and other 

important native fish species such as cutthroat trout (Peterson 

and Fausch, 2003; Peterson and others, 2004) and Chinook 

salmon (Levin and others, 2002; Izaak and others, 2007).

B. Rationale for Monitoring Fish Assemblages 

and Water Temperature as Indicators of 

Ecological Integrity

Rivers are among the most intensively managed and 

most severely degraded ecosystems on earth (Oberdorff and 

others, 2002). In the NCCN, rivers that drain from the large 

national parks are some of the last remaining free-flowing 

and unregulated systems in the lower 48 States. In the Pacific 

Northwest, there is limited information on fish assemblages 

from relatively pristine rivers such as those that drain from 

the NCCN parks. These rivers represent some of the largest 

tracts of contiguous, undisturbed aquatic habitat throughout 

the range of several west coast fish species, and are regionally 

important as freshwater habitat refuges for wild salmonids and 

other native fish species. These rivers serve as sanctuaries for 

critical life stages (for example, spawning and early rearing) 

of many species and many populations. The rivers also serve 

as relative undisturbed control systems to help gauge past 

and future changes in river systems throughout the Pacific 

Northwest.
6 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Every important aspect of the river ecosystem begins 

in headwater streams (Freeman and others, 2007). Protected 

river and stream corridors such as those at OLYM are rare in 

the Pacific Northwest where the best remaining habitats for 

native fish species are often restricted to higher elevations (Li 

and others, 1995). Habitat conditions in portions of rivers and 

streams identified in this protocol generally are undeveloped 

with little or no impervious surfaces, diversions, or 

hydroelectric projects inside the national parks. Consequently, 

the watersheds in OLYM are not subject to large-scale 

consequences of headwater alteration including downstream 

euthrophication, lower secondary productivity in downstream 

sites, and reduced viability of freshwater biota (see Freeman 

and others, 2007).

The fundamental sampling entity in this monitoring 

plan is the fish assemblage, which will serve as an indicator 

of ecological integrity. Fish assemblages in the NCCN are 

focal resources of parks (see Jenkins and others, 2003). 

Fish assemblages that inhabit rivers and streams represent 

critical components of biological integrity from ecosystem 

and public interest perspectives (Peck, D.V., and others, 

U.S. Environmental Protection Agency, unpub. data, 2000). 

These fish assemblages also can serve as excellent indicators 

of ecological conditions because they integrate effects from 

lower trophic levels (for example, fish being key predators and 

consumers in aquatic food webs), they integrate environmental 

variability at different spatial scales (Oberdorff and others, 

2002), and they are reasonably easy to identify (Plafkin and 

others, 1989). At the temporal scale, the longevity of fishes 

helps to “register” environmental alterations across long 

time periods (Schmutz and others, 2000). The life histories 

of many fish species are well understood, and therefore the 

presence or absence of specific taxa can be easily interpreted 

(Flotemersch and others, 2006). Freshwater and anadromous 

fish species also provide recreation for anglers and viewing 

by non-anglers. One disadvantage of using fishes as indicators 

in rivers is that fisheries management activities such as 

continuous stocking and harvest make it more difficult 

to distinguish between fishery-caused impacts and other 

anthropogenic alterations (Schmutz and others, 2000).

C. Monitoring Goals and Objectives

To guide monitoring in the National Park units, the 

goals for the National Park Service Inventory and Monitoring 

Program are to: (1) determine the status and trends in selected 

indicators of park ecosystems to allow managers to make 

better-informed decisions and to work more effectively 

with other agencies and individuals for the benefit of park 

resources, (2) provide early warning of abnormal conditions 

of selected resources to help develop effective mitigation 

measures and reduce costs of management, (3) provide data 

to better understand the dynamic nature and condition of park 

ecosystems, (4) provide reference points for comparisons with 

other, altered environments, (5) provide data to meet certain 

legal and Congressional mandates related to natural resource 

protection and visitor enjoyment, and (6) provide a means of 

measuring progress towards performance goals (http://science.

nature.nps.gov/im/monitor/docs/Vital_Signs_Overview.doc).

The primary goal of this monitoring protocol is to 

determine seasonal and annual trends in fish assemblages 

throughout reference sites of rivers and streams during 

summer months and disseminate that information to the public 

and decision makers. Trends are identified as continuing 

directional change in value of an indicator, generally up or 

down within season or among years (Larsen and others, 2004). 

Specific objectives of the protocol are to determine trends 

in: (1) fish species composition, (2) timing of migration of 

adult fish, (3) relative abundance, (4) age and size structure 

of juvenile fish, (5) extent of non-native fish and hatchery 

salmonids in reference sites throughout the park, and (6) water 

temperature.

D. Management Implications

This protocol is designed to provide an understanding 

of trends in fish assemblages from reference sites of OLYM 

rivers and streams. The protocol will provide insights at the 

individual, population, and assemblage level. Information 

derived from this monitoring may facilitate better management 

and conservation of native fishes in national parks. The 

scientific information obtained through this protocol has 

multiple applications for management decision-making, 

research, education, and promoting public understanding of 

park resources (http://science.nature.nps.gov/im/monitor/

Reporting.cfm). Specific management actions that may be 

linked to this protocol include harvest management, hatchery 

supplementation, control of non-native fish species, and 

habitat restoration projects.

This protocol will allow park managers to detect trends in 

high priority management species (for example, economically 

important species) with information on the number of fish 

species increasing and decreasing in abundance, the extent of 

non-native and hatchery fish invasions, and trends in federally 

threatened fish species (for example, bull trout). The protocol 

also provides information on magnitude of abundance of each 

fish species (10, 100, or 1,000), timing of migration of adult 

fishes, and growth of juvenile salmonids within reference 

sites. From a fish assemblage perspective, the protocol 

tracks changes in fish species composition within a river and 

allows general comparisons and correlations of trends in fish 

assemblages among rivers.

The seasonal and long-term trends in fish assemblages 

will provide specific and critical data to better inform park 

management. Knowledge of the presence, timing, and 

numbers of threatened fish species within a reference site 

can be used for compliance purposes and to establish work 

windows for road management projects along river corridors. 

Such information on fish assemblages also can be used to 

prioritize and maximize the benefits of habitat restoration 

projects such as culvert replacements and bridge constructions 

that improve fish passage.
2. Sampling Design 7

Information about migratory timing and relative 

abundance of fish species within reference sites can used to 

evaluate the most appropriate fishing regulations in a given 

river. As an example, the documentation of migratory timing 

of federally threatened North Fork Skokomish River bull trout 

was used to develop a fishing season (June to September) that 

provided recreational opportunity during summer months 

while protecting bull trout during their spawning migration 

from late September to December (for example, river closed).

Information on the relative numbers of hatchery fish in 

reference sites is critical to the successful management of 

wild fish. During pilot surveys for this protocol, we detected 

hatchery coho salmon and hatchery summer steelhead in the 

South Fork Hoh River—a river basin with no hatchery releases 

for those two species. That information was immediately 

used to attain funding to address the origin of those fish 

(for example, which hatchery) and to examine the extent of 

genetic introgression between hatchery and wild fish in that 

river. Additionally, information about hatchery fish inhabiting 

a reference site highlights the importance of implementing 

fishing regulations that target the harvest of hatchery salmon 

or steelhead in park waters.

Finally, the detection of non-native fish (for example, 

brook trout) in reference sites of rivers will provide an early 

warning signal for alien fish invasions in OLYM rivers. With 

annual sampling over several years, any future detection of 

non-native brook trout would prompt management actions that 

address the control of non-native fish in park rivers. 

2. Sampling Design

There is a lack of widely accepted sampling protocols 

for monitoring trends in fish assemblages in river systems. 

Aquatic environments are inherently difficult to sample 

(Fausch and others, 2002), and pose numerous challenges 

to sampling fish populations. Streams that are considered to 

be wadeable are relatively easy to sample when compared 

to sampling in rivers, and consequently the development of 

protocols for lotic systems has focused on wadeable streams 

(D.V. Peck and others, U.S. Environmental Protection Agency, 

unpub. data, 2000; Flotemersch and others, 2006). However, 

many of the sampling techniques for wadeable streams are 

infeasible in river systems (Flotemersch and others, 2006). In 

the NCCN, rivers are particularly challenging to sample using 

traditional fisheries techniques because of prolonged periods 

of high flow, low water visibility from glacial melt, poor 

access, safety concerns, and limitations on sampling methods 

that are allowed in National Park waters. Additionally, these 

challenges are compounded by the presence of migratory 

fishes, whose extensive movements in rivers add complexity to 

sampling (Torgersen, 2002).

The Environmental Monitoring and Assessment 

Program (EMAP; U.S. Environmental Protection Agency), 

Aquatic Riparian Effectiveness Monitoring Program 

(AREMP; U.S. Forest Service), and National Water-Quality 

Assessment Program (NAWQA; U.S. Geological Survey) 

are existing aquatic protocols that focus on monitoring fish, 

macroinvertebrates, and water quality metrics (Meador and 

others, 1993; D.V. Peck and others, U.S. Environmental 

Protection Agency, unpub. data, 2000; Moulton, 2002). 

Additionally, there are protocols designed to monitor fish in 

National Park units. Programs include the monitoring of coral 

reef fish in the South Florida and Caribbean Network and the 

monitoring of warmwater fish communities in the Buffalo 

National River and Ozark National Scenic Riverways in the 

Ozark Plateaus of Arkansas and Missouri (Menza and others, 

2006; Petersen and others, 2008). 

Many of the existing aquatic protocols use probabilitybased sampling (for example, EMAP) and are designed 

to evaluate changes in environmental conditions that vary 

across regions and change gradually over time (for example, 

pH in wadeable streams or mountain lakes) often with the 

explicit purpose of evaluating compliance with water quality 

standards. These protocols provide an understanding of the 

status or condition of natural resources, and allow inference 

over a large geographic area (for example, Western United 

States). Inferential designs in those protocols necessarily 

spread sampling across a broad area and focus on short sample 

reaches that are randomly chosen. This approach can be 

powerful because it avoids biases associated with selecting 

sites based on convenience and/or tradition. However, there 

are limitations to a probabilistic design.

Ideally, we want a monitoring program to provide 

meaningful extrapolation to an entire park and/or network 

of parks. However, given our program constraints, it is not 

possible to achieve an adequate sample size and/or frequency 

to be able to detect seasonal and annual trends in fish 

assemblages within an area as large as an entire park the size 

of MORA, NOCA, or OLYM. Under these circumstances, a 

viable alternative is to use a reference design, where sample 

size or frequency is adequate to detect the desired level of 

change. If changes are detected in the reference systems, 

additional work can confirm the scope of the change and 

suggest causal factors.

In this protocol, seasonal and annual trends in fish 

assemblages are determined by intensive and repeated 

sampling of reference sites in eight rivers and five wadeable 

streams. The general rationale for the repeated sampling 

of reference sites (about 10 surveys per river per year) is to 

ensure that we account for the high interannual variability 

in fish movements and abundances in rivers. We provide 

a sampling foundation of rivers distributed throughout the 

park from which additional reference sites may be added 

with additional funding. To detect seasonal and annual trends 

in fish assemblages in reference sites, we rely on repeated 

and consistent annual sampling at each monitoring location. 

One underlying assumption is that the monitoring program 

is designed in perpetuity, and consequently our capability to 

detect trends substantially increases with time. 
8 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

With respect to monitoring fish assemblages in NCCN 

parks, a probability-based design is not easily adapted to 

monitor fish movements or to examine seasonal and annual 

trends. A probability-based sampling design would only 

be effective to detect trends in OLYM rivers if sampling in 

both space and time were substantially increased. To attain 

A denser array and more frequent sampling of sites spread 

throughout the many aquatic habitats of OLYM would be 

desirable to attain, but the associated costs with this level 

of effort would increase by at least an order of magnitude. 

By annual sampling of all eight rivers that are conducive to 

snorkel methods during the summer, a large benefit is gained 

and allows for extrapolation of trends to the lower ends of 

OLYM rivers near the park boundary without the use of 

inferential statistics.

Because of the geographic diversity within OLYM (and 

the NCCN), we explored the possibility of a stratified design 

for sampling rivers in the four diverse regions of OLYM. A 

stratified design has some promise to intensify the efforts 

within a river, which would increase the ability to extrapolate 

to the watershed level. However, the uneven distribution of 

rivers within regions (n=1 to 4 per region) prevented extensive 

efficiency gained by stratification. 

Some limitations of the sampling approach in this 

protocol include: (1) reduced capability to extrapolate 

information gained to the watershed level, (2) lack of 

information on explanatory habitat variables (for example, 

flow, woody debris, habitat complexity), and (3) challenges in 

counting fish assemblages in shallow riffles during summer 

low-flow conditions.

A. Study Area

We include information on watersheds and fish 

assemblages for three large wilderness parks, OLYM, MORA, 

and NOCA. 

Olympic National Park 

Olympic National Park, a designated World Heritage Site 

and Biosphere Reserve located on the Olympic Peninsula, 

contains one of the largest contiguous areas of relatively 

pristine habitat throughout the range of several west coast 

fish species. Olympic National Park encompasses 373,133 

ha (922,000 acres) including the upper portions of 12 major 

river basins and 5,600 km of streams. The park is 96 percent 

designated wilderness, with roads, campgrounds, and 

structures comprising less than 1 percent of the total area of 

the park (Jenkins and others, 2003). The western part of the 

park receives the greatest precipitation in the conterminous 

United States with annual precipitation ranging from 180 

to 600 cm on Mount Olympus (Jenkins and others, 2003). 

Most of the precipitation occurs as rain in lowland areas and 

snowfall may exceed 1,300 cm. In most rivers, river discharge 

is strongly influenced by rainfall in winter and snowmelt in 

spring. Watersheds in the park generally are characterized 

as having steep slopes, short drainages, and high amounts of 

annual precipitation that cause river discharges to rise and 

decline rapidly with frequent high flows in the winter.

We identified four ecoregions within OLYM based on 

differences in climate, drainage aspect, downstream outlet, 

and accessibility to anadromous fish. Of the eight rivers in 

the protocol, four are located in the northwest region, two are 

located in the southwest region, and two are located in the 

southeast region (fig. 1). The remaining rivers that drain from 

OLYM were not included in this protocol because of poor 

water visibility during the summer months and/or high costs to 

access. These rivers include the Calawah, Duckabush, Elwha, 

Greywolf, Hamma Hamma, Hoh, Ozette, and Queets Rivers. 

Ranges of values for watershed characteristics for 

this protocol include 7,965 to 32,849 ha of watershed area, 

29 to 100 percent of watershed in the park, 103 to 329 m of 

elevation at park boundary, 1,288 to 2,245 m of elevation at 

headwaters, and 21 to 106 total river length in kilometers 

(table 1). Watersheds that drain the westside of the park 

(n=6) contain anadromous and non-anadromous species 

and watersheds that drain the eastside of the park (n=2) 

are inhabited strictly by potamodromous (for example, 

migrate entirely within freshwater) fish species because of 

natural barriers and dams that prevent upstream migration of 

anadromous fish.

Fish fauna in OLYM consists of primarily coldwater 

species in the families Salmonidae and Cottidae. There are 

nine species of Pacific salmonids and at least 70 unique 

populations (OLYM files). A total of 31 native and 5 nonnative freshwater fish species from 11 different families have 

been documented in OLYM waters (table 3). Both native wild 

populations and hatchery stocks of Pacific salmonids occur in 

OLYM. Photographs of fish species commonly observed in 

rivers and streams in this protocol are in appendix A.

On the western Olympic Peninsula, State and Tribal 

hatcheries produce and release millions of hatchery salmonids 

annually. There are widespread annual releases of hatchery 

winter steelhead, summer steelhead, fall coho salmon, 

summer coho salmon, sockeye salmon, chum salmon, and 

spring Chinook salmon in portions of rivers located outside 

park boundaries. As an example, more than 196 million 

hatchery sockeye salmon were released in the Quinault Basin 

since 1916 and about 1 million sockeye were released into 
2. Sampling Design 9

Figure 1. Location of eight reference sites for long-term monitoring of fish assemblages in OLYM rivers. 

Bars depict general location of reference sites that extend upstream of the park boundary.

Lake Ozette since 1937 (OLYM files). There also are total 

annual releases of 4.8 million coho salmon and 850,000 

winter steelhead into Peninsula rivers (National Oceanic and 

Atmospheric Administration, 1997; http://www.nwfsc.noaa.

gov/publications/techmemos/tm24/tm24.htm#toc). These 

released smolts are largely derived from only a few parent 

stocks (Busby and others, 1996). Recent estimates of the 

proportion of hatchery steelhead on natural spawning grounds 

in Olympic Peninsula rivers ranged from 16 (Quillayute River) 

to 44 percent (Quinault River) (Busby and others, 1996).

OLYM has exclusive jurisdiction over recreational fishing 

in the park, and generally permits fishing throughout the 

year. Coastal rivers provide popular sport fisheries for Pacific 

salmonids throughout the year, with angler effort typically 

the highest during periods when salmon and steelhead 

are migrating upstream. The park offers diverse fishing 

opportunities with an emphasis on catch-and-release of wild 

fish species and retention of hatchery and non-native fish. 

Tribal gill-net fisheries occur at the river mouths of coastal 

systems with netting scheduled during most weeks of the year. 
10 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Table 3. Native and non-native fish species that inhabit watersheds that drain from Olympic National Park with specific reference to 

river basins where species have previously been observed. 

[From OLYM files, Mongillo and Hallock (1997), Brenkman (1998), and Brenkman and others (2004). The presence of a fish species in a given watershed 

does not necessarily imply it occurs within OLYM. Abbreviations: OLYM, Olympic National Park; BOGA, Bogachiel; DOSE, Dosewallips; EFQR, East Fork 

Quinault; ELWH, Elwha; LCRES, Lake Crescent; NFQR, North Fork Quinault; NFSK, North Fork Skokomish; NFSR, North Fork Sol Duc; OZET, Ozette; 

QUEE, Queets; QUIL, Quillayute; QUIN, Quinault; SFHR, South Fork Hoh; SOLD, Sol Duc]

Common name Family Genus Species River(s)

Longnose sucker Catostomidae Catostomus catostomus NFSR

Largescale sucker Catostomidae Catostomus macrocheilus EFQR; QUIN

Largemouth bass1 Centrarchidae Micropterus salmoides NFSR, OZET

American shad1 Clupeidae Alosa sapidissima OZET

Riffle sculpin Cottidae Cottus gulosus BOGA; HOH; SOLD; QUIL; QUIN

Prickly sculpin Cottidae Cottus asper LCRES; NFSR; OZET; QUEE; QUIL; QUIN 

Shorthead sculpin Cottidae Cottus confusus BOGA; NFSR; NFQR; QUIN; SFHR; SOLD; 

Coastrange sculpin Cottidae Cottus aleuticus DOSE; HOH; QUIL; QUEE; QUIN 

Torrent sculpin Cottidae Cottus rhotheus BOGA; EFQR; HOH; NFQR; QUEE; QUIL; QUIN; SFHR; 

SOLD 

Reticulate sculpin Cottidae Cottus perplexus HOH; SFHR; QUEE; QUIL; QUIN; SOLD

Slimy sculpin Cottidae Cottus cognatus OZET 

Peamouth Cyprinidae Mylocheilus caurinus OZET; QUIN

Northern pikeminnow Cyprinidae Ptychocheilus oregonensis OZET; QUIN

Speckled dace Cyprinidae Rhynichthys osculus NFSR; QUEE; QUIN

Longnose dace Cyprinidae Rhynichthys cataractae HOH; QUEE; QUIL; QUIN

Redside shiner Cyprinidae Richardsonius balteatus OZET

Threespine stickleback Gasterosteidae Gasterosteus aculeatus ELWH; HOH; OZET; QUEE; QUIN 

Yellow bullhead1 Ictaluridae Ictalurus natalis OZET

Yellow perch1 Percidae Perca flavescens OZET

Pacific lamprey Petromyzontidae Lampetra tridentata BOGA, ELWH; HOH; OZET; QUIN; SOLD; SFHR

Western brook lamprey Petromyzontidae Lampetra richardsoni OZET; QUEE; QUIL; QUIN

Chinook salmon Salmonidae Oncorhynchus tshawytscha BOGA; EFQR; ELWH; HOH; NFSK2

; NFSR; NFQR; 

OZET; QUIN; QUIL; SFHR; SOLD

Pink salmon Salmonidae Oncorhynchus gorbuscha ELWH; HOH; SFHR; QUIN

Chum salmon Salmonidae Oncorhynchus keta BOGA; EFQR; ELWH; HOH; OZET; QUEE; QUIL; QUIN; 

SFHR

Sockeye salmon Salmonidae Oncorhynchus nerka BOGA; EFQR; ELWH; HOH; OZET; QUIL; QUIN; SOLD; 

SFHR 

Coho salmon Salmonidae Oncorhynchus kisutch BOGA; EFQR; ELWH; HOH; NFSR; NFQR; OZET; QUIL; 

QUIN; SFHR; SOLD

Steelhead Salmonidae Oncorhynchus mykiss BOGA; EFQR; ELWH; HOH; NFSR; NFQR; OZET; QUIL; 

QUIN; SFHR; SOLD

Rainbow trout3 Salmonidae Oncorhynchus mykiss DOSE; ELWH; LCRES; NFSR

Kokanee salmon Salmonidae Oncorhynchus nerka ELWH; NFSR; LCRES; OZET 

Cutthroat trout Salmonidae Oncorhynchus clarkii BOGA; EFQR; ELWH; LCRES; NFSK; NFSR; NFQR; 

SFHR; SOLD

Mountain whitefish Salmonidae Prosopium williamsoni BOGA; EFQR; HOH; NFSK; NFQR; QUIL; QUIN; SFHR; 

SOLD

Pygmy whitefish Salmonidae Prosopium coulteri LCRES

Atlantic salmon1 Salmonidae Salmo salar ELWH; QUIL

Bull trout Salmonidae Salvelinus confluentus EFQR; ELWH; HOH; NFSK; NFQR; SFHR; QUIN 

Dolly Varden Salmonidae Salvelinus malma EFQR; SOLD

Eastern brook trout1 Salmonidae Salvelinus fontinalis DOSE; ELWH; NFSR

Olympic mudminnow Umbridae Novumbra hubbsi HOH; OZET; QUIL QUIN; QUEE 

1

 Non-native fish species.

2

 Landlocked Chinook salmon.

3

 Landlocked rainbow trout.
2. Sampling Design 11

Table 4. Fish species known to occur in Mount Rainier National Park and their conservation status.

[From Barbara Samora, Mount Rainier National Park, written commun., November 14, 2007. N/A, not applicable]

Common 

name

Scientific 

name Origin Federal status

Coastal cutthroat trout Oncorhynchus clarkii Native None

Westslope cutthroat trout Oncorhynchus clarkii lewisi Introduced None

Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri Introduced None

Rainbow trout/Steelhead Oncorhynchus mykiss Native and introduced stock Steelhead threatened

Bull trout1 Salvelinus confluentus Native Threatened

Eastern brook trout Salvelinus fontinalis Non-native None

Coho salmon Oncorhynchus kisutch Native Species of concern

Chinook salmon Oncorhynchus tschawytscha Native Threatened

Sockeye salmon Oncorhynchus nerka Unknown None

Kokanee salmon Oncorhynchus nerka Introduced None

Mountain whitefish Prosopium williamsoni Native None

Shorthead sculpin Cottus confusus Native None

Torrent sculpin Cottus rhotheus N/A None

1

From Dehaan and others (2007).

Mount Rainier National Park

Mount Rainier National Park encompasses 95,357 ha 

(235,625 acres), is 97 percent designated Wilderness, and 

has 91 km2 (35 mi2) of permanent ice and snow. There are a 

total of 1,063 linear kilometers of rivers and creeks in MORA 

(151 km of rivers; 912 km of creeks; Barbara Samora, MORA, 

written commun., 2007). The major glacial rivers that drain 

from MORA include the Carbon, Nisqually, Puyallup (South 

and North Forks), Mowich (South and North Forks), Paradise, 

White (West Fork), Ohanapecosh, and Muddy Fork Rivers. 

The Ohanapecosh and Muddy Fork Rivers ultimately drain 

into the Columbia River and the other six rivers drain into the 

Puget Sound near Tacoma, Washington. The Ohanapecosh 

River is the only river at MORA that is conducive to sampling 

methods outlined in this protocol. It is not possible to conduct 

snorkel methods in the other rivers during summer months due 

to extreme flows, glacial melt, and low to no visibility.

The presence of hydroelectric dams precludes 

anadromous fish passage in the Puyallup, Mowich, 

Ohanapecosh, and Nisqually Rivers. Anadromous salmonids 

are transported above Mud Mountain Dam on the White 

River. The Carbon River is the only major basin that drains 

from MORA without a dam (http:/www.nps.gov/mora/

naturescience/fish.htm, accessed January 7, 2008). 

Fish fauna in MORA consists of coldwater species 

in the families Salmonidae and Cottidae. Mount Rainier 

National Park contains at least 10 species of fish (table 4). Of 

those 10 species, 7 are native to park waters and the others 

were introduced. There are three federally threatened fish 

species including Puget Sound Chinook salmon, Puget Sound 

steelhead and coastal and Puget Sound bull trout. Species 

that inhabit the park from previous hatchery plantings since 

around 1918 include brook trout, rainbow trout, Yellowstone 

cutthroat trout (Oncorhynchus clarkii bouvieri), and Westslope 

cutthroat trout (Oncorhynchus clarkii lewisi) (table 4). Brook 

trout and cutthroat trout inhabit the Ohanapecosh River. 

MORA maintains exclusive federal jurisdiction of recreational 

fisheries, and park fishing regulations generally are in 

accordance with those of the surrounding area waters of the 

State of Washington. The Ohanapecosh River is the only river 

with special regulations that limits it to fly fishing only. 
12 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

North Cascades National Park

North Cascades National Park was designated in 

1968 and encompasses 276,815 ha (684,000 acres). The 

park includes portions of the Baker, Cascade, Chilliwack, 

Nooksack, Skagit, and Stehekin Rivers. The upper Baker, 

Chilliwack, North Fork Cascade, Skagit, and Stehekin 

Rivers are systems at NOCA that may be conducive to 

snorkel sampling methods outlined in this protocol (Ashley 

Rawhouser, NOCA, written commun., December 31, 2007). 

Watersheds that drain from NOCA eventually flow into four 

major river systems: Columbia River, Fraser River, Skagit 

River and Nooksack River (Zyskowski, 2007). There are 

a total of about 6,500 km of rivers and creeks in NOCA 

(Zyskowski, 2007).

North Cascades National Park contains 28 fish species 

from seven different families (table 5). Of those 28 species, 

25 are native to park waters. Non-native fish species in 

NOCA include golden trout, lake trout, and brook trout. 

Table 5. Native and non-native fish species that inhabit watersheds that drain from North Cascades National Park.

[From Ron Holmes, North Cascades National Park, oral commun., December 18, 2007; National Park Service Species database]

Common name Family Genus Species Origin

Longnose sucker Catostomidae Catostomus catostomus Native

Largescale sucker Catostomidae Catostomus macrocheilus Native

Burbot Gadidae Lota lota Native

Prickly sculpin Cottidae Cottus asper Native

Coastrange sculpin Cottidae Cottus aleuticus Native

Torrent sculpin Cottidae Cottus rhotheus Native

Slimy sculpin Cottidae Cottus cognatus Native

Peamouth Cyprinidae Mylocheilus caurinus Native

Northern pikeminnow Cyprinidae Ptychocheilus oregonensis Native

Longnose dace Cyprinidae Rhynichthys cataractae Native

Redside shiner Cyprinidae Richardsonius balteatus Native

Threespine stickleback Gasterosteidae Gasterosteus aculeatus Native

Western brook lamprey Petromyzontidae Lampetra richardsoni Native

Chinook salmon Salmonidae Oncorhynchus tshawytscha Native

Pink salmon Salmonidae Oncorhynchus gorbuscha Native

Chum salmon Salmonidae Oncorhynchus keta Native

Sockeye salmon Salmonidae Oncorhynchus nerka Native

Coho salmon Salmonidae Oncorhynchus kisutch Native

Steelhead Salmonidae Oncorhynchus mykiss Native

Rainbow trout1 Salmonidae Oncorhynchus mykiss Native

Kokanee salmon Salmonidae Oncorhynchus nerka Native

Cutthroat trout Salmonidae Oncorhynchus clarkii Native

Golden trout Salmonidae Oncorhynchus aquabonita Non-native

Mountain whitefish Salmonidae Prosopium williamsoni Native

Pygmy whitefish Salmonidae Prosopium coulteri Native

Bull trout Salmonidae Salvelinus confluentus Native

Dolly Varden Salmonidae Salvelinus malma Native

Lake trout Salmonidae Salvelinus namaycush Non-native

Eastern brook trout Salmonidae Salvelinus fontinalis Non-native

1

Landlocked rainbow trout.

There are three federally listed and threatened fish species 

including Puget Sound Chinook salmon, Puget Sound 

steelhead and coastal and Puget Sound bull trout. NOCA 

maintains concurrent jurisdiction of recreational fisheries with 

Washington Department of Fish and Wildlife. The following 

was excerpted from http://198.238.33.67/fish/papers/north_

cascades_high_lakes/index.htm (accessed on January 7, 2008).

Introduction of fish into lakes within boundary of 

NOCA occurred as early as 1915 and by the early 

20th century, Federal and county agencies were 

stocking many wilderness lakes, including highelevation lakes within the current NOCA boundaries, 

with brook trout, rainbow trout, and cutthroat 

trout. By the time the Washington Department of 

Game was formed in 1933, several lakes within 

current park boundaries had already received fish 

introductions and harbored reproducing populations 

or were stocked periodically. Throughout the 1940s, 

1950s, and 1960s, the high lake fishery resource 

within current park boundaries continued to expand.
2. Sampling Design 13

B. Allocation of Sampling Effort Relative to 

Budget

The allocation of sampling effort in this protocol 

represents a balance between ecological considerations, a 

sound monitoring approach, and practical limitations caused 

by logistical and financial constraints. The general rationale 

for the repeated sampling of reference sites (about two surveys 

per month per river) is to ensure that we account for the high 

interannual variability in fish movements and abundances 

in rivers. The goal is to maximize the number of surveys 

in each reference site throughout the summer. Typically, 

snorkel counts are conducted every 7 to 10 days from June to 

September with as many as 10 surveys per reference site per 

year. Based on pilot fieldwork from 2004 to 2007, the sample 

design is repeatable and has minimal observer bias when using 

snorkel counts in rivers (McDonald, 2006). 

The sampling of NCCN rivers is difficult because of 

high costs, arduous logistics, safety concerns, and financial 

constraints. The sampling design in this protocol is designed 

to accommodate many of these challenges and is considered 

to be logistically feasible based on pilot studies conducted 

from 2004 to 2007. Substantial portions of rivers are rendered 

essentially inaccessible by prohibitively steep slopes, narrow 

canyons, periods of high flows, long distances from trails, and 

dangerous river crossings (Siegel and others, 2007). There are 

portions of rivers in the more remote parts of MORA, NOCA, 

and OLYM where a single fish sampling survey may require 

over a week of a crew’s time to reach, sample, and return. 

Constraints of funding necessitate the allocation of 

two field crews (four people total) to conduct snorkel 

and electrofishing surveys in reference sites from June to 

September. The protocol is cost effective and ensures that a 

number of sites are sampled under extremely limited budgets. 

Given the tight financial constraints currently anticipated for 

this project coupled with safety concerns, attempting to reach 

more remote places would consume an inordinate proportion 

of available resources and would greatly reduce the number of 

visits each year (see Siegel and others, 2007).

C. Number and Location of Sampling Sites

Fish assemblages will be monitored in reference sites 

located immediately upstream of the park boundary in each 

of eight rivers (fig. 1; table 1; appendix B). The protocol 

emphasizes portions of rivers immediately upstream of the 

park boundary as these reference sites typically minimize 

challenges to access. Specific locations of reference sites are 

included in table 6. The reference sites of rivers outlined in 

this protocol are comprised of mainstem and side-channel 

habitats with multiple types of habitat units (for example, 

pools, riffles, glides) throughout each reference site. Location 

of sites at the park boundary has the advantage of reflecting 

the integrated conditions of the watershed (appendix B). 

These river reference sites to be sampled in OLYM generally 

are characterized as unconstrained, productive floodplains 

that are utilized by numerous fish species when compared to 

remote reaches of upper watersheds that are largely confined 

and where physical barriers and waterfalls prevent upstream 

movements of migratory fish.

Table 6. Specific locations of river reference sites in Olympic National Park and Mount Rainier National Park 

based on Global Positioning System and pilot fieldwork.

[rkm, river kilometer]

River

Downstream 

boundary

Upstream 

boundary Location 

(rkm)

Latitude Longitude Latitude Longitude

Bogachiel 47.52.74 124.14.83 47.52.94 124.11.39 40.5–35.6

Dosewallips 47.43.58 123.09.15 47.44.14 123.00.07 25.9–23.5

East Fork Quinault 47.32.30 123.40.15 47.33.44 123.36.71 82.6–76.9

North Fork Quinault 47.32.31 123.40.18 47.34.11 123.38.93 4.4–0.0

North Fork Skokomish 47.30.13 123.19.06 47.31.19 123.20.04 48.1–45.5

South Fork Hoh 47.47.40 123.56.10 47.46.71 123.54.41 10.5–7.8

Sol Duc 47.59.19 123.53.70 47.59.19 123.53.70 101.6–97.2

North Fork Sol Duc 48.01.43 123.54.45 48.00.29 123.53.36 7.1–3.6

Ohanapecosh 46.45.36 121.33.53 46.46.98 121.33.31 10.1–6.3
14 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

The completion of pilot work in OLYM rivers (2004–07), 

OLYM wadeable streams (2005 to 2007), and MORA rivers 

(2006–07) provided opportunities to test and streamline field 

methodologies and analytical approaches. The pilot studies 

produced datasets that were used to allocate effort (table 7).

Selection criteria for reference sites included: no physical 

barriers to fish movements, high underwater visibility, and safe 

access. Minimum criteria for depth, river size, and visibility 

need to be met for snorkel surveys to be optimal (Johnson and 

others, 2007). The selected rivers and corresponding reference 

sites met the following criteria: minimum recommended depth 

of 20 cm (Johnson and others, 2007); underwater visibility of 

at least 5 m from June to September; and gradients of less than 

4 percent. Additionally, reference sites needed to be accessible 

by road or trail with hike times less than 4 h/d. 

The following are approximate drive times (round trip 

from Port Angeles), duration of hiking, and duration of 

snorkeling for each reference site: 

Table 7. Distribution of snorkel surveys in rivers in Olympic National Park and Mount Rainier National Park during pilot field work, 

2005–07.

[Dates of snorkel surveys: X, 2005; Y, 2006; Z, 2007]

Rivers

Dates of snorkel surveys

May 15 May 22 May 29 June 5 June 12 June 19 June 26 July 3 July 10 July 17

North Fork 

Skokomish

X X X X, Y X, Y, Z X, Y, Z X, Z

Dosewallips

North Fork 

Quinault

X X, Y, Z

East Fork Quinault X X X, Y Z

Sol Duc Y X X, Y X, Y, Z X, Y, Z Z X, Z

North Fork Sol Duc Y Y Z Z Y

Bogachiel Y X Y X, Z Y X, Y, Z Y X, Y, Z X, Z

South Fork Hoh X X,Y X, Z X X, Y

Ohanapecosh Z Y

Rivers

Dates of snorkel surveys

July 24 July 31 Aug. 7 Aug. 14 Aug. 21 Aug. 28 Sept. 4 Sept. 11 Sept. 18 Sept. 25

North Fork 

Skokomish

X X, Z X, Z Z X X, Y, Z Z Y

Dosewallips Z Y Y, Z Z Y, Z

North Fork 

Quinault

X,Y Y, Z Z Y X, Y Z X,Y Z Y, Z X, Z

East Fork Quinault X, Y X, Y, Z X, Z Y X, Y Z X, Z Y, Z Y, Z X

Sol Duc X, Y Y, Z Y, Z X, Z X, Y, Z X, Z Y

North Fork Sol Duc Z Y Y, Z

Bogachiel X, Y, Z X, Y Y, Z X Y X, Z Z X Y, Z

South Fork Hoh X, Y X, Y, Z Y, Z X, Z X, Y Z Z X X, Z Y, Z

Ohanapecosh Z Y Z Y

Reference site Drive 

time (h)

Duration of 

hiking (h)

Duration of 

snorkeling (h)

Bogachiel 3.0 7.5 mi in 2 h 2.0–3.5

Dosewallips 3.0 5–6 mi in 2 h 1.0–1.5

East Fork Quinault 5.5 0.50 2.0–3.75

North Fork Quinault 5.5 0.50 2.0–3.75

North Fork Skokomish 5.0 0.50 1.5–2.5

North Fork Sol Duc 2.0 1 2.5–4.0

Sol Duc 2.0 0.75 2.25–3.5

South Fork Hoh 4.5 1.75 1.5–3.0
2. Sampling Design 15

Table 8. Characteristics of stream reference sites that will be monitored for seasonal and annual trends in fish assemblages in 

Olympic National Park.

[Length: From Phinney and Bucknell (1975). Fish species: From Brenkman and others (2004) and OLYM files. Abbreviations: km, kilometer; ha, hectare; 

OLYM, Olympic National Park]

Creek/

river

Length 

(km) 

Estimated 

watershed 

area (ha)

Percent of 

watershed 

in OLYM

Fish species

Mink Lake Creek, Sol Duc 3.7 639 100 Brook trout, coho salmon, cutthroat trout, rainbow trout/ 

steelhead, and sculpin spp.

Slate Creek, North Fork Skokomish 4.2 688 100 Bull trout, cutthroat trout, and sculpin spp.

Indian Creek, Bogachiel 2.3 267 100 Cutthroat trout, rainbow/steelhead, riffle sculpin.

Big Creek, Quinault 16.2 2,226 100 Chinook salmon, coho salmon, sockeye salmon, rainbow/

steelhead, torrent sculpin, and prickly sculpin.

Pass Creek, Dosewallips 2.9 344 100 Rainbow trout.

D. Co-Location of Wadeable Stream Sites

Although snorkel surveys in this protocol provide key 

information on fish assemblages in rivers, they do not provide 

complete life history information because young-of-the-year 

and juvenile fish are not counted. An approach to document 

trends in early life history stages is to use electrofishing 

techniques in wadeable streams that are co-located with river 

sites. The complementary use of snorkel and electrofishing 

surveys provides a more complete understanding of adult and 

juvenile fish assemblages. 

Because tributary streams are highly linked to life 

history patterns and strategies for many of the fish species 

within park boundaries, it is considered important to include 

wadeable streams in the protocol. Many wadeable tributary 

streams represent natal and rearing areas for Pacific salmon, 

steelhead, bull trout, and other species. Juvenile and adult 

fish use small tributary for various lengths of time (hours to 

months) for various reasons (for example, spawning, feeding, 

predator avoidance, thermal refugia). Efficiency can be 

gained if sampling efforts in wadeable tributary streams are 

located near river sampling sites. Without this co-location, the 

additional effort to sample wadeable streams would likely be 

infeasible because of anticipated funding limits. If funding is 

not an issue, then the constraint of co-locating wadeable sites 

with river sites could be dropped, and in its place, could be 

a stratified design that includes enough wadeable streams to 

represent the inherent variability. 

Wadeable streams offer enhanced sampling opportunity. 

In small wadeable streams, backpack electrofishing is 

an effective way to collect fish under a defined sampling 

methodology that will allow important fish metrics to be 

collected. With fish in hand, samplers can readily measure 

length and weight, as well record species, take samples of 

tissue (for example, scales for ageing, fin clip for genetics), 

and make general observations of fish health.

Budget constraints limited sampling to five wadeable 

streams (table 8). Selection criteria for reference sites 

included: no physical barriers to fish movements, safe access, 

and the presence of anadromous and/or potamodromous fish 

species. Reference sites include Mink Lake Creek (Sol Duc), 

Slate Creek (North Fork Skokomish River), Indian Creek 

(Bogachiel River), Pass Creek (Dosewallips River), and Big 

Creek (Quinault River).

The following are approximate round trip drive times 

(from Port Angeles), hike times, and duration of electrofishing 

surveys in reference sites of wadeable streams.

Reference sites 

of wadeable 

streams

Drive 

time (h)

Duration of 

hiking (h)

Duration of 

electrofishing 

survey (h)

Mink Lake 2.0 0.5 2.0–3.5

Slate Creek 5.0 0.5 2.0–3.5

Indian Creek 3.0 10 mi in 3.5 h 2.0–3.5

Pass Creek 2.0 10 mi in 3.5 h 2.0–3.5

Big Creek 5.0 0.25 2.0–3.5

E. Frequency and Timing of Sampling

The frequency and timing of sampling differs with the 

gear being used (snorkeling or electrofishing) and with the 

type of site being sampled (wadeable stream or river). Snorkel 

surveys will be conducted every 7–10 days from June to 

September throughout the 5-km or less reference sites with 

as many as eight surveys per river per year. Sampling of 

wadeable streams by electrofishing will occur in five streams 

per year with each stream to be sampled once in July and once 

in September.
16 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

F. Selected Monitoring Variables

The following variables will be measured in each 

reference site of eight rivers: (1) relative abundance and 

density (fish/km) of each species by date, (2) species 

composition by date, (3) mean onset, peak, and end of 

migration, (4) percent of hatchery and wild salmonids, and 

(5) number of non-native fish species by date (table 9). For 

reference sites in streams, the following variables will be 

measured: (1) relative abundance, (2) fish biomass (g/m2), 

(3) fish density (fish/m2), (4) species composition by date, 

(5) and fish growth (July and September) (table 10). 

We will monitor continuous water temperature in rivers 

and streams. The reported metrics include daily maximum, 

daily minimum, and daily average water temperature at each 

reference site in rivers and streams. 

Table 9. Summary of response variables to detect seasonal and annual trends in fish assemblages in rivers.

Monitoring 

metric Response Data summary

Reported 

by 

Frequency of 

reporting

Fish Trends in relative 

abundance (rivers) 

Annual peak count; regression versus time Species for each river in 

each year

Annually

Species composition 

(rivers)

Mean monthly species composition 

(percent)

Species for each river in 

each month

Migration timing 

(rivers)

Mean onset, peak, and end of migration; 

smoothed counts versus Julian date

Species for each river 

Observer variability 

(rivers)

Estimate residual standard error; 

coefficients of variation

Species for each river during 

dates of replicate surveys

Once every 3–5 

years

Abrupt change 

detection (rivers)

Regression over time on past data and 

computation of 95 percent prediction 

interval for next point

Species for each river Once in 5 years

Continuous 

water 

temperature

Daily average

(rivers)

Average and averages over warmest and 

coolest 7-day period

River Annually

Daily maximum 

(rivers)

Average and maximum daily average; 

average over warmest consecutive 

7-day period

Daily minimum 

(rivers)

Average

Table 10. Summary of response variables to detect seasonal and annual trends in fish assemblages in wadeable streams. 

[g/m2., gram per square meter]

Monitoring 

metric Response Data summary

Reported 

by 

Frequency of 

reporting

Fish Age/size (streams) Length frequency distribution (ages 0 and 1) Species by month in each year Annually

Species composition 

(streams)

Mean monthly species composition (percent) Species for each river in each 

month

Fish growth (streams)

Fish biomass (streams)

Mean length (age 1 fish); g/m2 Species for each stream in each 

month

Continuous 

water 

temperature

Daily maximum 

(rivers and streams)

Average and maximum daily average; 

average over warmest consecutive 

7-day period

Stream Annually

Daily minimum 

(rivers and streams)

Average

Daily average 

(rivers and streams)

Average and averages over warmest and 

coolest; 7-day period
2. Sampling Design 17

Figure 2. Regression analysis used to detect long-term trend in run size of bull trout in 

the North Fork Skokomish River from 1994 to 2005. 

Statistical power is defined as the probability that the regression analysis correctly 

rejects the null hypothesis H0: slope = 0 (McDonald, 2006). Power=Probability that the null 

hypothesis of no trend is rejected when trend is actually occurring=probability of correctly 

detecting trend.

G. Level of Change That Can Be Detected for the 

Amount and Type of Sampling

The statistical power of the proposed sampling program 

to detect seasonal and annual trends in fish abundance within 

reference sites was evaluated by WEST Inc. We examined data 

from snorkel surveys conducted in the North Fork Skokomish 

River from 1994 to 2005. The snorkel methods used to collect 

these data were identical to those outlined in this protocol.

The following summary of results was taken from 

McDonald (2006). Given the importance of estimating trends 

in relative abundance, it was important to investigate the 

statistical power and which metric (for example, annual peak 

count, average of three peak counts) was most responsive to 

long-term trends in run size. This investigation involved a 

power analysis, which computed the ability of each estimator 

to detect trends when it was used as the response in a 

regression model. Power of each estimator was investigated at 

both the regional (multiple river) and individual river scales. 

To estimate power, appropriate regional and individual 

trend detection analyses were required. Using regression, 

annual trends in relative abundance was estimated as the slope 

of the line that resulted when abundance was fitted onto year 

of the survey. If slope of this regression line was significantly 

non-zero, a trend was defined to have been detected. Statistical 

power was the probability that this regression analysis 

correctly detected a trend. In other words, statistical power 

was the probability that the null hypothesis of no slope was 

rejected, assuming that the true slope was non-zero. The 

regression analysis used to detect trend in run size is illustrated 

in figure 2. 

Regional trend analyses were designed to detect a 

consistent change in the size of all runs in rivers that contained 

a certain fish species. Power to detect trends on a regional 

scale was estimated from a regression analysis that fitted a 

common slope to run sizes on all rivers in the analysis. Similar 

to the individual river analysis, power was defined as the 

probability of correctly rejecting the null hypothesis that the 

1994

200

0

400

600

800

1,000

Run Size Estimate

Linear Regression

POWER = Probability null hypothesis 

of no trend is rejected when trend is 

actually occurring = Probability of 

correctly detecting trend

Trend is occurring if true slope ≠ 0

1996 1998 2000

YEAR

2002 2004 2006

FISH PER KILOMETER
18 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

common slope across all rivers was 0. In general, the regional 

analysis should have more statistical power to detect a trend 

than individual river analyses because the regional regression 

analysis has many more points. The regression analysis that 

estimates a regional slope, assuming two rivers contained the 

same species of interest, is illustrated in figure 3.

Given these regional and individual river regression 

analyses, statistical power was computed using the statistical 

theory surrounding each analysis. Under the assumption 

that run size estimates follow a normal distribution and 

that correlation through time in residuals of the analysis 

Figure 3. Regional run size regression analysis used to detect long-term trends on multiple 

rivers. 

A common slope was estimated for the two rivers and regional trend was defined to be 

occurring if the common slope was significantly different from zero. Power=the probability 

that the null hypothesis of no common trend is rejected when the trend is actually 

occurring=probability of correctly detecting trend.

followed an exponential model, the probability of declaring 

an estimated slope to be significantly different from zero was 

computed. 

Power of the analysis to detect different sized true trends 

was computed and graphed. True trends were defined as 

total percent change after T years, where T was set to 5, 7, 10 

and 15 years. The trend (total percent change) that could be 

detected with 80 percent power after 10 years of sampling was 

also computed. The run size estimator with highest power for 

a given true trend, or the estimator detecting the lowest total 

percent change with 80 percent power after 10 years, was the 

estimator deemed most responsive to trends in run size. 

1994

200

0

400

600

800

1,000

 River 1

 River 2

Linear Regression

POWER = Probability null hypothesis of no 

common trend is rejected when trend is actually 

occurring = Probability of correctly detecting trend.

Common, or “average”, slope is found by

forcing estimated lines to be parallel

Trend is occurring if true 

common slope ≠ 0

1996 1998 2000

YEAR

2002 2004 2006

FISH PER KILOMETER

 Run Size Estimate
2. Sampling Design 19

The North Fork Skokomish was the only river with 

multiple years of snorkel surveys that could be used to 

estimate power to detect trends on an individual river. This 

river also dominated computation of means, variance, and 

correlations in the regional analysis. Consequently, the 

primary difference between reported power to detect trends at 

the regional scale and power to detect trend on an individual 

river was the reduced overall sample size of the individual 

analysis (for example, one river’s data versus n rivers’ data).

Mean run size statistics, variation, coefficient of 

variation, and auto-correlation estimated from a linear 

regression of fish density on year and river, and used in the 

regional power analysis are shown in table 11. The regional 

trend detectable with 80 percent power after 10 years of 

data collection using each of the three candidate run size 

estimators (maximum count, mean of three maximum counts, 

and smoothed maximum) also is included in table 11. Total 

change detectable with 80 percent power after 10 years was 

consistently smaller for maximum count than the other two 

run size statistics. This implied that maximum count on any 

single snorkel survey provided the highest power to detect 

regional trends (table 11). Power curves from which the 

numbers in table 11 were computed appear for maximum 

count only (appendix C). Power curves for the other two run 

size statistics were lower than those for maximum count. 

The three estimators of runs size performed similarly 

relative to one another when used to detect a trend on 

individual rivers. That is, maximum count on a single snorkel 

survey appeared to have the highest power to detect trends. 

Because of the reduced sample size when analyzing data from 

one river, power to detect trends on individual rivers was less 

than power to detect trends in a region (appendix D). Means, 

variance, and autocorrelations used in the power analysis, 

and estimated from North Fork Skokomish, are shown in 

appendix D.

From the power analysis, the maximum observed 

count (for example, annual peak count) provided the highest 

power to detect trends in regional and individual river fish 

populations. This result was somewhat unexpected. Little 

difference was expected a priori between power of maximum 

count and power of the mean of the three maximum counts, 

and the smoothed maximum. Although relatively little 

difference in power between these three estimators was 

observed (table 11), power of the maximum count was 

consistently higher than that of the others. The higher power 

of the maximum count was attributed to its responsiveness 

and ability to change quickly. The other estimators, being 

averages, were naturally less responsive and changed more 

slowly. Higher responsiveness can, in some cases, also mean 

higher variance, but apparently this was not true here. The 

maximum count apparently had low enough natural variation 

that it was able to respond to real changes in fish abundance 

quicker than the other two estimators. 

Although the power analysis was primarily designed to 

assess and compare power of the three run size estimators, 

it also can be used to gauge the relative number of rivers 

required to detect a certain sized trend. Assuming that trends 

are assessed after 10 years of data collection, the current level 

of effort (for example, about one survey every 2 weeks) can 

detect from 89 to 121 percent regional trend with 80 percent 

power using data from four to six rivers (table 11). These 

numbers indicate that a doubling or halving of the regional 

population in 10 years would be detected with 80 percent 

power.

Table 11. Values of mean, variance, CV, auto-correlation, and number of rivers used in the regional power analysis. 

[Total change detectable: Total percent change in run parameters detectable with 80 percent power after 10 years of data collection (adapted from McDonald, 

2006). Abbreviations: CV, coefficient of variation; %, percent; Max, maximum]

Species Response Mean Residual 

variance CV Auto-correlation (ρ)

Number of 

rivers (n)

Total change 

detectable (%)

Bull trout Max count 41.7 19.86 0.48 0.26 4 88.9

Mean max 27.9 20.24 .72 -.3 4 90.1

Smooth max 29.7 17.22 .58 .29 4 110.2

Mountain 

whitefish

Max count 222.1 196.59 0.89 -0.25 5 102.3

Mean max 157.4 119.40 .76 .19 5 120.7

Smooth max 164.2 138.82 .85 -.03 5 116.2

Cutthroat/ 

rainbow trout

Max count 66.5 51.78 0.78 -0.14 6 89.7

Mean max 49.3 45.70 .93 -.28 6 95.3

Smooth max 41.7 34.33 .82 -.14 6 94.9

Chinook salmon Max count 3.6 3.19 0.88 -0.18 6 99.1

Mean max 2.1 1.83 .88 -.11 6 103.3

Smooth max 2.2 2.32 1.03 -.19 6 114.6
20 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Decreasing the size of trend detected with 80 percent 

power further would require the sampling of more rivers. 

The results from pilot surveys included four to six rivers 

for each species. Power to detect long-term trends would 

not increase appreciably if more surveys were conducted 

annually in each river. Although not specifically estimated, 

eye-balled extrapolation of the values in appendix C indicates 

that the size of trend detectable with 80 percent power would 

decrease to approximately 50 percent if the number of rivers 

sampled doubled to 10 to 12 rivers. In this protocol, we 

intend to sample nine rivers. It is anticipated that the size of 

the detectable trend would not decrease appreciably less than 

50 percent if more than 10–12 rivers were sampled due to 

inherent year-to-year variation in run size.

H. Start-Up and Annual Costs

The annual budget for the protocol as designed is $55,154 

based on costs for fiscal year 2008, NPS personnel services 

(table 12). The protocol requires four seasonal employees for 

8 to 10 pay periods. 

monitoring program in the NCCN, methods such as boat 

electrofishing or gill-netting were not suitable for trend 

detection or repeat sampling because of lack of access and 

vulnerability of native fish to direct and indirect mortality.

A. Day Snorkeling in Rivers

The seasonal movements, assemblage structure, and 

relative abundances of riverine fishes during summer months 

will be determined by snorkel counts in each river. Day 

snorkeling from June through September has been shown 

to be an effective method to determine seasonal movements 

and enumerate fish during summer months based on reliable 

periods of high water visibility and pilot field work. Night 

snorkel surveys in relatively remote portions of rivers are too 

hazardous, and snorkeling during fall, winter, and spring is too 

difficult because of high flows and low water visibility.

Snorkel surveys are an important tool to study fish 

populations in lotic systems, and these surveys are known 

to provide precise and reliable estimates of fish abundance 

(Northcote and Wilkie 1963; Schill and Griffith 1984; Thurow 

1994). Snorkel surveys are feasible in deep, clear rivers where 

the effectiveness of other methods are limited. By design, 

snorkel surveys have a multi-species focus. Snorkel surveys 

also are feasible in logistically remote terrain and roadless 

areas because of the relatively small amount of equipment 

(Thurow, 1994). Snorkeling is a passive technique (that is, 

no handling of fish) that is conducive to sampling fish stocks 

that are protected or that inhabit natural areas where invasive 

sample methods are less desired. Day snorkel surveys are not 

effective at enumerating species typically observed at night 

(for example, juvenile bull trout) or species associated with the 

benthos such as sculpin spp. 

Two divers, one on each side of the river, will proceed 

downstream and count each species that is greater than 15 cm 

in length (fig. 4). Snorkelers will move downstream at the 

speed of the current, and look side to side to the farthest point 

visible. The diver on the left bank (looking downstream) will 

count and record fish from the midpoint of the river channel 

to the left bank. The diver on the right bank will count fish 

from the midpoint of the river channel to the right bank. The 

primary target species in this protocol are Pacific salmonids 

and mountain whitefish based on their relative abundance and 

ease of identification. We will record sculpins, longnose dace, 

lamprey or other fish species, but will not include those fish 

in the analysis because they are rarely observed. When fish 

species are observed in large aggregations, divers commonly 

will make two passes in their respective lanes and average 

the counts. Divers will make frequent data recording stops 

(about every 100 m) to compare observations and minimize 

duplication of counts. In portions of the river where wood 

jams exist, divers will move carefully and slowly and often 

average counts after two passes. Because of the difficulty 

in distinguishing between cutthroat trout and rainbow trout 

underwater, counts of these two species will be combined as 

Table 12. Proposed annual budget for implementation of the 

NCCN Fish Assemblages Protocol in eight OLYM rivers and five 

OLYM wadeable streams. 

[Abbreviations: NCCN, North Coast and Cascades Monitoring Network; 

OLYM, Olympic National Park; Tech., technician; GS, general schedule; 

pp, pay period]

Proposed annual budget for protocol implementation in OLYM 

rivers and wadeable streams

Personnel Cost

Biological Science Tech. GS-7/1, term (10 pp) $20,017

Biological Science Tech. GS-6/1 (9pp) $12,678

Biological Science Tech. GS-5/1 (8 pp) $10,004

Biological Science Tech. GS-5/1 (8pp) $10,004

Operations and Equipment

Wading shoes, drysuit/s, thermograph replacement $1,750

Travel

In park per diem/travel $701

Total annual cost $55,154

3. Methods of Sampling 

This protocol relies on a combination of snorkel and 

electrofishing methodologies to maximize detection of trends 

in juvenile and adult fish assemblages in NCCN rivers and 

wadeable streams. These methods are useful across nonglacial rivers and streams in the NCCN. For a long-term 
3. Methods of Sampling 21

cutthroat/rainbow trout. The sampling procedure of snorkel 

counts will be consistent within and among years and 

consistent among rivers.

To address observer variability in snorkel counts during 

pilot field work, we will conduct two-pass replicate snorkel 

counts in six rivers on the same date over the same <5-km 

reference site. Replication of snorkel surveys should be 

completed after fish have had time to recover from disturbance 

but before conditions of the river change (for example, flow 

or turbidity) (Johnson and others, 2007). Two divers typically 

conducted the second pass 20 to 60 minutes after divers began 

the first pass. Replicates surveys occurred on the following 

dates: 

– East Fork Quinault River (August 10, 2005), 

– North Fork Quinault River (August 11, 2005), 

– North Fork Skokomish River (August 9, 2005), 

– Bogachiel River (June 28, 2005) and 

– South Fork Hoh River (June 9, 2005). 

Replicate counts should occur in each river every 3 to 5 years 

to address observer variability in fish counts. 

B. Backpack Electrofishing in Wadeable 

Streams

To collect fish in wadeable streams, a crew of four will 

proceed upstream without block-nets from the start of the first 

riffle upstream of the mouth to 1-km upstream sampling from 

left to right streambank. One crew member will operate a 

backpack electrofisher (I-5 settings on unit), one to two-crew 

members will net fish using dip-nets, and one crew member 

will handle buckets (fig. 5). In general, the electrofishing 

settings should be: 60 Hz, 6 ms, and 400–600 v, which follows 

Connolly and Brenkman (2008), but these settings can be 

judiciously changed depending on conditions. When feasible, 

as many as 50 individuals per fish species should be collected. 

In the event that 50 fish of a species are not captured in the 

1-km section, surveyors should assess whether they can attain 

a total of 50 individuals by sampling a short distance more, 

but keeping these fish and their associated data separate in the 

field. 

Figure 4. Schematic diagram that depicts two divers snorkeling downstream to count fish species in the reference site in the 

North Fork Skokomish River, OLYM.
22 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

As the crew proceeds upstream, a few habitat measures 

will be taken. Observers will measure the length of pools 

and non-pools within the sampled 1-km section. Pools will 

be delineated by their smooth-water surface and by having a 

maximum depth >20 cm. Maximum depth of each pool will 

be measured. All data will be recorded as specified on the data 

sheet in appendix F.

C. Fish Handling and Measurements

Fish that are collected by backpack electrofisher will 

be immediately placed in aerated 5 gal buckets. Fish held 

in buckets will be monitored regularly to minimize stressful 

conditions. If necessary, fish will be lightly anesthetized 

with 50 mg/L MS-222 buffered with an equal amount of 

sodium bicarbonate. All fish will be identified to species 

(exceptions: sculpin and lamprey to genus; rainbow trout and 

cutthroat trout under 60 mm will be recorded as “trout”) and 

enumerated. Fish will be weighed to the nearest 0.1 g, and 

measured for fork length to the nearest millimeter. General 

observations of fish health and condition should be noted. All 

fish will be held in ambient temperature stream water until 

they fully recover, and then they will be released near their 

point of capture.

Figure 5. Sampling methods for electrofishing in streams (Mink Lake Creek, Sol 

Duc River, OLYM). 

Photograph taken by Philip RS Johnson.

D. Collection of Water 

Temperature Data

Water temperature will be monitored 

at all river and stream sites near the park 

boundary with the exception of the North 

Fork Skokomish River where water 

temperatures are recorded continuously 

and retrieved from the USGS gaging 

station 12056500 in OLYM. Use of 

continuous recording devices with twice 

yearly downloads will cost little additional 

effort or dollars beyond the initial cost 

of the devices and their replacement 

every 5 years. Water temperature will be 

monitored throughout the year using the 

Stowaway® Tidbit® devices by Onset® 

and following guidelines outlined in 

Dunham and others (2005). The Tidbit® 

model TBI32-05+37 has the following 

specifications: range -4 to 37oC; accuracy 

±0.2 at 20oC; resolution 0.6 at 20oC; and 

has a 5-year non-replaceable battery. The 

loggers are set to record a value every 30 

minutes, and will last 165 days. The data 

logger will be submersed and placed in 

each reference site from June to September. 

The temperature loggers will be placed near the park 

boundary of each reference site. The location of each logger 

will be determined by GPS and in accordance with SOP #1: 

Use of GPS and Data Downloading. The loggers will be 

attached to a flow-through PVC pipe with pre-drilled holes 

and placed in the river or wadeable stream. Data loggers 

placed in solid housing units will not be in direct contact 

with the water and will be recording air temperature within 

the sealed housing (Dunham and others, 2005). The PVC 

pipe will be attached to a metal fence post and the PVC 

pipe will be secured to the post with plastic zip ties. It is 

important to maintain an exchange of water through the 

housing to minimize bias in temperature readings (Dunham 

and others, 2005). The metal fence posts will be pounded 

into the substrate in a protected area of the river. Ideally, the 

logger will remain in an area of significant flow throughout 

the summer and will be sheltered from occasional high flow 

events in the fall. One should avoid tributary junctions and 

known ground-water springs when selecting the sample site. 

All temperature loggers should be calibrated prior to 

deployment using the “ice bucket” method. The following 

steps are necessary (excerpted from Dunham and others, 

2005):

1. Deploy the data logger at a 1-min sampling interval;

2. Submerge data logger in a large cooler with fresh water 

and ice; 
4. Pre-Field Operations 23

3. Ensure water temperature in water bath is 0°C using 

thermometer;

4. After 1 h, remove data logger and download the data. The 

temperature readings of a calibrated logger should level 

out at 0°C.

Error screening should be conducted after retrieval of 

the logger, and any observations that exceed 3°C per hour 

or a daily mean change of greater than 3°C between two 

consecutive days should be flagged. Flagged observations 

should then be reverified with personnel involved in the 

programming and field sampling (Dunham and others, 2005). 

E. GPS Mapping of Reference Sites 

Rivers and wadeable streams within OLYM and other 

NCCN parks are subject to seasonal and annual changes in 

channel morphology that typically occur during winter storm 

events (Bureau of Reclamation, 2004, 2005). Little changes 

occur during summer months when there are prolonged 

periods of low flows. As channel sinuosity increases or 

decreases from year to year, the lineal river distance between 

any two fixed points on the river changes accordingly. In 

some cases, these changes may be significant, and can result 

in changes to the length of a reference site. It is important 

to have an accurate measurement of distance surveyed each 

year because fish per kilometer is a key metric of relative 

abundance in this protocol. These measurements also will 

provide a means to monitor channel sinuosity and length in the 

reference sites over the years. 

Each year, the lineal distance and location of the wetted 

channel will be determined for each reference site based on 

waypoints collected with a Thales® MobleMapper® handheld 

Global Positioning Systems (GPS) receiver. Waypoints will 

be recorded in the mid-channel of the thalweg of the river on 

every meander bend or every 200 m (about 25 waypoints/

reference site), which ever is more frequent. Each GPS 

waypoint will be collected within 3 min. We expect to achieve 

10 m horizontal accuracy at 95 percent confidence (Roger 

Hoffman, GIS Specialist, OLYM, written commun., 2008). 

Sampling will occur in each reference site during periods 

of low riverflows in August or September. Waypoints will 

be transferred to the ArcMap GIS data system for use in 

determining the length of the survey reach.

4. Pre-Field Operations

A. Personnel and Operational Requirements

The success of the Monitoring Program for Fish 

Assemblages is dependent on hiring well-qualified crew 

members from GS-05 to GS-07 levels with prior snorkeling 

and electrofishing experience, preferably in Pacific Northwest 

rivers and streams. General sampling methods and fish 

identification skills can be honed, but it is essential that all 

crew members are experienced fisheries technicians who 

are very physically fit, comfortable with spending extensive 

periods of time in water, and are educated in aquatic sciences. 

It is desirable to maintain consistency of the crew from year 

to year, to minimize annual start-up costs and to improve data 

quality. The process of advertising, interviewing, and hiring 

should begin by March of each year (table 13).

Once personnel are hired, they should be sent the 

Protocol, species lists, and other introductory materials that 

will enable them to be as familiar as possible with the park and 

fish communities that inhabit each river. In March, equipment 

should be inventoried and any needed items should be 

purchased. Data forms should be printed or copied (all on rainproof paper), and topographic maps (1:24,000 scale) secured. 

 A government vehicle will be provided for each crew 

from June through September of each year. Crew members 

will be provided office space in the Natural Resources South 

Building at Olympic National Park headquarters in Port 

Angeles. At present, two computers are available in the 

Fisheries Office of that building. Crews will be provided park 

housing if available.

Table 13. Monthly schedule for hiring, training, field operations, data entry, and reporting for monitoring of rivers and wadeable 

streams. 

[Abbreviations: X, month when activity takes place; S, snorkel surveys in references sites in rivers; E, electrofishing surveys in Olympic National Park 

wadeable streams that are co-located with river reference sites; QA/QC, quality assurance/quality control]

Activity January February March April May June July August September October November December

Hiring X

Apply for permits X

Training X

Data collection S S S, E S S, E

Data entry X X X X

QA/QC X X X X

Analysis and reporting X X X
24 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

B. Roles and Responsibilities

[OLYM, Olympic National Park; GS, General Schedule; GIS, geographic 

information systems; NCCN, North Coast and Cascades Monitoring Network]

Role and Responsibilities Name / Position

Project Lead Supervisory 

Fishery 

Biologist, 

OLYM

•	 Project administration, operations, and implementation

•	 Track project objectives, budget, requirements, and 

progress toward meeting objectives

•	 Coordinate and ratify changes to protocol

•	 Assist or Lead training of field crews

•	 Maintain and archive project records

•	 Assist in performing data summaries or analysis

•	 Certify each season’s data for quality and completeness

•	 Complete reports, metadata, and other products 

according to schedule

•	 Facilitate logistics planning and coordination

•	 Review reports, data and other project deliverables

•	 Train and ensure safety of field crew

•	 Insure compliance is up-to-date

Data analyst

•	 Perform data summaries and analysis, assist 

interpretation and report preparation

Field crew lead Seasonal 

technician 

(GS-7, term). •	 Assist in training and ensuring safety of field crew

•	 Plan and execute field visits

•	 Acquire and maintain field equipment

•	 Oversee data collection and entry, verify accurate data 

transcription into database

•	 Complete a field season report

Technicians Seasonal 

technicians 

(GS 5-6), 

volunteers 

and interns

•	 Collect, record, enter and verify data

Data manager Data Manager, 

OLYM •	 Consultant on data management activities

•	 Facilitate check-in, review and posting of data, metadata, 

reports, and other products to national databases and 

clearinghouses according to schedule

•	 Maintain and update database application

•	 Provide database training as needed

GIS specialist GIS Specialist, 

OLYM •	 Consultant on GPS use and spatial analysis techniques

•	 Facilitate map and figure output generation

•	 Primary steward of GIS data and products

Network Coordinator NCCN Network 

Coordinator

•	 Review annual reports for completeness and 

compliance with I&M standards and expectations

C. Training

In June, a 5-day training session will be given 

on snorkel methods, river safety, electrofishing, fish 

identification, First-Aid and CPR, and use of radios each 

year. To gain familiarity with reference sites, it will be 

necessary to conduct pre-season reconnaissance at river and 

stream by all crew members. Crew members also will be 

given fish identification books (Pollard and others, 1997; 

Moyle, 2002; and Wydoski and Whitney, 2003) and species 

lists for each river, and will be trained to ensure familiarity 

with fish species commonly encountered in reference 

sites for each river. Additionally, crews will review digital 

photographs in OLYM files, and watch underwater video of 

fish assemblages from OLYM rivers.

D. Equipment Needs 

Snorkel Equipment:

The following equipment is necessary for safe 

snorkeling: 

•	 Park-issued waterproof radio with back-up batteries 

•	 Felt-soled wading shoes

•	 Knee and elbow pads

•	 Dry suits, dive mask, snorkel, and PVC dive slate for 

recording data

•	 Fleece liner, neoprene gloves, neoprene snorkel hood, 

#2 pencils, and an eraser

•	 Liquid silicone (“Seal-Saver”) to protect gaskets on 

dry suit 

•	 A stick of wax for drysuit zippers 

•	 NRS dry bag backpack, size 3.3 

•	 Camping equipment (tent, stove, sleeping bag, and 

water filter) 

•	 Fish identification books 

•	 Snorkel data sheets (appendix E) 

•	 GPS unit 

•	 Dive throwbags and First-Aid kit for safety
5. Field Operations 25

Electrofishing Equipment

The following equipment is necessary for safe 

electrofishing:

•	 Park issued waterproof radio with back-up batteries 

•	 Felt soled wading shoes 

•	 Chest waders 

•	 Collapsible buckets with oxygen aerators 

•	 Plexi-glass view tube 

•	 Smith-Root Model 12A electrofisher with extra 

batteries 

•	 Two sets of anodes and cathodes and two dip-nets 

•	 Rubber gloves rated to 10,000 volts 

•	 A calibrated conductivity meter 

•	 Scale accurate to nearest 0.1 g, capable of weighing 

fish as much as 300 g, with extra batteries

•	 Hand-held scale capable of weighing fish as much as 

4.5 kg

•	 Electrofishing data sheets (appendix F) 

•	 GPS unit and pencils 

Water Temperature Equipment

The following equipment is necessary to install 

temperature loggers:

•	 Water temperature logger 

•	 Fence posts 

•	 Post pounder

•	 Twist ties (large size)

•	 Flow-through PVC pipe 

•	 Pliers

•	 Wrench

•	 Stainless steel washers, nuts, and bolts with extras of 

each

•	 Software on computer 

•	 GPS unit

E. Collection of Permits

To conduct electrofishing in OLYM and MORA, it is 

necessary to obtain Section 10A1a research sampling permits 

under the Endangered Species Act from NOAA (Puget Sound 

Chinook salmon, Puget Sound Steelhead) and USFWS (Puget 

Sound and Coastal bull trout). These permits may be obtained 

on an annual basis, and “take” coverage may be requested 

for as many as 5 years. It also is necessary to fulfill reporting 

requirements associated with each permit by the end of the 

calendar year. Currently, OLYM and MORA have permits 

from USFWS valid through 2010 and MORA has a permit 

from NOAA valid through 2011 (appendix G).

5. Field Operations 

A. Sequence of Events During Field Cycle

The monitoring will occur daily on a continual basis 

from early June to September 30 each year. The field season 

and extent of sampling effort will depend on flows in each 

river. Certain rivers are more conducive to sampling in early 

June (for example, Bogachiel River) although others may not 

be sampled until late July (for example, Dosewallips River). 

Crews will conduct snorkel surveys in each river at 7- to 

10-day intervals. Sampling of the five co-located, wadeable 

streams will occur in July and September.

The team leader will be responsible for the review of 

site information with the crew. Team leaders also will contact 

local area rangers prior to each survey. The team leader will 

prepare the itinerary for day and week. Team members will 

prepare and load sampling gear and check equipment to ensure 

appropriate operation.

B. Safety Guidelines for Field Operations

Personnel at OLYM specialize in sampling relatively 

remote rivers and have developed and adopted a safety-based 

work culture that places safety of workers above all project 

objectives.

Personal safety of the crew is the highest priority and 

must be emphasized in safety plans for the field, laboratory, 

and driving. Risks to personal safety and health include 

drowning, electrical shock, hypothermia, pathogens, 

contusions, slips, trips, and falls.
26 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Safe behavior along rivers and during river crossings is 

paramount to the success of this program. It is important to 

recognize that every river is different and flows vary from day 

to day and even from hour to hour. We outline the relative 

range of safe flows for snorkeling each river in this protocol 

(table 1). The range of safe flows for each river should be 

re-evaluated on an annual basis due to regular geomorphic 

changes in channel conditions.

High flows increase the danger associated with log jams 

and other obstacles (fig. 6). Due to the overall increased 

hydraulic force of the river at higher flows, speed and power 

increase dramatically, thus decreasing the ability and time to 

react to situations that may not be safe. Compensation must be 

made for these conditions.

Fisheries staff at OLYM prepared a Job Hazard Analyses 

for snorkeling, electrofishing, and wading in rivers and 

streams (OLYM files). The following safety guidelines for 

work in lotic systems must be strictly adhered to at all times:

1. Record location of survey, time of departure, and time of 

expected return on fisheries scheduling board and inform 

Supervisor of planned activities each day. 

2. When crossing a river or stream, examine the waterway 

from the highest vantage point possible and pick a route 

through the widest channels or where there are multiple 

channels that distribute the flow. Always wear felt soled 

boots for traction and a dry suit with snorkel and mask. 

Braided areas and areas of smaller substrate generally 

are best for crossing when compared to deep channels or 

swift areas with larger substrate. Try to find an exit area 

on the far riverbank. It also is important to plan an option 

for a retreat back to the shore should the crossing become 

too difficult. Do not cross in areas of whitewater.

3. Always unbuckle the waist and chest straps on your 

drybag and carefully note substrate size (smaller generally 

is better), depth, and velocity prior to crossing. If wearing 

waders, ensure that the waistbelt is properly secured to 

reduce the likelihood of filling waders.

4. Only cross the river at slow flowing portions of the river 

when water depth is no more than about knee deep. To 

cross moderately fast portions of rivers, the water depth 

should be less than ankle-deep and where one can clearly 

see the river bottom. Areas of whitewater, fast flowing 

water, significant depth, velocity, or large substrate should 

be avoided.

5. When crossing, stand sideways and cross the river with 

a partner. Never face downstream as flowing water can 

cause knees to buckle. Move one foot at a time and plant 

each foot firmly before each step. One may use a stout 

stick to increase balance in the river. If swept away: stay 

calm, drop pack, use whistle, and attempt to float feet first 

with head slightly raised. Remember to swim across the 

current to the riverbank and not against the current.

6. Know your limits as a snorkeler.

7. Maintain hydration throughout the day and know early 

signs and symptoms of heat exhaustion and dehydration 

in hot weather.

8. Never attach ropes or straps to a 

diver.

9. At the beginning of each day, 

check current river flow conditions 

on the USGS real-time river data 

page located on the web (http://

waterdata.usgs.gov/wa/nwis/nwis) 

or at the Washington Department of 

Ecology streamflow site. Check the 

maximum acceptable flows for each 

individual river. These guidelines 

were established during summer 

2005 to 2007. Never snorkel when 

maximum established flow is 

exceeded in any river. 

10. No survey shall be conducted if one 

diver is uncomfortable with existing 

flow conditions.

11. Always carry waterproof radios 

and First Aid kits in dry bags at all 

times.

12. There shall be at least two divers 

at all times and a third person on 

riverbank whenever available.

Figure 6. A large woody debris complex in the Sol Duc River that would be potentially 

hazardous at flows higher than those depicted.

This photograph was taken during record low summer flows in 2005.
6. Data Handling, Analysis, and Reporting 27

Figure 7. Idealized flow schematic of the cyclical stages of project information management, 

from pre-season preparation to season close-out. 

Note that quality assurance and documentation are thematic and not limited to any particular 

stage.

13. Move slowly and take time to scout questionable sections 

of the river before attempting to survey them. 

14. Always walk around hazardous areas if there is any 

question as to the safety of the section or the comfort level 

of the survey crew.

C. Equipment Care

After each field season, sampling and camping equipment 

will be repaired as needed and stored in the Fisheries storage 

area at OLYM headquarters in Port Angeles. Electrofishing 

equipment (including probes and batteries) should be 

checked by the manufacturer to identify needs for repair or 

replacement.

D. End of the Season Procedures

At the end of the season, the Field Crew Leader will 

prepare a brief (less than 3 pages) summary report that 

includes the following:

•	 A table that depicts the allocation of surveys for each 

river during the season.

•	 Local precipitation and climatic conditions for each 

watershed attained from the NCCN Climate Protocol.

•	 Description of any logistic difficulties and safety 

concerns for each river. 

•	 Clear documentation and explanation of any diversions 

from established protocols.

Field Crew Leader reports will be archived. The 

Field Crew Leader will be responsible for ensuring that all 

equipment is properly inventoried, cleaned, and stored. The 

Field Crew Leader also will ensure that all close-out materials 

(keys, park passes, personnel forms) are completed by each 

crew member prior to their departure.

6. Data Handling, Analysis, and 

Reporting 

This section describes the procedures for data handling, 

analysis, and report development. Additional details and 

context for this section are provided in the NCCN Data 

Management Plan (Boetsch and others, 2005), which describes 

the overall information management strategy for the network. 

The NCCN website also contains guidance documents on 

various information management topics (for example, report 

development, GIS development, GPS use).

A. Project Information Management Overview

Project information management may be best understood 

as an ongoing or cyclic process, as shown in figure 7. Specific 

yearly information management tasks for this project and 

their timing are described in appendix H: Yearly Project Task 

List. Readers also may refer to each respective section for 

additional guidance and instructions.

•	 Points out any interesting 

or potentially important 

observations about the 

parks’ fish communities 

that may have been noted 

during the field season (for 

example, apparent changes 

in phenology from previous 

years, or notable changes 

in apparent abundance of 

particular species).

•	 Provides suggestions for 

improving the training 

session or field season 

logistics in the future.
28 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

The stages of this cycle are described in greater depth in 

later sections of this chapter, but can be briefly summarized as 

follows:

•	 Preparation – Training, logistics planning, print forms 

and maps

•	 Data acquisition – Field trips to acquire data

•	 Data entry & processing – Data entry and uploads 

into the working copy of the database, GPS data 

processing, etc.

•	 Quality review – Data are reviewed for quality and 

logical consistency 

•	 Metadata – Documentation of the year’s data collection 

and results of the quality review

•	 Data certification – Data are certified as complete for 

the period of record

•	 Data delivery – Certified data and metadata are 

delivered for archiving and upload to the master project 

database

•	 Data analysis – Data are summarized and analyzed

•	 Product development – Reports, maps, and other 

products are developed

•	 Product delivery – Deliver reports and other products 

for posting and archiving

•	 Posting and distribution – Distribute products as 

planned and/or post to NPS clearinghouses

•	 Archiving and records management – Review analog 

and digital files for retention (or destruction) according 

to NPS Director’s Order 19. Retained files are renamed 

and stored as needed.

•	 Season close-out – Review and document needed 

improvements to project procedures or infrastructure, 

complete administrative reports, and develop work 

plans for the coming season.

B. Pre-Season Preparations for Information 

Management

Project Workspace Setup

A section of the networked file server at OLYM 

is reserved for this project, and access permissions are 

established so that project staff members have access to 

needed files within this workspace. Prior to each season, the 

Project Lead should make sure that network accounts are 

established for each new staff member, and that the Data 

Manager is notified to ensure access to the project workspace 

and databases. The recommended file structure within this 

workspace is shown in figure 8. Certain folders—especially 

those for GPS data and images—should be retained in separate 

folders for each calendar year as shown in figure 8. This will 

make it easier to identify and move these files to the project 

archives at the end of each season.

Figure 8. Recommended file structure for project workspace.

Note: The workspace folder name includes ‘FIa10’, the NCCN project code.
6. Data Handling, Analysis, and Reporting 29

Each major subfolder is described as follows:

•	 Analysis – Contains working files associated with data 

analysis.

•	 Database – Contains the working database file for the 

season. The master database for the project is stored in 

the enterprise data management system (Boetsch and 

others, 2005).

•	 Documents – Contains subfolders to categorize 

documents as needed for various stages of project 

implementation.

•	 GPS data – Contains GPS data dictionaries and raw 

and processed GPS data files. 

Note: This folder contains subfolders to arrange files 

by year. Each of these subfolders also contains the 

project code (that is, ‘FIa10’) to make it easier to select 

the correct project folder within the GPS processing 

software (refer to SOP #1: Use of GPS and Data 

Downloading).

•	 Images – For storing images associated with the 

project. The following structure contains subfolders 

to arrange files by year, and permits data images to be 

stored and managed separately from non-record and 

miscellaneous images collected during the course of 

the project. This structure also provides separate space 

for image processing and storage of originals.

[Year] The appropriate year – 2008, 2009, etc.

_Processing Processing workspace

Data Data images

[Site_code] Arranged by reach, for images taken 

at reaches

[Date] Arranged by date, for images not 

taken at reaches

Miscellaneous Non-data images taken by project 

staff

[Site_code] Arranged by reach, for images taken 

at reaches

[Date] Arranged by date, for images not 

taken at reaches

Originals Renamed but otherwise unedited 

image file copies

[Site_code] Arranged by reach, for images taken 

at reaches

[Date] Arranged by date, for images not 

taken at reaches

Non-NPS Images acquired from other sources

•	 Spatial info – Contains files related to visualizing and 

interacting with GIS data.

◦ GIS data – New working shapefiles and coverages 

specific to the project.

◦ GIS layers – Pointer files to centralized GIS base 

themes and coverages.

◦ Map documents – Map composition files (.mxd).

Folder Naming Standards

In all cases, the following guidelines should be followed 

for folder names: (1) no spaces or special characters in the 

folder name, (2) use the underbar (“_”) character to separate 

words in folder names, (3) try to limit folder names to 

20 characters or fewer, and (4) dates should be formatted as 

YYYYMMDD for better sorting.

GPS Preparation

The GIS Specialist and Project Lead should work 

together to ensure that target coordinates and data dictionaries 

are loaded into the GPS units prior to the onset of field work, 

and that GPS download software is available and ready for 

use. Additional details on GPS use and GPS data handling 

are provided in SOP #1: Use of GPS and Data Downloading, 

and in NCCN GPS Guidelines (North Coast and Cascades 

Network-National Park Service 2006a).

Implementing Working Database Copy

Prior to the field season, the Data Manager will 

implement a blank copy of the working database and ensure 

proper access on the part of the project staff. Refer to Section 

6C, Overview of Database Design for additional information 

about the database design and implementation strategy.

C. Overview of Database Design

We maintain a customized relational database application 

to store and manipulate the data associated with this project. 

The design of this database is consistent with NPS I&M 

and NCCN standards (see the data dictionary and other 

documentation in Appendix I: Database Documentation). 

The Data Manager is responsible for development and 

maintenance of the database, including customization of data 

summarization and export routines.
30 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

The database is divided into two components—one for 

entering, editing, and error-checking data for the current 

season (“working database copy”), and another that contains 

the complete set of certified data for the monitoring project 

(“master project database”). A functional comparison of these 

two components is provided in table 14.

Each of these components is based on an identical 

underlying data structure (tables, fields and relationships, as 

documented in Appendix I: Database Documentation). The 

working database is implemented in Microsoft© Access to 

permit greater flexibility when implementing on computers 

with limited or unreliable network access. The master database 

is implemented in Microsoft© SQL Server to take advantage 

of the backup and transaction logging capabilities of this 

enterprise database software. 

Both components have an associated front-end database 

application (“user interface” with forms, queries, etc.) 

implemented in Microsoft© Access. The working database 

application has separate screens for data entry, data review, 

and quality validation tools. The master database application 

contains the analysis and summarization tools, including 

pre-formatted report output and exports to other software (for 

example, for analysis and graphics production).

During the field season, each project crew will be 

provided with their own copy of a working database into 

which they enter, process, and quality-check data for the 

current season (refer to Section 6D, Data Entry and Processing

and SOP #2: Data Entry and Verification). Once data for 

the field season have been certified, they will be uploaded 

into the master database, which is then used for all reporting 

and analysis. This upload process is performed by the Data 

Manager, using a series of pre-built append queries.

D. Data Entry and Processing

After each field trip, technicians should enter data in 

order to keep current with data entry tasks, and to identify 

any errors or problems as close to the time of data collection 

as possible. The working database application is found in 

the project workspace. For enhanced performance, it is 

recommended that users copy the front-end database onto their 

workstation hard drives and open it there. This front-end copy 

may be considered “disposable” because it does not contain 

any data, but rather acts as a pointer to the data that reside 

in the back-end working database. Whenever updates to the 

front-end application are made available by the Data Manager, 

an updated front-end database should be copied from the 

project workspace to the workstation hard drive.

The functional components for data entry into the 

working database are described in SOP #2: Data Entry 

and Verification. Each data entry form is patterned after the 

structure of the field form, and has built-in quality assurance 

components such as pick lists and validation rules to test for 

missing data or illogical combinations. Although the database 

permits users to view the raw data tables and other database 

objects, users are strongly encouraged only to use these prebuilt forms as a way of ensuring the maximum level of quality 

assurance.

Regular Data Backups

Upon opening the working database, the user will be 

prompted to make a backup of the underlying data (see 

SOP #2: Data Entry and Verification). It is recommended 

that backups be made on a regular basis – perhaps every day 

that new data are entered – to save time in case of mistakes or 

Table 14. Functional comparison of the master project database and 

the working database copy.

Project database 

functions and capabilities

Working 

database

Master 

database

Software platform for back-end data Microsoft©

Access

Microsoft© SQL 

Server.

Contains full list of sampling locations and taxa X X

Portable for remote data entry X

Forms for entering and editing current year data X

Quality assurance and data validation tools X X

Preliminary data summarization capabilities X

Full analysis, summarization and export tools X

Pre-formatted report output X

Contains certified data for all observation years X

Limited editing capabilities, edits are logged X

Full automated backups and transaction logging X

database file corruption. These periodic backup 

files should be compressed to save drive space, 

and may be deleted once enough subsequent 

backups are made. All such backups may be 

deleted after the quality review and certification 

of the data.

Data Verification

As data are being entered, the person 

doing the data entry should visually review 

them to make sure that the data on screen match 

the field forms. This should be done for each 

record prior to moving to the next form for data 

entry. At regular intervals and at the end of the 

field season, the Field Lead should inspect the 

data being entered to check for completeness 

and perhaps identify avoidable errors. The Field 

Lead also may periodically run the Quality 
6. Data Handling, Analysis, and Reporting 31

Assurance Tools that are built into the front-end working 

database application to check for logical inconsistencies 

and data outliers (this step is described in greater detail in 

Section 6E, Quality Review and also in SOP #3: Data Quality 

Review and Certification).

Field Form Handling Procedures

As field data forms are part of the permanent record for 

project data, they should be handled in a way that preserves 

their future interpretability and information content. If 

changes to data on the forms need to be made subsequent to 

data collection, the original values should not be erased or 

otherwise rendered illegible. Instead, changes should be made 

as follows:

•	 Draw a horizontal line through the original value, and 

write the new value adjacent to the original value with 

the date and initials of the person making the change.

•	 All corrections should be accompanied by a written 

explanation in the appropriate notes section on the field 

form. These notes also should be dated and initialed.

•	 If possible, edits and revisions should be made in a 

different color ink to make it easier for subsequent 

viewers to be able to retrace the edit history.

•	 Edits should be made on the original field forms and on 

any photocopied forms.

These procedures should be followed throughout data 

entry and data revision. On a 5-year basis, data sheets are to 

be scanned as PDF documents and archived (see the product 

delivery specifications in Section 6J, Product Delivery, 

Posting and Distribution). The PDF files may then serve as a 

convenient digital reference of the original if needed.

Image Handling Procedures

This section covers photographic images collected by 

project staff or volunteers during the course of conducting 

project-related activities. Images that are acquired by other 

means—for example, downloaded from a website or those 

taken by a cooperating researcher—are not project records and 

should be handled separately.

Data photographs are often linked to specific records 

within the database, and are stored in a manner that permits 

the preservation of those database links. Other photographs—

for example, of field crew members at work, or photographs 

showing the morphology of a certain fish species—also 

may be retained but are not necessarily linked with database 

records.

Effectively managing hundreds of photographic images 

requires a consistent method for downloading, naming, editing 

and documenting. The general process for managing data 

photographs proceeds as follows:

1. Image file structure setup – Set up the file organization 

for images prior to acquisition, according to the project 

workspace structure indicated in Section 6B, Pre-Season 

Preparations.

2. Image acquisition – Capture images at an appropriate 

resolution that balances space limitations with the 

intended use of the images. Although photographs taken 

to facilitate future navigation to the site do not need to be 

stored at the same resolution as those that may be used to 

indicate gross environmental change at the site, it may be 

more efficient to capture all images at the same resolution 

initially. A recommended minimum raw resolution is 

1600 × 1200 pixels (approximately 2 megapixels).

3. Download and process – Note: Large groups of 

photographs acquired under sub-optimal exposure or 

lighting can be batch processed to enhance contrast or 

brightness. Batch processing can also be used to rename 

groups of photographs according to a convention, or to 

resize images for use on the web. Batch processing may 

be done in ThumbsPlus, Extensis© Portfolio or a similar 

image software package.

a. Download the raw, unedited images from the camera 

into the appropriate “_Processing” folder.

b. Rename the images according to convention (refer 

to the image naming standards section). If image 

file names were noted on the field data forms, be 

sure to update these to reflect the new image file 

name prior to data entry. In cases where there are 

small quantities of photographs it is practical to 

individually rename these files. However, for larger 

numbers, it may be useful to rename files in batches. 

This may be done in ThumbsPlus, Extensis©

Portfolio or a similar image software package. A 

somewhat less sophisticated alternative is to batch 

rename files in Windows Explorer©, by first selecting 

the files to be renamed and then selecting File > 

Rename. The edits made to one file will be made to 

all others, although with the unpleasant side effect 

of often adding spaces and special characters (for 

example, parentheses) that will then need to be 

removed manually. Renaming photographs may 

be most efficient as a two part event – first a batch 

process to insert the date and transect number at 

the beginning of the photo name, after which a 

descriptive component is manually added to each file 

name.
32 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

c. Copy the images to the ‘Originals’ folder and set the 

contents as read-only by right clicking in Windows 

Explorer© and checking the appropriate box. These 

originals are the image backup to be referred to in 

case of unintended file alteration or deletion.

d. Delete any poor quality photographs, repeats, or 

otherwise unnecessary photographs. Low quality 

photographs might be retained if the subject is 

highly unique, or the photograph is an irreplaceable 

data photograph.

e. Rotate the image to make the horizon level.

f. Photographs of people should have ‘red eye’ glare 

removed.

g. Photographs should be cropped to remove edge areas 

that grossly distract from the subject.

h. When finished, move the image files that are to 

be retained and possibly linked in the database 

to the appropriate folder—data images under the 

Data folder, other images under the Miscellaneous 

folder. Photographs of interest to a greater audience 

should be copied to the park Digital Image Library. 

To minimize the chance for accidental deletion or 

overwriting of needed files, no stray files should 

remain in the processing folder between downloads.

i. Depending on the size of the files and storage 

limitations, contents of the Originals folder may be 

deleted once all desired files are accounted for after 

processing.

4. Establish database links—During data entry and 

processing, the database application will provide the 

functionality required to establish a link between each 

database record and the appropriate image file(s). To 

establish the link, the database prompts the user to 

indicate the root project workspace directory path, the 

specific image folder within the project workspace, and 

the specific file name. This way, the entire workspace 

may be later moved to a different directory (that is, the 

NCCN Digital Library) and the links will still be valid 

after changing only the root path. Refer to SOP #2: 

Data Entry and Verification for additional details on 

establishing these links. 

Note: Files must keep the same name and relative 

organization once these database links have been 

established. Users should not rename or reorganize the 

directory structure for linked image files without first 

consulting with the Data Manager.

5. Deliver image files for final storage—At the end of the 

season, and once the year’s data are certified, data images 

for the year may be delivered along with the working copy 

of the database to the Data Manager on a CD or DVD. To 

do this, simply copy the folder for the appropriate year(s) 

and all associated subfolders and images onto the disk. 

These files will be loaded into the project section of the 

NCCN Digital Library, and the database links to data 

images will be updated accordingly. Prior to delivery, 

make sure that all processing folders are empty. Upon 

delivery, the delivered folders should be made read-only 

to prevent unintended changes. Refer to Section 6J, 

Product Delivery, Posting, and Distribution for additional 

information.

GPS Data Procedures Image Handling 

Procedures

The following general procedures should be followed for 

GPS data (see SOP #1: Use of GPS Data and Downloading

and Appendix H: Yearly Project Task List):

1. GPS data should be downloaded by the field crew from 

the units at the end of each field trip and stored in the 

project workspace.

2. Raw files should be sent in a timely manner to the GIS 

Specialist for processing and correction.

3. The GIS Specialist will process the raw GPS data and 

store the processed data in the project workspace.

4. The GIS Specialist will upload corrected coordinate 

information into the database and create any GIS data 

sets.

The Field Lead should periodically review the processed 

GPS data to make sure that any errors or inconsistencies are 

identified early.

E. Quality Review

After the data have been entered and processed, 

they need to be reviewed by the Project Lead for quality, 

completeness and logical consistency. The working database 

application facilitates this process by showing the results of 

pre-built queries that check for data integrity, data outliers 

and missing values, and illogical values. The user may then 

fix these problems and document the fixes. Not all errors 

and inconsistencies can be fixed, in which case a description 

of the resulting errors and why edits were not made is then 

documented and included in the metadata and certification 

report (see Sections 6F, Metadata Procedures and 6G, Data 

Certification and Delivery, and SOP #3: Data Quality Review 

and Certification).
6. Data Handling, Analysis, and Reporting 33

Data Edits Before and After Certification

Due to the high volume of data changes and/or 

corrections during data entry, it is not efficient to log all 

changes until after data are certified and uploaded into the 

master database. Prior to certification, daily backups of the 

working database provide a crude means of restoring data to 

the previous day’s state. After certification, all data edits in the 

master database are tracked in an edit log (refer to appendix I: 

Database Documentation) so that future data users will be 

aware of changes made after certification. In case future users 

need to restore data to the certified version, we also retain a 

separate, read-only copy of the original, certified data for each 

year in the NCCN Digital Library (see Section 6J, Product 

Delivery, Posting and Distribution).

Geospatial Data

The Project Lead and GIS Specialist may work together 

to review the surveyed coordinates and other geospatial data 

for accuracy. The purpose of this joint review is to make sure 

that geospatial data are complete and reasonably accurate, 

and also to determine which coordinates will be used for 

subsequent mapping and field work.

F. Metadata Procedures

Data documentation is a critical step toward ensuring 

that data sets are usable for their intended purposes well into 

the future. This involves the development of metadata, which 

can be defined as structured information about the content, 

quality, condition and other characteristics of a given data 

set. Additionally, metadata provide the means to catalog 

and search among data sets, thus making them available 

to a broad range of potential data users. Metadata for all 

NCCN monitoring data will conform to Federal Geographic 

Data Committee (FGDC) guidelines and will contain all 

components of supporting information such that the data may 

be confidently manipulated, analyzed, and synthesized.

At the conclusion of the field season (according to 

the schedule in Appendix H: Yearly Project Task List), the 

Project Lead will be responsible for providing a completed, 

up-to-date metadata interview form to the Data Manager. 

The Data Manager and GIS Specialist will facilitate metadata 

development by consulting on the use of the metadata 

interview form, by creating and parsing metadata records from 

the information in the interview form, and by posting such 

records to national clearinghouses.

An up-to-date metadata record is a required deliverable 

that should accompany each season’s certified data. For longterm projects such as this one, metadata creation is most time 

consuming the first time it is developed – after which most 

information remains static from one year to the next. Metadata 

records in subsequent years then only need to be updated 

to reflect changes in contact information and taxonomic 

conventions, to include recent publications, to update data 

disposition and quality descriptions, and to describe any 

changes in collection methods, analysis approaches or quality 

assurance for the project. 

Specific procedures for creating, parsing and posting 

the metadata record are provided in NCCN Metadata 

Development Guidelines (North Coast and Cascades 

Network—National Park Service, 2006b). General procedures 

are as follows:

1. After the annual data quality review has been performed 

and the data are ready for certification, the Project Lead 

(or a designee) updates the metadata interview form.

a. The metadata interview form greatly facilitates 

metadata creation by structuring the required 

information into a logical arrangement of 15 primary 

questions, many with additional sub-questions.

b. The first year, a new copy of the NCCN Metadata 

Interview form should be downloaded. Otherwise 

the form from the previous year can be used as a 

starting point, in which case the Track Changes tool 

in Microsoft© Word should be activated in order 

to make edits obvious to the person who will be 

updating the XML record.

c. Complete the metadata interview form and maintain 

it in the project workspace. Much of the interview 

form can be filled out by cutting and pasting material 

from other documents (for example, reports, protocol 

narrative sections, and SOPs).

d. The Data Manager can help answer questions about 

the metadata interview form.

2. Deliver the completed interview form to the Data 

Manager according to the product delivery specifications 

in Section 6J, Product Delivery, Posting, and Distribution.

3. The Data Manager (or GIS Specialist for spatial data) will 

then extract the information from the interview form and 

use it to create and update an FGDC- and NPS-compliant 

metadata record in XML format. Specific guidance for 

creating the XML record is contained in NCCN Metadata 

Development Guidelines (North Coast and Cascades 

Network—National Park Service, 2006b).

4. The Data Manager will post the record and certified data 

to the NPS Data Store, and maintain a local copy of the 

XML file for subsequent updates. The NPS Data Store 

has help files to guide the upload process.

5. The Project Lead should update the metadata interview 

content as changes to the protocol are made, and each 

year as additional data are accumulated.
34 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

G. Data Certification and Delivery

Data certification is a benchmark in the project 

information management process that indicates that: (1) data 

are complete for the period of record, (2) data have undergone 

and passed the quality assurance checks (Section 6E, Quality 

Review), and (3) data are appropriately documented and 

in a condition for archiving, posting, and distribution as 

appropriate. Certification is not intended to imply that the data 

are completely free of errors or inconsistencies that may or 

may not have been detected during quality assurance reviews.

To ensure that only quality data are included in reports 

and other project deliverables, the data certification step is 

an annual requirement for all tabular and spatial data. The 

Project Lead is the primary person responsible for completing 

an NCCN Project Data Certification Form, available on the 

NCCN website. This form should be submitted with the 

certified data according to the timeline in Appendix 1: Yearly 

Project Task List. Refer to SOP #3: Data Quality Review and 

Certification and the delivery specifications in Section 6J, 

Product Delivery, Posting, and Distribution for instructions.

Water Quality Data Procedures

All water quality data collected for this monitoring 

project will be managed according to guidelines from the 

NPS Water Resources Division (WRD). NPSTORET (http://

www.nature.nps.gov/water/infoanddata) and Environmental 

Protection Agency (EPA) STORET (http://www.epa.gov/

storet/) are, respectively, the NPS and national enterprise data 

warehouses for water quality data. NPSTORET is maintained 

by WRD and is synchronized with EPA STORET on a 

regular basis. NPS WRD also maintains a desktop version 

of NPSTORET in Microsoft© Access to manage local data 

entry, documentation, and transfer. After the season's data 

are entered and reviewed in the project database, water 

temperature data will be uploaded to the local, desktop version 

of NPSTORET. We will then transfer the contents of this local 

copy at least annually to NPS Water Resource Division for 

upload to the STORET database. Once certified project data 

have been synchronized with WRD NPSTORET, they are 

automatically made available to the public through the EPA 

STORET data warehouse (http://www.epa.gov/storet/).

H. Data Analysis and Summaries

Seasonal and annual trends in fish assemblages are 

characterized by quantitative estimates of the relative 

abundance, species composition, fish biomass, and fish density 

in river and stream reference sites. To demonstrate the types 

of summaries to be constructed on an annual basis, we present 

actual data in graphical and tabular format from surveys 

conducted during pilot fieldwork and from an existing longterm data set from the North Fork Skokomish River (1994 to 

present). The results from these surveys shall be interpreted 

cautiously, and inferences are limited to individual reference 

sites within a river.

Comparisons of Seasonal Abundances of Fish 

Species Within and Among Rivers

The relative seasonal abundances of each fish species 

are determined within a river and general comparisons can 

be made among rivers in this protocol. Seasonal trends in 

abundance are reported as the number of each fish species 

(or fish/km) on a given sample date in each river. Graphics 

can be constructed for individual fish species in each river or 

graphics can be constructed to represent seasonal trends in 

relative abundances of multiple fish species in a given river 

(fig. 9). In the North Fork Skokomish River, there are distinct 

monthly changes in composition of mountain whitefish, 

cutthroat/rainbow trout, and adult bull trout that correspond 

to fish movements between the Lake Cushman (reservoir) and 

the river (fig. 9). To generally characterize seasonal changes in 

relative abundance or fish densities (fish/km) among reference 

sites, graphics are made for each river. 

To characterize seasonal or monthly trends in fish/km 

for a given species among rivers, the mean monthly counts 

for each species are reported (fig. 10). Such information 

can provide a relative gauge of productivity for each species 

among reference sites. Graphics are made annually for fish 

species that are present in multiple rivers. 

Comparisons of Seasonal Fish Species 

Composition Within and Among Rivers

The relative seasonal composition (for example, fish 

assemblage) of fish species is determined within each river 

and general comparisons can be made among rivers in this 

protocol. Seasonal trends in fish species composition are 

reported as the percent of each fish species in a given month in 

each river. Graphics can be constructed to represent seasonal 

trends in fish species composition (fig. 11).
6. Data Handling, Analysis, and Reporting 35

Figure 9. Numbers of adult bull trout, cutthroat/rainbow trout, and mountain whitefish in the reference site in the North 

Fork Skokomish River based on snorkel surveys conducted from April to December 1996.

Figure 10. Comparisons of mean monthly densities (fish/km) of mountain whitefish in the East Fork Quinault (EFQR), 

North Fork Quinault (NFQR), North Fork Skokomish (NFSR), and South Fork Hoh Rivers (SFHR), Washington based on 

snorkel surveys in reference sites from June to September 2005.

tac08-0232_fig09

0

50

100

150

200

250

300

350

400

450

500

550

04/13/9605/15/9606/05/9606/18/9607/01/9607/17/9607/25/9607/31/9608/08/9608/14/9608/21/9608/28/9609/06/9609/12/9609/19/9609/26/9610/09/9610/12/9610/19/9610/26/9611/16/9611/23/9612/07/96

Number of Fish

Bull Trout

Rainbow/Cutthroat Trout

Mountain Whitefish

0

50

100

150

200

250

300

350

June July Aug Sept

Mountain Whitefish

 per kilometer

NFSR SFHR

EFQR NFQR

BOGA
36 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Figure 11. Mean monthly composition of adult bull trout, cutthroat/rainbow trout, and mountain whitefish in the 

South Fork Hoh River, Washington, based on 11 snorkel surveys conducted in the reference site from June to 

September 2005. 

tac08-0232_fig11

0

10

20

30

40

50

60

70

80

90

100

 June July Aug Sept

Percentage of Fish Species Composition

n=2 n=4 n=3 n=2

Mountain Whitefish

Cutthroat/Rainbow Trout

Adult Bull Trout

Trends in Annual Peak Counts and Fish Species 

Composition in Rivers

Annual trends in relative abundances are determined 

by comparing the maximum density or peak count for 

each species in a given year. To properly estimate the peak 

count, at least one snorkel survey at or near the peak is 

required. Because the true peak count of some species may 

occur outside our sampling frame (June–September), the 

comparisons among years are a measure of trends in relative 

abundance. Trends in annual peaks counts are reported for 

each species in each river every year (fig. 12). 

To generally characterize migratory timing of each 

species among rivers, a comparison of peak counts is made 

among rivers (fig. 13). For instance, the general timing of 

peak counts for cutthroat/rainbow trout generally is consistent 

among rivers, and peak counts for bull trout are more variable 

in 2005 (fig. 13).

Annual trends in relative composition of each fish species 

over several years are determined by comparing the percent 

of each fish species in a given month among years. Trends in 

fish species composition are reported for each river every year 

(fig. 14). 

After collection of multiple years (for example 10–20 

years) of information, the fish assemblage in each river can 

be characterized with decadal information on: numerically 

abundant species (percent of each fish species; number of 

fish species; number of families); number of extirpated 

fish species; extent of faunal similarity within a river; and 

assemblage evenness that describes whether fish fauna is one 

with high species evenness and diversity or one with few, but 

abundant species. 

Trends in Migratory Timing in Rivers

To estimate onset, peak, and end of migrations for 

selected species, multiple snorkel surveys within years are 

required. In this protocol, we expect to attain information on 

migratory timing of adult fish that migrate during the sampling 

period (for example June through September). Snorkel counts 

by species are converted to densities (fish/km) due to varying 

lengths of reference reaches among rivers. Average run timing 

parameters are estimated by plotting reach densities derived 

from snorkel counts against Julian day of the year. Julian 

day is the number of days after January 1 each year. Data are 

smoothed using a locally weighted non-parametric scatterplot. The smooth line is an estimate of the average number of 

fish observed each day of the year.
6. Data Handling, Analysis, and Reporting 37

Figure 12. Trends in annual peak counts for adult bull trout and mountain whitefish in the 

North Fork Skokomish River, OLYM from 1994 to 2006.

Figure 13. Comparisons of relative dates of peak counts for mountain whitefish, bull trout, and 

cutthroat/rainbow trout among five rivers.

tac08-0232_fig12

0

25

50

75

100

125

150

175

200

225

250

275

300

325

350

375

400

425

450

475

500

199419951996199819992000200120022003200420052006

Annual Peak Counts of Bull Trout and Cutthroat/Rainbow Trout

0

200

400

600

800

1,000

1,200

1,400

1,600

1,800

2,000

2,200

2,400

2,600

Annual Peak Counts of Mountain Whitefish

Adult Bull Trout

Cutthroat/Rainbow Trout

Mountain Whitefish

Bogachiel

Mountain whitefish

Bull trout

Cutthroat/rainbow trout

10-15-2005

9-5-2005

8-16-2005

7-27-2005

7-7-2005

6-17-2005

5-28-2005

5-8-2005

9-25-2005

East Fork

Quinault

North Fork

Quinault

South Fork

Hoh

North Fork

Skokomish
38 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Table 15. Average run timing statistics for bull trout, mountain 

whitefish, cutthroat/rainbow trout, and Chinook salmon in North 

Fork Skokomish River based on snorkel counts in a 5 km reference 

site, 1994–2005.

[Maximum smoothed density: This estimator was computed by smoothing 

all densities collected during the year using “Super Smoother”, and observing 

the maximum smoothed estimate. Abbreviations: km, kilometer]

River Species

Maximum 

smoothed 

density 

(fish/km)

Average run date

Start Peak End 

North Fork 

Skokomish

Bull trout 32.44 Sept. 26 Nov. 14 Dec. 31

Mountain 

whitefish 

232.76 April 5 July 24 Sept. 15

Cutthroat/

Rainbow 

trout 

55.75 June 16 Aug. 28 Oct. 17

Chinook 

salmon 

1.38 Aug. 3 Oct. 16 Dec. 3

Figure 14. Mean monthly composition of adult bull trout, cutthroat/rainbow trout, and mountain whitefish in the North Fork 

Skokomish River, Washington based on 108 snorkel surveys conducted from June to December, 1994 to 2006. 

N=number of surveys in each month.

0

10

20

30

40

50

60

70

80

90

100

June July Aug Sept Oct Nov Dec

Percentage of Fish Species Composition

Mountain Whitefish

Cutthroat/Rainbow Trout

Adult Bull Trout

 n=11 n=18 n=15 n=15 n=26 n=14 n=9 

The average timing of each species’ peak is estimated as 

the day on which the smoothed average density of fish was 

highest. Average onset of the migration is estimated as the 

day prior to the peak during which average density of fish 

was 25 percent of the maximum average density. Similarly, 

the average end of the migration is estimated as the day post 

peak when the average density is 25 percent of the maximum 

average density (fig. 15). Estimates of the overall average 

migratory timing (start, peak, and end) by date for four fish 

species in the North Fork Skokomish appear in table 15 using 

data collected from 1994 to 2005. 
6. Data Handling, Analysis, and Reporting 39

Figure 15. The estimated onset, peak, and end of migrations of adult bull 

trout (SACO) and mountain whitefish (PRWI) in the North Fork Skokomish 

River using snorkel data from 1994 to 2005. 

The thickened red line is a smoothed estimate of the average density each 

day of the year and the vertical red lines represent the estimated start, peak, 

and ending dates of the average run.

NF Skokomish SACO

Fish per kilometer

1994

1995

1996

1998

1999

2000

2001

2002

2003

2004

2005

NF Skokomish 

PRWI

Date

Fish per kilometer

Feb01 Apr01 June 01 Aug01 Oct01 Dec01

100

120

80

60

40

20

0

800

600

400

200

0

1,000
40 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Public Highlights

Every year, a narrative will be submitted to Congress 

that summarizes findings and public highlights (table 16). The 

following is an example based on pilot fieldwork: from 2005 

to 2007, fisheries biologists conducted the most intensive 

monitoring efforts (n=180 surveys) of fish communities in 

NCCN rivers to date. Fisheries crews snorkeled 900 river 

kilometers in 10 rivers and made 57,000 individual fish 

observations from June through September each year. Some 

preliminary observations from snorkel surveys revealed that: 

(1) mountain whitefish were more abundant than any other 

fish species observed in OLYM rivers, (2) adult summer 

steelhead were in extremely low numbers in all coastal rivers 

that drain from OLYM, (3) hatchery steelhead were more 

abundant than wild steelhead in selected rivers, and (4) nonnative fish species were observed in only 1 of the 10 rivers, the 

Ohanapecosh at MORA. Results from the River Monitoring 

Program have management and conservation implications, 

particularly for Pacific salmonids that have high ecological 

and cultural importance and significantly contribute to 

recreational, commercial, and subsistence fisheries.

Abrupt Change Analysis

Abrupt change in fish abundance can be detected by 

fitting a weighted regression to past data, constructing a 

95 percent prediction interval for the current value, and 

observing whether the measured value is outside the interval 

(fig. 16).

Variation of Replicate Snorkel Counts in Rivers

The variation of repeated snorkel surveys will be 

determined every 3 to 5 years and is computed as a measure 

of the reproducibility of snorkel counts. Statistically, this 

variation was an estimate of the measurement error associated 

snorkel counts. Variation is computed among replicate 

counts for each of the primary species, and is reported as 

both the coefficient of variation (CV) and the 1⁄2 width of an 

approximate 95 percent confidence interval on the mean count. 

The CV for replicate counts x1 and x2 of the same species was

cv x

x x x x

x x

( ) ( ) . ( )

. ( ) = + − +

+

1

2

2

2

1 2

2

1 2

0 5

0 5

The 1⁄2 width of an approximate 95 percent confidence 

interval was computed as 2 times the standard error, or 

2cv(x)[0.5(x1 + x2)].

In our analysis from pilot studies, mountain whitefish 

(PRWI) were by far the most abundance species during 

replicate surveys among rivers in 2005 (table 17). Precision 

of replicate surveys was generally good, with coefficients of 

variation ranging from 0.097 to 0.241 across the four species 

analyzed here (table 17). The coefficient of variation for 

mountain whitefish was the smallest among the four species, 

but also had the largest confidence interval 1⁄2 width due to the 

large numbers.

The coefficients of variation observed during repeated 

surveys of the same river reach were surprisingly low given 

the variable nature of fish population, their mobility, and 

the difficulty identifying fish while snorkeling. Average 

coefficients of variation for the four species were less than 

25 percent, with 3 out of 4 less than18 percent. This level 

of variation in repeated counts is acceptable given the high 

variation in run timing and size that was observed. This 

level of observed variation in replicate counts is acceptable 

and largely inconsequential toward meeting the objectives 

of determining seasonal and annual trends in community 

composition and relative abundance. It would be surprising if 

an alternative fish counting methodology had lower inherent 

variability yet was as easy to conduct as snorkel surveys. 

Table 16. Summary of the number of fish observed by river and total number of snorkel 

surveys from May through September 2005, based on pilot fieldwork.

[NA, not applicable}

River

Total number

Fish 

observed

Percentage

 of total

Snorkel

surveys

Chinook Bull 

trout

Chum 

salmon

Mountain 

whitefish

North Fork Skokomish 10,351 39 18 0 756 NA 8,506

North Fork Quinault 1,715 6 9 8 102 0 1,227

East Fork Quinault 6,482 25 10 100 365 0 5,081

Sol Duc 1,084 4 12 2 NA 0 NA

Bogachiel 3,044 12 11 15 NA 19 1,651

South Fork Hoh 3,740 14 12 56 155 5 3,001

Total 26,416 100 72 181 1,378 24 19,466
6. Data Handling, Analysis, and Reporting 41

Table 17. Means and coefficient of variations observed during replicate surveys of the same river reach on the same day in 2005 for 

each of six rivers.

[Abbreviations: CV, coefficient of variation; std, standard; SACO, bull trout; PRWI, mountain whitefish; ONXX, cutthroat/rainbow trout; ONTS, Chinook 

salmon. NA indicates that the species was not found in that river]

River

Mean CV=std/mean Confidence Interval Width=2*std

SACO PRWI ONXX ONTS SACO PRWI ONXX ONTS SACO PRWI ONXX ONTS

Bogachiel NA 139.5 137.5 NA NA 0.096 0.231 NA NA 26.87 63.64 NA

East Fork 

Quinault

32.5 740.0 150.5 8.0 0.239 .141 .127 0.177 15.56 209.30 38.18 2.83

North Fork 

Quinault

9.5 178.0 70.0 NA .223 .072 .162 NA 4.24 25.46 22.63 NA

North Fork 

Skokomish

13.0 658.0 128.5 NA .000 .120 .083 NA .00 158.39 21.21 NA

South Fork 

Hoh

9.0 183.5 8.5 NA .157 .058 .749 NA 2.83 21.21 12.73 NA

Sol Duc NA NA 79.5 NA NA NA .098 NA NA NA 15.56 NA

Average 16.0 379.8 95.8 8.0 .155 .097 .241 .177 5.66 88.25 28.99 2.83

Figure 16. Regression method for detecting 

abrupt change. 

Filled circles are previous estimates of relative 

abundance for a given species. Bars are ±1 

standard error. Assuming uncorrelated errors, 

weighted regression can be used to fit a linear 

regression to data from 2005 through 2012, and a 

prediction interval for 2013 can be constructed. 

Abrupt change would be detected if the 

measured value for 2013 fell outside this interval, 

that is, in one of the ‘Abrupt Change Detection 

Zones’.
42 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Trends in Proportions of Hatchery and Wild Fish 

in Rivers

Seasonal and annual trends of proportions of hatchery 

(that is, fin clipped) versus wild salmonids are determined by 

observations of marked and unmarked fish a reference site 

on a given date. The observations of marked fish provide a 

relative gage to the extent of hatchery fish invasions in park 

rivers (table 18). These observations only apply to adult 

salmonids. Annual observations of the proportion of hatchery 

to wild salmonids will be evaluated by species within a given 

river.

Juvenile Fish Data from Wadeable Streams

We will examine young-of-the-year and juvenile fish 

assemblages and determine changes in relative densities 

[(fish/100 g)/m2

] and length frequency distributions for each 

species in reference sites of streams. Seasonal trends in fish 

species composition are reported as the number and percent 

of each fish species in a given month in each river (table 19). 

Length-frequency analysis can show a clear distinction in size 

distribution and growth of age-0 rainbow trout during summer 

months (fig. 17; Connolly and Brenkman, 2008). Additionally, 

relative timing of emergence of age-0 trout is evident from 

plots of length frequency distributions. 

Water Temperatures

Water temperature is a readily obtained and relatively 

inexpensive metric that is important for understanding 

fish assemblage structure, fish growth, and productivity. 

Water temperature also is of widespread interest in aquatic 

ecosystems, and is affected by many different natural and 

anthropogenic influences (Dunham and others, 2005). For 

detailed information on water temperature monitoring (for 

example measurement interval, field sampling, error screening, 

data summaries), see Dunham and others (2005).

We summarize continuous water temperature in reference 

sites of rivers and streams. The following metrics will be 

analyzed: daily maximum water temperature (maximum daily 

average), the highest average temperatures over a continuous 

7 days during summer, average daily minimum temperature, 

and the average temperature recorded across all observations 

from June to September 30.

Table 18. Example of annual summary of the relative proportions of hatchery (marked) and wild (unmarked) adult Chinook salmon, 

coho salmon, and steelhead among reference sites in three coastal rivers.

[The relative number of marked versus unmarked fish is based on the total number of observations from June through September, using data collected during 

pilot surveys in 2006. NA, not applicable]

River

Chinook salmon Coho salmon Summer steelhead

Marked Unmarked Marked Unmarked Marked Unmarked

East Fork Quinault 7 23 NA NA 5 35

North Fork Quinault 0 16 NA NA 2 3

South Fork Hoh1 16 23 0 0 15 11

1

There are no hatchery releases of Chinook salmon, coho salmon, or summer steelhead in the Hoh River Basin.

Table 19. Example of a summary of the number of fish observed in a stream reference site during electrofishing surveys in July and 

September of a given year. 

Creek

Coho salmon Bull trout Rainbow/Steelhead Brook trout Sculpin spp.

July Sept. July Sept. July Sept. July Sept. July Sept.

Mink Lake Creek, Sol Duc 569 754 0 0 246 278 0 0 238 278

Big Creek, Quinault 350 91 0 0 16 29 0 0 15 198

Pass Creek, Dosewallips 0 0 0 0 0 0 28 38 0 0

Indian Creek, Bogachiel 293 349 0 0 126 479 0 0 45 123

Slate Creek, North Fork 

Skokomish

0 0 129 198 28 79 0 0 18 38
6. Data Handling, Analysis, and Reporting 43

Figure 17. Length-frequency histograms for rainbow trout in the middle and upper Elwha River in 

June, July, August, and September 2004 and 2005 based on backpack electrofishing. 

(From Connolly and Brenkman, 2008.)
44 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Calibration of data loggers is important, and a relatively 

simple process. The procedure involves the following steps 

from Dunham and others (2005):

1. Deploy the data loggers at a short sampling interval (for 

example, 1 minute);

2. Submerge data loggers in an insulated, well-mixed water 

bath with a generous amount of melting ice (for example, 

large cooler with ice water);

3. If possible, record water temperatures using a 

thermometer to ensure the temperature of the water bath is 

0oC; 

4. After at least 1 hour, remove the data loggers and 

download the data. If calibrated correctly, the temperature 

readings should level out at 0oC.

Data archiving is one of the most important steps in 

temperature monitoring (Dunham and others, 2005; table 20). 

There are three important types of information to include in 

water temperature databases: (1) pre-deployment information, 

(2) field deployment information, and (3) post-deployment 

information (Dunham and others, 2005).

I. Reporting and Product Development

We recommend that a summary report be produced 

annually, with a more detailed report produced every 5 years. 

Standard Report Format

Annual reports and trend analysis reports will use 

the NPS Natural Resource Publications template, a preformatted Microsoft© Word template document based on 

current NPS formatting standards. Annual reports will use 

the Natural Resource Report template, and trend analysis and 

other peer-reviewed technical reports will use the Natural 

Resource Technical Report template. These templates and 

documentation of the NPS publication standards (National 

Park Service, 2005) are available at: http://www.nature.nps.

gov/publications/NRPM/index.cfm.

Table 20. Example of a relational database application for storage of temperature data collected using data loggers.

[From Dunham and others, 2005]

Table name Field name Description

Site Site ID Auto number assigning consecutive numbers to sites

Stream name Name of stream sampled

Site Number of descriptor of site within stream

Basin River basin

Quad 24K Quad name

UTM X UTM easting coordinate

UTM Y UTM northing coordinate

Elevation Elevation in meters of site

Logger Logger ID Unique ID or serial number of logger

Type Manufacturer and/or model of logger

Year Year of sample

Deployed Site ID Site ID of stream and site (relates back to Site table)

Logger ID Unique ID of logger deployed in the stream (relates back to Logger table)

Date Date logger placed in water

Time Time logger placed in water

Interval Time interval of samples

Depth Depth of logger

Removal Site ID Site ID of stream and site (relates back to Site table)

Date Date logger removed from water

Time Time logger removed from water

Comments Any site differences from time of deployment to time of removal

Temperature Site ID Site ID of stream and site (relates back to Site table)

Date Date of sample

Time Time of sample

Temperature Temperature (in Celsius or Fahrenheit) of sample
6. Data Handling, Analysis, and Reporting 45

•	 To share information as broadly as legally possible, 

and to provide a consistent, tractable approach for 

handling sensitive information, the following shall 

apply if a project is likely to collect and store sensitive 

information:

◦ Random coordinate offsets of up to 2 km for data 

collection locations, and

◦ Removal of data fields from the released copy that 

are likely to contain sensitive information.

a. What Kinds of Information Can and Can Not Be 

Shared?

•	 Do not share: Project staff and cooperators should not 

share any information outside NPS that reveals details 

about the “nature or specific location” of protected 

resources, unless a confidentiality agreement is in 

place. Specifically, the following information should be 

omitted from shared copies of all data, presentations, 

reports, or other published forms of information.

◦ Exact coordinates – Instead, public coordinates are 

to be generated that include a random offset azimuth 

and distance. These offset coordinates can be shared 

freely.

◦ Other descriptive location data – Examples may 

include travel descriptions, location descriptions, or 

other fields that contain information that may reveal 

the specific location of the protected resource(s).

◦ Protected resource observations at disclosed 

locations – If specific location information has 

already been made publicly available, the occurrence 

of protected resources at that location cannot 

be shared outside NPS without a confidentiality 

agreement. For example, if the exact coordinates for 

a monitoring station location are posted to a website 

or put into a publication, then at a later point in time 

a spotted owl nest is observed at that monitoring 

station, that nest cannot be mentioned or referred to 

in any report, presentation, data set, or publication 

that will be shared outside NPS.

•	 Do share: All other information about the protected 

resource(s) may be freely shared, so long as the 

information does not reveal details about the “nature 

or specific location” of the protected resource(s) that 

are not already readily available to the general public 

in some form (for example, other published material). 

Species tallies and other types of data presentations 

that do not disclose the precise locations of protected 

resources may be shared, unless by indicating the 

presence of the species the specific location is also 

revealed (for example, in the case of a small park).

Sensitive Information Procedures

Certain project information related to the specific 

locations of rare or threatened taxa may meet criteria for 

protection and as such should not be shared outside NPS 

except where a written confidentiality agreement is in place 

prior to sharing. Before preparing data in any format for 

sharing outside NPS – including presentations, reports, and 

publications – the Project Lead should refer to the information 

contained in this section. Information that may convey specific 

locations of sensitive resources may need to be screened or 

redacted from public versions of products prior to release. 

There also will be adherence to USGS policy on information 

dissemination.

Although it is the general NPS policy to share 

information widely, the NPS also realizes that providing 

information about the location of park resources may 

sometimes place those resources at risk of harm, theft, or 

destruction. This can occur, for example, with regard to 

federally threatened fish species. Therefore, information will 

be withheld when the NPS foresees that disclosure would be 

harmful to an interest protected by an exemption under the 

Freedom of Information Act (FOIA). The National Parks 

Omnibus Management Act, Section 207, 16 U.S.C. 5937, is 

interpreted to prohibit the release of information regarding 

the “nature or specific location” of certain cultural and natural 

resources in the national park system. Additional details and 

information about the legal basis for this policy are in the 

NPS Management Policies (National Park Service, 2006), and 

in Director’s Order #66.

These guidelines apply to all NCCN staff, cooperators, 

contractors, and other partners who are likely to obtain or 

have access to information about protected NPS resources. 

The Project Lead has primary responsibility for ensuring 

adequate protection of sensitive information related to this 

project. Additionally, USGS staff shall adhere to policies on 

information dissemination.

The following are highlights of the strategy for protecting 

this information: 

•	 Protected resources, in the context of the NCCN 

Inventory and Monitoring Program, include species 

that have State- or Federally-listed status, and other 

species deemed rare or sensitive by local park taxa 

experts.

•	 Sensitive information is defined as information about 

protected resources that may reveal the “nature 

or specific location” of protected resources. Such 

information must not be shared outside the National 

Park Service, unless a signed confidentiality agreement 

is in place.

•	 In general, if information is withheld from one 

requesting party, it must be withheld from anyone else 

who requests it, and if information is provided to one 

requesting party without a confidentiality agreement, it 

must be provided to anyone else who requests it.
46 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Whenever products such as databases and reports are 

being generated, handled, and stored, they should be created 

explicitly for one of the following purposes:

1. Public or general-use – Intended for general distribution, 

sharing with cooperators, or posting to public websites. 

They may be derived from products that contain sensitive 

information so long as the sensitive information is either 

removed or otherwise rendered in a manner consistent 

with other guidance in this document.

2. Internal NPS use – These are products that contain 

sensitive information and should be stored and distributed 

only in a manner that ensures their continued protection. 

These products should clearly indicate that they are solely 

for internal NPS use by containing the phrase: “Internal 

NPS Use Only – Not For Release.” These products 

can only be shared within NPS or in cases where a 

confidentiality agreement is in place. They do not need to 

be revised in a way that conceals the location of protected 

resources.

b. Data Sets

To create a copy of a data set that will be posted or shared 

outside NPS:

1. Make sure the public offset coordinates have been 

populated for each sample or observation location in 

tbl_Locations.

2. Remove tbl_Coordinates, tbl_Target_Coordinates, and 

tbl_GPS_Info.

3. Delete the following database objects to ensure consistent 

omission of fields that may contain specific, identifying 

information about locations of protected resources:

a. tbl_Sites.Site_notes

b. tbl_Locations.Travel_notes

c. tbl_Locations.Elevation, Elev_units, Elev_source

d. tbl_Locations.Location_desc

e. tbl_Locations.Location_notes

f. tbl_Features

g. tbl_Markers

The local, master copy of the database contains the exact 

coordinates and all data fields. The Data Manager and/or GIS 

Specialist can provide technical assistance as needed to apply 

coordinate offsets or otherwise edit data products for sensitive 

information.

c. Presentations and Reports

Public or general-use reports and presentations should 

adhere to the following guidelines:

1. Do not list exact coordinates or specific location 

information in any text, figure, table, or graphic in the 

report or presentation. If a list of coordinates is necessary, 

use only offset coordinates and clearly indicate that 

coordinates have been purposely offset to protect the 

resource(s) as required by law and NPS policy.

2. Use only general use maps as specified in the section on 

maps and other GIS output.

3. Indicate whether the information has been peer reviewed 

or whether results are preliminary.

If a report is intended for internal use only, these 

restrictions do not apply. However, each page of the report 

should be clearly marked with the following phrase: “Internal 

NPS Use Only – Not For Release.”
6. Data Handling, Analysis, and Reporting 47

J. Product Delivery, Posting, and Distribution

Product Delivery Schedule and Specifications

[Abbreviations: NCCN, North Coast and Cascades Monitoring Network; GPS, global positioning system; GIS, geographic information system; NPS, National 

Park Service; EPA, Environmental Protection Agency; XML, Extensible Markup Language; I&M, inventory and monitoring; PDF, portable document format]

Deliverable product Primary responsibility Target date Instructions

Field season report Field Crew Lead September 30 of the 

same year

Upload digital file in Microsoft© Word format to the 

NCCN Digital Library1

 submissions folder.

Raw GPS data files Field Crew Lead September 30 of the 

same year

Zip and send all digital files to the GIS Specialist.

Processed GPS data files GIS Specialist October 30 of the 

same year

Zip and upload raw and processed files to the NCCN 

Digital Library1

.

Digital photographs Project Lead November 30 of the 

same year

Organize, name and maintain photographic images 

in the project workspace according to the image 

handling procedures in Section 6D, Data Entry and 

Processing.

Certified working database Project Lead Delivered by 

November 30 of the 

same year, data are 

not posted to public 

sites until June of 

the second year

Refer to the following section on delivering certified 

data and related materials. The final destination 

is the master project database and GIS data sets, 

NPSTORET2

 and EPA STORET2 (for water 

temperature data), NPSpecies3

, the NCCN Digital 

Library1

, and the NPS Data Store4.

Certified geospatial data Project Lead with 

GIS Specialist

Data certification report Project Lead

Metadata interview form Project Lead

Full metadata (parsed XML) Data Manager and 

GIS Specialist

March 15 of the 

following year

Upload the parsed XML record to the NPS Data 

Store4

, and store in the NCCN Digital Library1.

Annual I&M report Project Lead May 1 of the 

following year

Refer to the following section on reports and 

publications. The final destination is NatureBib5

, 

NCCN Digital Library1

, and printout to local park 

collections. 5-year analysis report Project Lead and 

Data Analyst

Every 5 years by May

Other publications Project Lead and 

Data Analyst

As completed

Field data forms Project Lead Every 5 years by 

January 31

Scan original, marked-up field forms as PDF files 

and upload these to the NCCN Digital Library1

submissions folder. Originals go to the Park 

Curator for archival.

Other records Project Lead Review for retention 

every January

Organize and send analog files to Park Curator for 

archival. Digital files that are slated for permanent 

retention should be uploaded to the NCCN Digital 

Library1

. Retain or dispose of records following 

NPS Director’s Order #196.

1

 The NCCN Digital Library is a hierarchical digital filing system stored on the NCCN file servers (Boetsch and others, 2005). Network users have read-only 

access to these files, except where information sensitivity may preclude general access.

2

 NPSTORET (http://www.nature.nps.gov/water/infoanddata) and EPA STORET (http://www.epa.gov/storet/) are, respectively, the NPS and national 

enterprise data warehouses for water quality data. NPSTORET is maintained by NPS-Water Resources Division (WRD) and is synchronized with EPA STORET 

on a regular basis.

3

 NPSpecies is the NPS database and application for maintaining park-specific species lists and observation data (http://science.nature.nps.gov/im/apps/npspp/

index.htm).

4

 NPS Data Store is a clearinghouse for natural resource data and metadata (http://science.nature.nps.gov/nrdata). Only non-sensitive information is posted to 

NPS Data Store. Refer to the section on sensitive information in Section 6J, Product Delivery, Posting and Distribution for details.

5

 NatureBib is the NPS bibliographic database (http://www.nature.nps.gov/nrbib/index.htm). This application has the capability of storing and providing 

public access to image data (for example, PDF files) associated with each record.

6

 NPS Director’s Order 19 provides a schedule indicating the amount of time that the various kinds of records should be retained. Available at: http://data2.itc.

nps.gov/npspolicy/DOrders.cfm.
48 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

All digital file submissions that are sent by email should 

be accompanied by a product submission form, which briefly 

captures the following information about the products:

•	 Submission date

•	 Name of the person submitting the product(s)

•	 Name and file format of each product

•	 Indication of whether or not each product contains 

sensitive information (see Section 6I, Reporting and 

Product Development for a definition). 

This form can be downloaded from the NCCN website or 

obtained from the Data Manager. People who submit digital 

files directly to the NCCN Digital Library will be prompted 

for the same information, and so a submission form is not 

required.

Upon notification and/or receipt of the completed 

products, the Data Manager or GIS Specialist will check them 

into the NCCN project tracking application.

Delivering Certified Data and Related Materials

Data certification is a benchmark in the project 

information management process that indicates that: 

(1) data are complete for the period of record, (2) data have 

undergone and passed the quality assurance checks; and 

(3) data are appropriately documented and in a condition 

for archiving, posting and distribution as appropriate. To 

ensure that only quality data are included in reports and 

other project deliverables, the data certification step is an 

annual requirement for all tabular and spatial data. For more 

information, refer to SOP #3: Data Quality Review and 

Certification.

The following deliverables should be delivered as a 

package:

•	 Certified working database – Database in Microsoft©

Access format containing data for the current season 

that has been through the quality assurance checks 

documented in SOP #3: Data Quality Review and 

Certification.

•	 Certified geospatial data – GIS themes in ESRI 

coverage or shapefile format. Refer to NCCN 

GIS Development Guidelines (North Coast and 

Cascades Network, 2006c) and NCCN GIS Product 

Specifications (North Coast and Cascades Network, 

2005a) for more information.

•	 Data certification report – A brief questionnaire in 

Microsoft© Word that describes the certified data 

product(s) being submitted. A template form is 

available on the NCCN website at: http://science.

nature.nps.gov/im/units/nccn/datamgmt_guide.cfm.

•	 Metadata interview form – The metadata interview 

form is a Microsoft© Word questionnaire that greatly 

facilitates metadata creation. It is available on the 

NCCN website at: http://science.nature.nps.gov/im/

units/nccn/datamgmt_guide.cfm. For more details, 

refer to Section 6F, Metadata Procedures.

After the quality review is completed, the Project Lead 

should package the certification materials for delivery as 

follows:

1. Open the certified back-end database file and compact 

it (in Microsoft© Access, Tools > Database Utilities > 

Compact and Repair Database). This will make the file 

size much smaller. Back-end files are typically indicated 

with the letters “_be” in the name (for example, Fish_

Assemblages_FIa10_be_2007.mdb).

2. Rename the certified back-end file with the project 

code (“FIa10”), the year or span of years for the data 

being certified, and the word “certified”. For example: 

FIa10_2007_certified.mdb.

3. Create a compressed file (using WinZip® or similar 

software) and add the back-end database file to that file. 

Note: The front-end application does not contain project 

data and as such should not be included in the delivery 

file.

4. Add the completed metadata interview and data 

certification forms to the compressed file. Both files 

should be named in a manner consistent with the naming 

conventions described elsewhere in this document.

5. Add any geospatial data files that are not already in the 

possession of the GIS Specialist. Geospatial data files 

should be developed and named according to NCCN 

GIS Naming Conventions (North Coast and Cascades 

Network, 2005b).

6. Upload the compressed file containing all certification 

materials to the new submissions folder of the NCCN 

Digital Library. If the Project Lead does not have intranet 

access to the NCCN Digital Library, then certification 

materials should be delivered as follows:

a. If the compressed file is under 5 mb in size, it may 

be delivered directly to the NPS Lead and Data 

Manager by email.

b. If the compressed file is larger than 5 mb, it should 

be copied to a CD or DVD and delivered in this 

manner. Under no circumstances should products 

containing sensitive information be posted to an 

FTP site or other unsecured web portal (refer to 

Section 6I, Reporting and Product Development for 

a definition of sensitive information).

7. Notify the Data Manager by email that the certification 

materials have been uploaded or otherwise sent.
6. Data Handling, Analysis, and Reporting 49

Upon receiving the certification materials, the Data 

Manager will:

1. Review them for completeness and work with the Project 

Lead if there are any questions.

2. Notify the GIS Specialist if any geospatial data are 

submitted. The GIS Specialist will then review the 

data, and update any project GIS data sets and metadata 

accordingly.

3. Check in the delivered products using the NCCN project 

tracking application.

4. Store the certified products together in the NCCN Digital 

Library.

5. Upload the certified data to the master project database.

6. Export temperature data and submit these to NPS Water 

Resources Division (WRD) staff to be uploaded to WRD 

NPSTORET and EPA STORET.

7. Notify the Project Lead that the year’s data have been 

successfully uploaded and processed. The Project Lead 

may then proceed with data summarization, analysis, and 

reporting.

8. Update species observation data records in NPSpecies.

9. Develop, parse, and post the XML metadata record to the 

NPS Data Store.

10. After a holding period of 2 years, the Data Manager 

will upload the certified data to the NPS Data Store. 

This holding period is to protect professional authorship 

priority and to provide sufficient time to catch any 

undetected quality assurance problems.

No sensitive information (for example, information 

about the specific nature or location of protected resources) 

may be posted to the NPS Data Store or another publiclyaccessible website, or otherwise shared or distributed outside 

NPS without a confidentiality agreement between NPS and 

the agency, organization, or person(s) with whom the sensitive 

information is to be shared. Only products that are intended 

for public/general-use may be posted to public websites and 

clearinghouses–these may not contain sensitive information.

Instructions for Reports and Publications

In general, the procedures for reports and publications are 

as follows:

1. The document should be formatted using the NPS Natural 

Resource Publications template. Formatting according to 

NPS standards is easiest when using the template from 

the very beginning, as opposed to reformatting an existing 

document.

2. The document should be peer reviewed at the appropriate 

level. For example, I&M Annual Reports should be 

reviewed by other members of the appropriate project 

work group. The Network Coordinator also will review 

all annual reports for completeness and compliance with 

I&M standards and expectations.

3. Upon completing the peer review, acquire a publication 

series number from the NPS Technical Information Center 

or the appropriate local or regional key official (currently 

the Regional I&M Coordinator).

4. Upload the file in PDF and Microsoft© Word formats to 

the NCCN Digital Library submissions folder.

5. Send a printout to each Park Curator.

6. The Data Manager or a designee will create a 

bibliographic record and upload the PDF document to 

NatureBib according to document sensitivity.

File Naming Standards

Prior to submitting digital products, files should be 

named according to the naming conventions appropriate to 

each product type.

a. Images

The image file name should consist of the following 

parts:

1. Date of data capture (formatted as YYYYMMDD)

2. Reference name

3. Optional: a brief descriptive word or phrase

4 Optional: a sequential number if multiple images were 

captured

5. Optional: time (formatted as HHMM)

b. Reports and Publications

•	 No spaces or special characters in the file name.

•	 Use the underbar (“_”) character to separate file name 

components.

•	 Try to limit file names to 30 characters or fewer, up to a 

maximum of 50 characters. 

•	 Dates should be formatted as YYYYMMDD.

•	 As appropriate, include the project code (for example, 

“FIa10”), network code (“NCCN”) or park code, and 

year in the file name. Examples: NCCN_FIa10_2007_

Annual_report.pdf

•	 NCCN_FIa10_2007_Field_season_report.doc; NCCN_

FIa10_2007_Certification_report.doc
50 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

c. Other Files

Unless otherwise specified, files for other product types 

should be named as follows:

•	 No spaces or special characters in the file name.

•	 Use the underbar (“_”) character to separate file name 

components.

•	 Try to limit file names to 30 characters or fewer, up to a 

maximum of 50 characters. 

•	 Dates should be formatted as YYYYMMDD.

•	 Correspondence files should be named as 

YYYYMMDD_AuthorName_subject.ext.

Holding Period for Project Data

To permit sufficient time for priority in publication, 

certified project data will be held upon delivery for a period 

not to exceed 2 years after it was originally collected. After the 

2-year period has elapsed, all certified, non-sensitive data will 

be posted to the NPS Data Store. 

Note: This hold only applies to raw data, and not to metadata, 

reports or other products that are posted to NPS clearinghouses 

immediately after being received and processed.

To protect professional authorship priority and to provide 

sufficient time to complete quality assurance measures, 

there is a 2-year holding period before posting or otherwise 

distributing finalized data. This means that certified data 

sets are first posted to publicly accessible websites (that is, 

the NPS Data Store) approximately 24 months after they are 

collected (for example, data collected in June 2008 becomes 

generally available through the NPS Data Store in June 2010). 

In certain circumstances, and at the discretion of the Project 

Lead, data may be shared before a full 2 years have elapsed. 

Note: This hold only applies to raw data; all metadata, reports, 

or other products are to be posted to NPS clearinghouses in a 

timely manner as they are received and processed.

Responding to Data Requests

Occasionally, a park or project staff member may be 

contacted directly regarding a specific data request from 

another agency, organization, scientist, or from a member of 

the general public. The following points should be considered 

when responding to data requests:

•	 NPS is the originator and steward of the data, and the 

NPS Inventory and Monitoring Program should be 

acknowledged in any professional publication using 

the data.

•	 NPS retains distribution rights; copies of the data 

should not be redistributed by anyone but NPS.

•	 Data that project staff members and cooperators collect 

using public funds are public records and as such can 

not be considered personal or professional intellectual 

property.

•	 No sensitive information (for example, information 

about the specific nature or location of protected 

resources) may be posted to the NPS Data Store or 

another publicly accessible website, or otherwise 

shared or distributed outside NPS without a 

confidentiality agreement between NPS and the 

agency, organization, or person(s) with whom 

the sensitive information is to be shared. Refer to 

Section 6I, Reporting and Product Development for a 

definition of sensitive information.

•	 For quality assurance, only certified, finalized versions 

of data sets should be shared with others. In cases 

where a provisional data set needs to be shared 

with others prior to certification: any accompanying 

communications should clearly indicate that the data 

set is provisional and subject to change according 

to our quality review process; and file names and 

the media it is sent on should be clearly labeled as 

containing provisional data not for distribution.

The Project Lead will handle all data requests as follows:

1. Discuss the request with other Park Biologists as 

necessary to make those with a need to know aware of the 

request and, if necessary, to work together on a response.

2. Notify the Data Manager of the request if s/he is needed 

to facilitate fulfilling the request in some manner.

3. Respond to the request in an official email or memo.

4. In the response, refer the requestor to the NPS Data 

Store (http://science.nature.nps.gov/nrdata), so they may 

download the necessary data and/or metadata. If the 

request can not be fulfilled in that manner – either because 

the data products have not been posted yet, or because 

the requested data include sensitive information – work 

with the Data Manager to discuss options for fulfilling 

the request directly (for example, burning data to CD 

or DVD). Ordinarily, only certified data sets should be 

shared outside NPS.

5. It is recommended that documents and presentation files 

be converted to PDF format prior to distribution. This is to 

maximize portability and to reduce the ability for others 

to alter and redistribute files.

6. If the request is for data that may reveal the location 

of protected resources, refer to the next section in 

this document about sensitive information and also to 

Section 6I, Reporting and Product Development for a 

definition of sensitive information.
6. Data Handling, Analysis, and Reporting 51

7. After responding, provide the following information to the 

Data Manager, who will maintain a log of all requests in 

the NCCN Project Tracking database:

a Name and affiliation of requestor

b Request date

c Nature of request

d Responder

e Response date

f Nature of response

g List of specific data sets and products sent (if any)

7. Freedom of Information (FOIA) Requests

All official FOIA requests will be handled according 

to NPS policy. The Project Lead will work with the Data 

Manager and the park FOIA representative(s) of the park(s) 

for which the request applies.

8. Special Procedures for Sensitive Information

Products that have been identified upon delivery by 

the Project Lead as containing sensitive information will 

normally be revised into a form that does not disclose the 

locations of protected resources – most often by removing 

specific coordinates and only providing coordinates that 

include a random offset to indicate the general locality of the 

occurrence. If this kind of measure is not a sufficient safeguard 

given the nature of the product or the protected resource 

in question, the product(s) will withheld from posting and 

distribution.

If requests for distribution of products containing 

sensitive information are initiated by the NPS, by another 

Federal agency, or by another partner organization (for 

example, a research scientist at a university), the unedited 

product (that is, the full data set that includes sensitive 

information) may only be shared after a confidentiality 

agreement is established between NPS and the agency, 

organization, or person(s) with whom the sensitive information 

is to be shared. All data requests will be tracked.

Once a confidentiality agreement is in place, products 

containing sensitive information may be shared following 

these guidelines:

•	 Always clearly indicate in accompanying 

correspondence that the products contain sensitive 

information, and specify which products contain 

sensitive information.

•	 Indicate in all correspondence that products containing 

sensitive information should be stored and maintained 

separately from non-sensitive information, and 

protected from accidental release or re-distribution.

•	 Indicate that NPS retains all distribution rights; copies 

of the data should not be redistributed by anyone but 

NPS.

•	 Include the following standard disclaimer in a text file 

with all digital media upon distribution: 

The following files contain protected information. 

This information was provided by the National Park 

Service under a confidentiality agreement. It is not 

to be published, handled, re-distributed or used in a 

manner inconsistent with that agreement.

The text file also should specify the file(s) containing 

sensitive information.

•	 If the products are being sent on physical media (for 

example, CD or DVD), the media should be marked in 

such a way that clearly indicates that media contains 

sensitive information provided by the National Park 

Service.

a. Confidentiality Agreements

Confidentiality agreements may be created between NPS 

and another organization or individual to ensure that protected 

information is not inadvertently released. When contracts or 

other agreements with a non-federal partner do not include 

a specific provision to prevent the release of protected 

information, the written document must include the following 

standard Confidentiality Agreement: 

Confidentiality Agreement – I agree to keep 

confidential any protected information that I may 

develop or otherwise acquire as part of my work 

with the National Park Service. I understand that 

with regard to protected information, I am an agent 

of the National Park Service and must not release 

that information. I also understand that by law I 

may not share protected information with anyone 

through any means except as specifically authorized 

by the National Park Service. I understand that 

protected information concerns the nature and 

specific location of endangered, threatened, rare, 

commercially valuable, mineral, paleontological, 

or cultural patrimony resources such as threatened 

or endangered species, rare features, archeological 

sites, museum collections, caves, fossil sites, 

gemstones, and sacred ceremonial sites. Lastly, I 

understand that protected information must not be 

inadvertently disclosed through any means including 

websites, maps, scientific articles, presentation, and 

speeches.
52 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

K. Archiving and Records Management

All project files should be reviewed, cleaned up, and 

organized by the Project Lead on a regular basis (for example, 

annually in January). Decisions on what to retain and what to 

destroy should be made following guidelines stipulated in NPS 

Director’s Order 19, which provides a schedule indicating the 

amount of time that the various kinds of records should be 

retained. Many of the files for this project may be scheduled 

for permanent retention, so it is important to isolate and 

protect them, rather than lose them in the midst of a large, 

disordered array of miscellaneous project files. Because this 

is a long-term monitoring project, good records management 

practices are critical for ensuring the continuity of project 

information. Files will be more useful to others if they are 

well organized, well named, and stored in a common format. 

In addition, files containing sensitive information must be 

stored in a manner that will enable quick identification. Refer 

to Section 6I, Reporting and Product Development for a 

definition for a definition of sensitive information.

To help ensure safe and organized electronic file 

management, NCCN has implemented a system called the 

NCCN Digital Library, which is a hierarchical digital filing 

system stored on the NCCN file servers (Boetsch and others, 

2005). The typical arrangement is by project, then by year to 

facilitate easy access. Network users have read-only access to 

these files, except where information sensitivity may preclude 

general access.

As digital products are delivered for long-term storage 

according to the schedule in Section 6J, Product Delivery, 

Posting and Distribution, they will be catalogued in the NCCN 

project tracking database and filed within this the NCCN 

Digital Library. Analog (non-digital) materials are to be 

handled according to current practices of the individual park 

collections.

l. Season Close-out

After the conclusion of the field season, the Project Lead, 

Data Manager, and GIS Specialist should meet to discuss the 

recent field season, and to document any needed changes to 

the field sampling protocols, the working database application, 

or to any of the SOPs associated with the protocol.

7. Revisions to Protocol 

All protocol revisions will be documented in the revision 

logs. Small changes to the protocol (for example, adding or 

modifying a variable) will be reviewed by the Project Lead, 

and approved by the Network Coordinator. More drastic 

changes (for example, modifications to the sample design or 

analytical methods for trend detection) will trigger an outside 

review to be conducted by the NPS Pacific West Regional 

Office or designated review panel as directed by the NPS 

Inventory and Monitoring Program.

This section explains how to make and track changes 

to the NCCN Fish Assemblages Monitoring Protocol, 

including its accompanying SOPs. Project staff should refer 

to these guidelines whenever edits are necessary, and should 

be familiar with the protocol versioning system in order to 

identify and use the most current versions of the protocol 

documents. Required revisions should be made in a timely 

manner to minimize disruptions to project planning and 

operations.

This protocol attempts to incorporate the best and 

most cost-effective methods for monitoring and information 

management. As new technologies, methods, and equipment 

become available, this protocol will be updated as appropriate, 

by balancing current best practices against the continuity of 

protocol information. All changes will be made in a timely 

manner with the appropriate level of review.

All edits require review for clarity and technical 

soundness. Small changes to existing documents – for 

example, formatting, simple clarification of existing content, 

small changes in the task schedule or project budget, or 

general updates to information management handling SOPs 

– may be reviewed in-house by project cooperators and 

NCCN staff. However, changes to data collection or analysis 

techniques, sampling design, or response design will trigger an 

outside review to be coordinated by the Pacific West Regional 

Office. 
7. Revisions to Protocol 53

Procedures

1. Discuss proposed changes with other project staff prior 

to making modifications. It is especially important to 

consult with the Data Manager prior to making changes 

because certain types of changes may jeopardize data set 

integrity unless they are planned and executed with data 

set integrity in mind. Because certain changes may require 

altering the database structure or functionality, advance 

notice of changes is important to minimize disruptions to 

project operations. Consensus should be reached on who 

will be making the changes and in what timeframe.

2. Make the agreed-upon changes in the current, primary 

version of the appropriate protocol document (that is, not 

the most recent versioned copy – see below). 

Note that the protocol is split into separate documents for 

each appendix and SOP. 

Note: A change in one document also may necessitate 

other changes elsewhere in the protocol. For example, a 

change in the narrative may require changes to several 

SOPs; similarly renumbering an SOP may mean changing 

document references in several other documents. The 

project task list and other appendixes also may need to be 

updated to reflect changes in timing or responsibilities for 

the various project tasks.

3. Document all edits in the Revision History Log embedded 

in the protocol narrative and each SOP. Log changes only 

in the document being edited (that is, if there is a change 

to an SOP, log those changes only in that document). 

Record the date of the changes (that is, the date on 

which all changes were finalized), author of the revision, 

describe the change and cite the paragraph(s) and page(s) 

where changes are made, and briefly indicate the reason 

for making the changes.

4. Circulate the changed document for internal review

among project staff and cooperators.

5. Upon ratification and finalizing changes:

a. Ensure that the version date (last saved date field 

code in the document header) and file name (field 

code in the document footer) are updated properly 

throughout the document.

b. Make a copy of each changed file to the protocol 

archive folder (that is, a subfolder under the Protocol 

folder in the project workspace).

c. The copied files should be renamed by appending 

the revision date in YYYYMMDD format. In this 

manner, the revision date becomes the version 

number, and this copy becomes the ‘versioned’ copy 

to be archived and distributed.

d. The current, primary version of the document (that 

is, not the versioned document just copied and 

renamed) does not have a date stamp associated with 

it.

e. To avoid unplanned edits to the document, reset 

the document to read-only by right-clicking on the 

document in Windows Explorer and checking the 

appropriate box in the Properties popup.

f. Inform the Data Manager so the new version 

number(s) can be incorporated into the project 

metadata. 

6. As appropriate, create PDF files of the versioned 

documents to post to the Internet and share with others. 

These PDF files should have the same name and be made 

from the versioned copy of the file.

7. Post the versioned copies of revised documents to 

the NCCN Digital Library and forward copies to all 

individuals who had been using a previous version of the 

affected document.

Example of Document Revision

1. SOP_1_GPS_Use.doc is revised on October 31, 2008, and 

circulated for review.

2. Changes are accepted by the group and changes are 

finalized on November 6, 2008.

3. The revised SOP is:

a. Copied into the Archive folder.

b. That versioned copy is renamed as SOP_1_GPS_

Use_20081106.doc.

c. Both the current, primary version and the versioned 

copy are set to read-only.

d. A PDF of the document is created from the 

versioned copy and named SOP_1_GPS_

Use_20081106.pdf.

e. Both the PDF and the versioned document are 

uploaded to the NCCN Digital Library.

The PDF is sent to any cooperators.
54 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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56 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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nps.gov/im/units/nccn/datamgmt_guide.cfm

Northcote, T.G., and Ennis, G.L., 1994, Mountain whitefish 

biology and habitat use in relation to compensation and 

improvement possibilities: Reviews in Fisheries Sciences, 

v. 2, no. 4, p. 347-371.

Northcote, T.G., and Wilkie, D.W., 1963, Underwater census 

of stream fish populations: Transactions of the American 

Fisheries Society, v. 92, p. 146-151.

Oakley, K.L., Thomas, L.P., and Fancy, Steven G., 2003, 

Guidelines for long-term monitoring protocols: Wildlife 

Society Bulletin, v. 31, no. 4, p. 1000-1003.

Oberdorff, T., Pont, D., Hugueny, B., and Porchers, J., 2002, 

Development and validation of a fish-based index for the 

assessment of “river health” in France: Freshwater Biology, 

v. 47, p. 1720-1734.

Peterson, D.P., and Fausch, K.D., 2003, Upstream movement 

by nonnative brook trout (Salvelinus fontinalis) promotes 

invasion of native cutthroat trout (Oncorhynchus clarki) 

habitat: Canadian Journal of Fisheries and Aquatic 

Sciences, v. 60, p. 1502-1516.

Peterson, D.P., Fausch, K.D., and White, G., 2004, Population 

ecology of an invasion: Effects of brook trout on native 

cutthroat trout: Ecological Applications, v. 14, p. 754-772.
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Petersen, J.C., Justus, B.J., Dodd, H.R., Bowles, D.E., 

Morrison, L.W., Williams, M.H., and Rowell, G.A., 2008, 

Methods for monitoring fish communities of Buffalo 

National River and Ozark National Scenic Riverways in the 

Ozark Plateaus of Arkansas and Missouri:Version 1: U.S. 

Geological Survey Open-File Report 2007-1302, 94 p.

Phinney, L., and Bucknell, P., 1975, A catalog of Washington 

streams and salmon utilization–Vol. 2, Coastal region: I and 

E Division, Washington Department of Fisheries, Olympia.

Plafkin, J.L., Barbour, M.T., Porter, K.D., Gross, S.K., and 

Hughes, R.M., 1989, Rapid bioassessment protocols for use 

in streams and rivers: Benthic macroinvertebrates and fish: 

Washington, D.C., U.S. Environmental Protection Agency, 

EPA/440/4-89/001.

Pollard, W.R., Hartman, G.F., Groot, C., and Edgell, P., 

1997, Field identification of coastal juvenile salmonids: 

Department of Fisheries and Oceans and Weyerhauser ltd., 

British Columbia, Canada.

Reisenbichler, R.R., and McIntyre, J.D., 1977, Genetic 

differences in growth and survival of juvenile hatchery 

and wild steelhead trout, Salmo gairdneri: Journal of the 

Fisheries Research Board of Canada, v. 34, p. 123-128.

Rieman, B.E., and McIntyre, J.D., 1993, Demographic and 

habitat requirements for conservation of bull trout: U.S. 

Forest Service General Technical Report INT-302, Ogden, 

Utah, U.S. Department of Agriculture, Forest Service, 

Intermountain Research Station, 37 p.

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observations to estimate cutthroat trout abundance in the 

Yellowstone River: North American Journal of Fisheries 

Management, v. 4, p. 479-487.

Schmutz, S., Kaufmann, M., Vogel, B., Jungwirth, M., and 

Muhar, S., 2000, A multi-level concept for fish-based, 

river-type-specific assessment of ecological integrity: 

Hydrobiologia, v. 422/423, p. 279-289.

Siegel, R.B., Wilkerson, R.L., Jenkins, K.J., Kuntz II, R.C., 

Boetsch, J.R., Schaberl, J.P., and Happe, P.J., 2007, 

Landbird monitoring protocol for national parks in the 

North Coast and Cascades Network: U.S. Geological 

Survey Techniques and Methods 2-A6, 208 p.

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salmonids in the Intermountain West: Ogden, Utah, U.S. 

Forest Service, Intermountain Research Station, General 

Technical Report INT-GTR-307.

Torgersen, C.E., 2002, A geographical framework for 

assessing longitudinal patterns in stream habitat and fish 

distribution: Corvallis, Oregon State University, PhD 

dissertation.

Williams, J.E., Johnson, J.E., Hendrickson, D.A., ContrerasBalderas, S., Williams, J.D., Navarro-Mendoza, M., 

McAllister, D.E., and Deacon, J.E., 1989, Fishes of North 

America endangered, threatened, or of special concern: 

1989: Fisheries, v. 14, no. 6, p. 2–19.

Wydoski, R.S., and Whitney, R.R., 2003, Inland fishes of 

Washington, 2nd edition, revised and expanded: American 

Fisheries Society and University of Washington Press, 

322 p.

Zyskowski, S.E., 2007, Stream fish inventories 2001 to 2003, 

North Cascades National Park Complex and Mount Rainier 

National Park, Washington: Sedro-Woolley, Washington, 

U.S. Department of Interior, National Park Service, 51 p.
58 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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SOP 1: Use of GPS and Data Downloading 59

Protocol for Monitoring Fish Assemblages in 

Pacific Northwest National Parks

Standard Operating Procedure (SOP) #1: Use of GPS and Data Downloading 

Revision History Log 

Revision Date Author Changes Made Reason for Change 

This SOP provides step-by-step instructions for collecting position information using 

Thales MobileMapper GPS receivers, as well as downloading that information in 

preparation for sending it to the GIS Specialist. The material in this SOP is excerpted from 

the document NCCN Global Positioning System Data Acquisition and Processing, 2006 

(http://www1.nature.nps.gov/im/units/nccn/datamgmt_guide.cfm), which also provides 

information on processing GIS data once the data have been downloaded and given to the 

GIS specialist.

1. General Practices for GPS Data Collection 

Regardless of GPS receiver type, certain data collection standards must be followed. 

Most of the quality control measures below can be established by the user and should be 

followed whenever possible to produce the most accurate data possible. 

• Satellite availability and satellite geometry (PDOP):

GPS users can increase mapping accuracy by using planning charts and targeting 

their data collection to the times of day when satellite availability and geometry 

are best. Such timing however does not always work in the field. 

• Length of time GPS data file is open

Positional accuracy will be better the longer a file is open and the more GPS 

positions are collected and averaged. 

• Multipath error, or signal interference

Although mostly beyond a user’s control, some adjustments can be made to 

minimize multipath error. These include positioning the GPS in the most 

unobstructed view of the sky as possible, using offsets from better satellite 

reception areas to the target location, and using an external antenna. 

• Signal to Noise Ratio (SNR)

This is out of a user’s control, although adjusting for less multipath also will 

create a better SNR.
60 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

GPS file names should be recorded on hard copy datasheets or in field computers. GPS 

field coordinates (coordinates shown on a GPS receiver while a GPS is receiving satellite 

signals) and datum also should be recorded on hardcopy datasheets. In the event a GPS file is 

lost or corrupted, the coordinates recorded in the field from the GPS unit display window will 

become the best measure of location. Be aware that these coordinates can not be differentiallycorrected and are in the coordinate system and datum that were chosen for the unit’s display. 

2. Thales MobileMapper Operating Instructions

Contact NCCN GIS staff to have MobileMapper Office software installed and to have 

MobileMapper GPS receivers initialized. The User Manual (.pdf) found under the Help section 

of MobileMapper Office is a useful reference.

Battery Options

MobileMapper GPS receivers use two AA batteries that will last approximately 8 hours with the 

backlight on and 14-16 hours with the backlight off. 

External Antenna

MobileMapper GPS units have internal antenna at the top of the unit. External antennas are not 

necessary in the field, but can be used in areas with significant satellite signal obstructions. 

External antennas are required for mapping from aircraft or road vehicle. With the unit facing

you, the antenna jack is on the upper right side underneath a small black rubber flap. Hold the 

unit vertically so that the internal antenna is oriented correctly.

Projection and Datum

GPS units receive coordinate data from satellites in latitude and longitude in the WGS-84 datum, 

but can display coordinate in various projections and datums. NCCN GPS units should be set up 

to display coordinate information in UTM zone 10, North American Datum 1983 (NAD83). 

Configuration Settings

Configuration settings in MobileMapper receivers consist of setting map display scales, selected 

navigation screens, coordinate display, selected background maps, and power options. Contact 

NCCN GIS Specialists for assistance with setting receiver configurations.

Receiver Operation and Data Collection

Power On and Off 

Push PWR button to power on. Push ENTER when the disclaimer/warning screen appears or the 

unit will automatically shut off. To turn off the receiver, push PWR twice. Most NCCN 

MobileMapper units have been configured to prevent accidental shut off by forcing users to push 

the PWR button once and then push the ENTER button once. 
SOP 1: Use of GPS and Data Downloading 61

Backlight

The backlight can be adjusted by using the PWR button. Push the PWR button for more than 2 

seconds and then release it to change the backlight from high to low. Push the PWR button again 

for more than 2 seconds and then release it to change the backlight from low to off. Push the 

PWR button again for more than 2 seconds and then release it to turn the backlight on again. 

Receiver Screens

The NAV button scrolls through navigation screens. Many navigation screens have been turned 

off (such as the road view) during the configuration/initialization process. The screens that will 

be used most are the satellite chart, the background map, the position screen, and the heading and 

bearing screen. The ESC key steps back through previous screens. 
62 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Look for the Satellite Status screen. This shows the status of the battery power, how many 

satellites are being tracked (the solid bars in the graph) and whether the GPS is calculating 

positions in 2D or 3D mode (upper right corner). If there are four or more satellites being tracked 

and the 3D indicator appears then data recording can proceed. 

Check Signal Reception and Current Location 

Push the NAV button until the Position screen appears. This also will show the status of the 

strength of the satellite signals. The line that reads “Averaging” will indicate, whether the GPS is 

“Search – 1st sat”, “Search – 2nd sat” ... or Averaging. Averaging will only show up if the GPS is 

getting good signals and is stationary. If it is averaging, it will also show the duration at which 

the unit has been receiving satellite data at that point on the next line (for example, 9 minutes and 

6 seconds). 

Current Position Information

Use the position screen to see current coordinates and obtain a running average of your current 

position. It will show the duration and average UTM’s during that duration. Relatively small 

movement (like shoulder width distance) will reset the duration clock and create a new running 

coordinate average. This screen shows a primary (at the top) and secondary (at the bottom) 

coordinate system (these displays are set during the configuration process). NCCN units have 

UTM zone 10, NAD 1983 as the primary coordinate screen. The “10” preceding the easting at 

the top is the UTM zone. 
SOP 1: Use of GPS and Data Downloading 63

Background Maps

Background maps are useful reference for fieldwork. For example, a background map can show 

target points where field crews will place plots, roads, trails, and park boundaries. Background 

maps will display at scales set during map creation in MobileMapper Office and at a level set in 

the GPS unit configuration. 

MobileMapper GPS receivers can display vector data (points, lines, polygons) in a background 

map. One attribute can be displayed for each vector feature in the background map. Shapefiles 

are imported in MobileMapper Office and saved as a map file (.mmp). Background maps are 

transferred to the receiver. Contact NCCN GIS staff for background map creation, imports, and 

proper configuration settings. 

To view a background map in the GPS receiver, use the IN and OUT buttons to zoom in and out. 

Use the scroll arrows to move around the map and to set a center point for zooming in and out. A 

black triangle will show your present position (the triangle is really big and it is unclear if it can 

be made smaller). Zoom out beyond a certain scale will show a more general map. Zooming in to 

the scale set during map creation in MobileMapper Office will show more detail.

NOTE: The black cursor on the background map will not zoom in beyond 10 meters on 

the display. 

Open a File 

When you are ready to collect a data file, 

1. push the LOG button. 

2. highlight Create New Job and push ENTER 

3. use the scroll arrows to get to Clear (bottom of the keyboard) 
64 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

 

4. Push ENTER

5. Use the scroll arrows and ENTER button to type in a job file name 

job files should be named the following standard way: 

Xyymmdd

Where:

X = GPS unit letter (see the back of the GPS unit for its letter-code) 

Yy = last two digits of the year (for example, “08” for 2008) 

Mm = month (use two digits; for example “06” for June) 

Dd = day (use two digits; for example, “03” for the third day of the month) 

6. Scroll to OK when finished typing in the job file name

7. Push ENTER

NOTE: There is an 8 character limit in file names. After naming the job file, 

8. Select a feature library (called a data dictionary in Trimble’s realm)

9. Select XXXXX.mmf where XXXXX is the specific feature library. For example, select 

FIa10.mmf to map features of interest to the fish assemblages monitoring program.

10. Push Enter and the Job Mode screen will appear

11. Select Post-processing

12. Push ENTER

The New Feature screen will appear

13. Select the feature for which data will be collected (a point or a line feature)

14. Push ENTER

Change file name from 

“Job1” to, for example, 

“M080710” 

Select the data dictionary 

created for a specific project
SOP 1: Use of GPS and Data Downloading 65

NOTE: if the default data dictionary is being used, then the screen will display choices 

“Point, Line, Area, Grid”. 

NOTE: Positions will not begin to collect in a file until the GPS unit begins receiving 

three or four satellite signals.

NOTE: Hold the unit vertically so that the antenna is oriented correctly 

15. Once the GPS unit receives sufficient satellite signals, pushing ENTER on the selected 

feature in the New Feature screen will change the screen from showing feature type 

information (e. g. New Feature/FIa10_pt or FIa10_line) to a screen for specific feature data 

collection that shows: data dictionary attributes that need data entry, logging time, number of 

satellites, and PDOP

NOTE: The MobileMapper does not show the number of points collected in a file like Trimble 

files do. Try to watch the elapsed time window and keep an eye on the PDOP. Try to collect at 

least three minutes of PDOP =<8.0 (make your best guess). 

Data Entry for a Point Feature 

To map a start point or an end point of a survey reach, or to map a temperature logger location, 

1. Scroll to the feature named FIa10_pt and push ENTER 

2. Don’t move during data collection! 

3. Use the scroll keys and Enter button to type in attribute data 

4. Push ENTER when finished entering attribute data

5. Try to collect approximately 2-3 minutes of location data with relatively low (=<8) PDOP

6. Select OK when finished with data collection

Close the Feature 

1. Scroll to CLOSE when finished logging the feature 

2. Push ENTER

This returns to the New Feature screen.

NOTE: This closes the feature, not the file.

3. Write the GPS file name on a hardcopy datasheet

Data Entry for a Line Feature 

A line feature can be opened within the same GPS file as the point feature. When a point feature 

is closed, the New Feature screen will appear again. From that screen a new line feature can be 

opened. 

1. Scroll to the feature named FIa10_line and push ENTER 

2. Use the scroll keys and Enter button to type in attribute data 

Example of an attribute called 

“depth” that needs a value 

entered
66 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

3. Push ENTER when finished entering attribute data 

4. Slowly walk the stream or river channel

5. Stop moving if you lose satellite signals and wait for reception to improve 

6. Select OK when finished

7. Close the feature (see Close the Feature above)

8. Write the GPS file name on a hardcopy datasheet

Close a File

To close out of the entire job file, 

1. Push MENU 

2. Scroll to Close Job 

3. Push ENTER

Open File Again to Collect New Feature (either a point location or a line)

To open a job file again and add further point or line features, 

1. Push the LOG button 

2. Select Open Existing Job 

3. Push ENTER

4. Select the job file name 

5. Push ENTER

6. Push LOG to get to the New Feature/Plot screen and wait for satellite signals

7. Push ENTER and log another point or line feature 

8. Write the GPS file name on a hardcopy datasheet

To close out of the entire job file, 

1. Push MENU 

2. Scroll to Close Job 

3. Push ENTER

NOTE: You also can re-open a job from pushing the MENU button and selecting Open 

Job. 

NOTE: There is no set rule for how many jobs to create and how many features (plot 

locations or line segments) to log per job. Typically, one job file per day works well for 

field operations and for data management considerations. 

NOTE: Turning off the unit will close an open job file (unlike the Trimble units, the file 

will not stay open).

NOTE: If batteries die during a job file, replace batteries, open a new job file and begin 

data collection again.
SOP 1: Use of GPS and Data Downloading 67

3. Transferring GPS Receiver Data to a Computer

Processing differentially correctable GPS rover files requires a computer, a data transfer cable, 

and GPS software. GPS receivers typically come with manufacturer-specific software and data 

transfer cables. Each software package operates differently, but the basic process is the same.

It is extremely important that whenever field crews return from the field, GPS files are 

transferred from GPS receivers to computers or network folders that are routinely backed-up. 

Files should be transferred to an appropriately named folder (such as, under the project’s main 

network folder, \GPS_data\FIa10_2008\Rover_files\Raw or Backup). 

Contact NCCN GIS staff to help set-up file folders, GPS software default settings, and hardware 

configurations for GPS data transfers. Differential processing will be done by NCCN GIS staff. 

Upon completion of GPS file transfers, notify GIS staff about GPS files that are ready for 

processing.

NOTE: Files collected on the MobileMapper GPS receivers are termed “jobs” and files saved 

via MobileMapper Office are named “jobs” (both have .mmj extensions). 

1. Open MobileMapper Office program from the computer and create a job file

MobileMapper Office Project Set-up 

a) Click on the File menu

b) Select New

c) Click on the File menu again

d) Select Save As

e) Navigate to a computer or network directory in which a PC job file will be stored 

f) Name the file

g) Push Save 

2. Set the coordinate system

a) Click on the Options menu 

b) Select Coordinate System

c) Click the drop-down arrow in the Spatial Reference System window

d) Select UTM/WGS84/UTM zone 10N 

i. If no coordinate system has been selected yet, click <new> from the dropdown list 

ii. Select “SELECT a PRE-DEFINED system”

iii. Click the Next button

iv. Scroll down to UTM in the left pane of the Coordinate System Wizard – 

Select window and double click 

v. Double click on WGS 84 

vi. Select UTM/WGS 84/UTM zone 10N from the right pane in the 

Coordinate System Wizard – Select window 

vii. Click on the Finish button 

viii. Click on the browse button to the right of the drop-down list 
68 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

ix. Click on the Datum tab

x. Select NAD83 from the Datum Name: pick-list

xi. Click OK

xii. Make sure the new option is selected in the Select Coordinate System 

window 

e) Click OK

NOTE: MobileMapper Office does not display the pick-list as NAD83; it displays as 

UTM/WGS 84/UTM zone 10N 

3. Set the units

a) Click on the Options menu 

b) Select Units

c) Select m, km/hectare

Open this job file each time GPS job files are downloaded from the GPS unit to the PC desktop. 

1. Connect the GPS to the computer using the serial cable 

Data Transfer between GPS and MobileMapper Office

2. Turn on the GPS unit 

3. Launch MobileMapper Office if it is not already open

4. In MobileMapper Office, click on the File menu 

5. Select Download from GPS 

6. Click on the File menu within the MobileMapper Transfer window 

7. Select Connect 

8. Select GPS Device via Cable

This will bring up a list of all the files in the GPS unit on the left side pane.

9. Use the dropdown box in the right side pane to navigate to the directory to which GPS files 

will be copied and stored (e. g. “Raw” or “Unprocessed” folder) 

10. Copy files from the left pane to the right pane by 

a) Highlighting the job(s) name (use Shift or Ctrl keys to highlight multiple files), 

b) Right clicking, 

c) And selecting Copy to 

This will automatically begin the file(s) transfer from the GPS unit to the 

directory in the right pane. 

NOTE: Use the Copy option, not the Move option. It appears to be safer to copy, not 

move. The Move option takes the files out of the GPS unit and into the directory shown 

in the right pane. NCCN has experienced transfer errors that corrupt GPS receiver job 

files using the Move option. 

NOTE: Highlight and copy only the GPS receiver job files. There is no need to copy 

background map and feature library files. 

11. Close the data transfer window. This will return to the main MobileMapper Office job 

window. 

12. Close the MobileMapper Office software program

13. Contact GIS staff about newly transferred files that are now ready for post-processing

Delete Files from GPS Receiver
SOP 1: Use of GPS and Data Downloading 69

Delete GPS files from GPS receivers only after files have been transferred to computers, backedup, and differentially corrected (field crews may have to verify GPS file correction status with 

NCCN GIS staff). 

Delete Files from MobileMapper Receiver

With the GPS receiver turned on, 

1. Push MENU 

2. Scroll to Delete Files

3. Push ENTER

4. Scroll to the file to be deleted

5. Push ENTER

6. Scroll to Yes to confirm deletion

7. Push ENTER

NOTE: Files must be deleted one at a time. There is no option for deleting all files at once from 

the receiver.

Delete Files from MobileMapper Receiver using MobileMapper Office

With MobileMapper Office open and the GPS receiver connected to the computer, 

1. Click on the File menu

2. Select Download from GPS 

3. Click on the File menu within the MobileMapper Transfer window 

4. Select Connect 

5. Select GPS Device via Cable

This will bring up a list of all files in the GPS unit on the left side pane.

6. Highlight the job(s) name (use Shift or Ctrl keys to highlight multiple files) that will be 

deleted 

7. Right click

8. Select Delete 

 This will delete the selected job files from the GPS receiver.
70 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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SOP 2: Data Entry and Verification 71

Protocol for Monitoring Fish Assemblages in 

Pacific Northwest National Parks

Standard Operating Procedure (SOP) #2: Data Entry and Verification 

Revision History Log 

Revision Date Author Changes Made Reason for Change

Overview Guidelines for Data Entry and Verification

This document describes the general procedures for entry and verification of field data in the 

working project database. Refer also to protocol Section 6C – Overview of Database Design, 

and Section 6D – Data Entry and Processing for related guidance and a clarification of the 

distinction between the working database and the master database. The following are general 

guidelines to keep in mind: 

1. Data entry should occur as soon after data collection as possible so that field crews keep 

current with data entry tasks, and catch any errors or problems as close to the time of data 

collection as possible.

2. The working database application will be found in the project workspace. For enhanced 

performance, it is recommended that users copy the front-end database onto their 

workstation hard drives and open it there. This front-end copy may be considered 

“disposable” because it does not contain any data, but rather acts as an interface with data 

residing in the back-end working database. 

3. Each data entry form is patterned after the layout of the field form, and has built-in 

quality assurance components such as pick lists and validation rules to test for missing 

data or illogical combinations. Although the database permits users to view the raw data 

tables and other database objects, users are strongly encouraged only to use the pre-built 

forms as a way of ensuring the maximum level of quality assurance.

4. As data are being entered, the person entering the data should visually review each data 

form to make sure that the data on screen match the field forms. This should be done for 

each record prior to moving to the next form for data entry. 

5. At regular intervals and at the end of the field season, the Field Lead should inspect the 

data that have been entered to check for completeness and perhaps catch avoidable errors.

The Field Lead also may periodically run the Quality Assurance Tools that are built into 

the front-end working database application to check for logical inconsistencies and data 

outliers (this step is described in greater detail in Section 6E: Quality Review and also in 

SOP #3: Data Quality Review and Certification).
72 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Database Instructions 

Getting Started

The first action to be taken is to make sure the data entry workspace is set up properly on a 

networked drive. If you are unclear about where this should be, contact either the local park 

wildlife biologist or the Data Manager.

• Store the back-end database file on the server so that others can enter data into the same 

back end file. The back-end file has “_be_” as part of its name. Upon saving this backend, the user may want to append the local park code to distinguish it from other backend files associated with other crews (for example, ForestVeg_VCa02_be_2007_ 

OLYM.mdb). 

• The crew’s copy of the front-end database also may be stored in the same folder. 

• If it does not already exist, also create a folder in the same network folder named 

“backups” or “backup_copies” for storing daily backups of the back-end database file.

Prior to using the database: 

• Open the front-end database. The first thing it will do is to ask to update the links to the 

back-end database file. This will only need to be done once for each new issue of the 

front-end database. 

Important Reminders for Daily Database Use

• A fresh copy of the front-end will need to be copied to your workstation every day. Do 

not open up and use the front-end on the network

• Backups should be made consistently at some point every day that data entry occurs.

Normally, the front-end application will automatically prompt you to make a backup 

either upon initially opening or upon exiting the application. Backups also can be made 

on demand by hitting the “Back up data” button on the main menu and storing the backup 

file in the “backups” folder.

as this ‘bloats’ the database file and 

makes it run more slowly. 

• To save drive space and network resources, backup files should be compacted by rightclicking on the backup file in Windows Explorer and selecting the option: “Add to Zip 

file”. Older files may be deleted at the discretion of the project crew lead.

• New issues of the front-end application may be released as needed through the course of 

the field season. If this happens, there should be no need to move or alter the back-end 

file. Instead, the front-end file may be deleted and replaced with the new version, which 

will be named in a manner reflecting the update (for example, ForestVeg_2007_v2.mdb). 

• If the front-end database gets bigger and slower, compact it periodically by selecting 

Tools > Database Utilities > Compact and Repair Database.
SOP 2: Data Entry and Verification 73

Database Components

The working front-end application has the following functional components, which are accessed 

from the main application switchboard form that opens automatically when the application starts:

• Enter / edit data – Opens a form to confirm default settings (for example, park, coordinate 

datum) prior to continuing to the project-specific data entry screens.

• Site task list – Keeps track of unfinished tasks associated with sample locations (for 

example, forgotten equipment, unfinished data collection) that one field crew can use to 

communicate with a future field crew.

• Lookup tables – Opens a tool for managing the lookup values for the project data set (for 

example, species list, list of project personnel, etc.). 

• QA checks – Opens the data validation tool, which shows the results of pre-built queries 

that check for data integrity, missing data, and illogical values, and allows the user to fix 

these problems and document the fixes. See SOP #3: Data Quality Review and 

Certification.

• View db window – Allows the user to view database objects (tables, queries, and forms).

• Back up data – Creates a date-stamped copy of the back-end database file.

• Connect data tables – Verifies the connection to the back-end working database file, and 

provides the option to redirect or update that connection. 
74 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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SOP 3: Data Quality Review and Certification 75

Protocol for Monitoring Fish Assemblages in 

Pacific Northwest National Parks

Standard Operating Procedure (SOP) #3: Data Quality Review and Certification 

Revision History Log 

Revision Date Author Changes Made Reason for Change 

Overview

This document describes the procedures for validation and certification of data in the working 

project database. Refer also to protocol narrative Section 6C – Overview of Database Design, 

Section 6E – Quality Review, and Section 6G – Data Certification and Delivery for related 

guidance and a clarification of the distinction between the working database and the master 

database.

After the season’s field data have been entered and processed, they need to be reviewed and 

certified by the Project Lead for quality, completeness, and logical consistency. Data validation 

is the process of checking data for completeness, structural integrity, and logical consistency. 

The working database application facilitates this process by showing the results of pre-built 

queries that check for data integrity, data outliers, missing values, and illogical values. The user 

may then fix these problems and document the fixes. 

Once the data have been through the validation process and metadata have been developed for 

them, they are to be certified by completing the NCCN Project Data Certification Form, 

available on the NCCN website. The completed form, certified data and updated metadata may 

then be delivered to the NPS Lead and the Data Manager according to the timeline in 

Appendix 2: Yearly Project Task List. 

Data Quality Review 

The following table shows the automated validation checks that are performed on the data prior 

to certification. These queries are designed to return records that need to be fixed, so ideally – 

once all data checks have been run and any errors have been fixed – none of the queries will 

return records. However, not all errors and inconsistencies can be fixed, in which case a 

description of the resulting errors and why edits were not made is then documented and included 

in the metadata and certification report.
76 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

The queries are named and numbered hierarchically so that high-order data – for example from 

tables on the parent side of a parent-child relationship such as sample locations – should be fixed 

before low-order data (for example, individual species observations). The rationale for this is that 

one change in a high-order table affects many downstream records, and so proceeding in this 

fashion is the most efficient way to isolate and treat errors.

Query name Type Returns records meeting the following criteria

qa_a113_Overview_sampling_visit_

summary

information Summary of the number of visits made for each 

location, grouped by location type and survey type

qa_a113_Overview_sampling_visit_

summary

information Summary of the number of visits made for each 

location, grouped by location type and survey type

qa_a123_Overview_locations_visited information Full list of sampling events

qa_a123_Overview_locations_visited information Full list of sampling events 

qa_a133_Overview_monitoring_locations_

visited

information Subset showing only the reference reaches visited

qa_a133_Overview_monitoring_locations_

visited

information Subset showing only the reference reaches visited

qa_a203_Sampling_event_date_ranges information Returns the earliest and latest sample dates in the data 

set

qa_a203_Sampling_event_date_ranges information Returns the earliest and latest sample dates in the data 

set

qa_a213_Quality_assurance_status information Quality assurance status (i.e., unverified, verified, or 

updated) of all sampling events in the data set

qa_a213_Quality_assurance_status information Quality assurance status (i.e., unverified, verified, or 

updated) of all sampling events in the data set

qa_a902_Unverified_events warning List of unverified sampling events in the data set

qa_a902_Unverified_events warning List of unverified sampling events in the data set

qa_d101_Locations_missing_critical_info critical Missing park code, location code, location type, 

watershed name, or watercourse type

qa_d101_Locations_missing_critical_info critical Missing park code, location code, location type, 

watershed name, or watercourse type

qa_d111_Locations_park_inconsistencies critical Park code inconsistent with watersheds table - may be 

assigned to wrong watershed

qa_d111_Locations_park_inconsistencies critical Park code inconsistent with watersheds table - may be 

assigned to wrong watershed

qa_d121_Locations_duplicates_on_park_

and_loc_code

critical Duplicate records on park code and location code

qa_d121_Locations_duplicates_on_park_

and_loc_code

critical Duplicate records on park code and location code

qa_d132_Locations_duplicates_on_park_

and_loc_name

warning Duplicate records on park code and loc name

qa_d132_Locations_duplicates_on_park_

and_loc_name

warning Duplicate records on park code and loc name

qa_d152_Locations_missing_establishment_dates warning Sampled locations with loc type = 'reference' or nonblank discontinued dates, but without establishment 

dates

qa_d152_Locations_missing_establishment_dates warning Sampled locations with loc type = 'reference' or nonblank discontinued dates, but without establishment 

dates
SOP 3: Data Quality Review and Certification 77

Query name Type Returns records meeting the following criteria

qa_d162_Locations_status_inconsistencies warning Missing location status; sampled locs w/ status = 

'rejected' or 'proposed'; locs w/ establishment dates 

and status = 'proposed'; 'retired' locs w/o discont. 

dates; discont. dates w/ status other than 'retired' or 

'rejected'

qa_d162_Locations_status_inconsistencies warning Missing location status; sampled locs w/ status = 

'rejected' or 'proposed'; locs w/ establishment dates 

and status = 'proposed'; 'retired' locs w/o discont. 

dates; discont. dates w/ status other than 'retired' or 

'rejected'

qa_d172_Locations_info_inconsistencies warning Missing WRIA code, or the downstream kilometer 

bounding value is greater than the upstream value

qa_d172_Locations_info_inconsistencies warning Missing WRIA code, or the downstream kilometer 

bounding value is greater than the upstream value

qa_d203_Locations_without_coordinates information Sampled locations without coordinate records

qa_d203_Locations_without_coordinates information Sampled locations without coordinate records

qa_d243_Locations_missing_sampling_

events

information Unsampled locations

qa_d243_Locations_missing_sampling_

events

information Unsampled locations

qa_d901_Location_illogical_dates critical Updated date prior to created date, or discontinued 

date prior to established date

qa_d901_Location_illogical_dates critical Updated date prior to created date, or discontinued 

date prior to established date

qa_f101_Events_missing_critical_info critical Missing location ID, project code, or start date

qa_f101_Events_missing_critical_info critical Missing location ID, project code, or start date

qa_f111_Events_duplicates_on_location critical Duplicate event records on location ID

qa_f111_Events_duplicates_on_location critical Duplicate event records on location ID

qa_f132_Events_without_observers warning Events without associated observers

qa_f132_Events_without_observers warning Events without associated observers

qa_f163_Events_missing_declination information Sampling events with missing declination correction 

values

qa_f163_Events_missing_declination information Sampling events with missing declination correction 

values

qa_f203_Events_missing_QA_info information Event records without entered date/by entries, or 

incomplete updated date/by or verified date/by 

entries

qa_f203_Events_missing_QA_info information Event records without entered date/by entries, or 

incomplete updated date/by or verified date/by 

entries

qa_f222_Events_with_more_than_one_

coord

warning Events with more than one coordinate record - verify 

that these are intended

qa_f222_Events_with_more_than_one_

coord

warning Events with more than one coordinate record - verify 

that these are intended

qa_f302_Events_sample_cycle_

inconsistencies

warning Sample cycle or visit in cycle is blank for monitoring 

locations, or non-blank where loc type <> 'monitoring'

qa_f302_Events_sample_cycle_ 

inconsistencies

warning Sample cycle or visit in cycle is blank for monitoring 

locations, or non-blank where loc type <> 'monitoring'

qa_f303_Events_snorkel_data_summary information Monitoring locations that are missing data flags for 

tree data, DWM data, canopy cover or plot 
78 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Query name Type Returns records meeting the following criteria

completion; or having these flags where loc type <> 

'monitoring'

qa_f303_Events_snorkel_data_summary information Monitoring locations that are missing data flags for 

tree data, DWM data, canopy cover or plot 

completion; or having these flags where loc type <> 

'monitoring'

qa_f901_Events_illogical_dates critical Events with end dates prior to start date, or updated 

or verified dates prior to the record entry date

qa_f901_Events_illogical_dates critical Events with end dates prior to start date, or updated 

or verified dates prior to the record entry date

qa_g101_Coordinates_missing_critical_

values

critical Records missing event ID or coord creation date

qa_g101_Coordinates_missing_critical_

values

critical Records missing event ID or coord creation date

qa_g122_Coordinates_missing_field_UTMs warning Field UTMs are missing

qa_g122_Coordinates_missing_field_UTMs warning Field UTMs are missing

qa_g131_Coordinates_incomplete_

field_UTMs

critical A portion of the field coordinate pair is missing, field 

datum or field coordinate source is missing, or only a 

portion of offset distance or azimuth is filled in

qa_g131_Coordinates_incomplete_

field_UTMs

critical A portion of the field coordinate pair is missing, field 

datum or field coordinate source is missing, or only a 

portion of offset distance or azimuth is filled in

qa_g142_Coordinates_duplicates_on_

field_UTMs

warning Returns instances where multiple records have the 

same exact final UTMs

qa_g142_Coordinates_duplicates_on_

field_UTMs

warning Returns instances where multiple records have the 

same exact final UTMs

qa_g152_Coordinates_missing_field_horiz_

error

warning Field horizontal error is missing

qa_g152_Coordinates_missing_field_horiz_

error

warning Field horizontal error is missing

qa_g191_Coordinates_inconsistent_field_

source_info

critical Field coordinate source = 'map', however there is a 

GPS file name, a field horizontal error, or GPS model 

filled in to suggest that the source is GPS

qa_g191_Coordinates_inconsistent_field_

source_info

critical Field coordinate source = 'map', however there is a 

GPS file name, a field horizontal error, or GPS model 

filled in to suggest that the source is GPS

qa_g202_Coordinates_incomplete_GPS_

info

warning Field coordinate source = 'GPS' but missing GPS model 

or GPS file name

qa_g202_Coordinates_incomplete_GPS_

info

warning Field coordinate source = 'GPS' but missing GPS model 

or GPS file name

qa_g901_Coordinates_illogical_dates critical Coordinates with updated dates before creation dates

qa_g901_Coordinates_illogical_dates critical Coordinates with updated dates before creation dates

qa_h101_Observers_missing_critical_info critical Missing event ID or contact ID

qa_h101_Observers_missing_critical_info critical Missing event ID or contact ID

qa_i101_Project_crew_missing_critical_info critical Missing contact ID, project code, last name, or first 

name

qa_i101_Project_crew_missing_critical_info critical Missing contact ID, project code, last name, or first 

name

qa_i112_Project_crew_missing_info warning Missing organization or position title

qa_i112_Project_crew_missing_info warning Missing organization or position title
SOP 3: Data Quality Review and Certification 79

Query name Type Returns records meeting the following criteria

qa_j101_Project_taxa_missing_or_illogical_

info

critical Missing taxon ID, project code, species code, category, 

record status, or both scientific and common name; or 

updated date prior to created date

qa_j101_Project_taxa_missing_or_illogical_

info

critical Missing taxon ID, project code, species code, category, 

record status, or both scientific and common name; or

updated date prior to created date

qa_j111_Project_taxa_duplicate_sci_name critical Duplicates on scientific name

qa_j111_Project_taxa_duplicate_sci_name critical Duplicates on scientific name

qa_j121_Project_taxa_duplicate_species_

code

critical Duplicates on species code

qa_j121_Project_taxa_duplicate_species_

code

critical Duplicates on species code

qa_j131_Project_taxa_duplicate_TSN critical Duplicates on TSN

qa_j131_Project_taxa_duplicate_TSN critical Duplicates on TSN

qa_j202_Project_taxa_without_park_

records

warning Lookup taxa (excluding temporary and grouped taxa) 

that do not have an associated park record

qa_j202_Project_taxa_without_park_

records

warning Lookup taxa (excluding temporary and grouped taxa) 

that do not have an associated park record

qa_j211_Park_taxa_missing_or_illogical_info critical Missing taxon ID, park code, park status, park origin, or 

record status; or updated date prior to created date

qa_j211_Park_taxa_missing_or_illogical_info critical Missing taxon ID, park code, park status, park origin, or 

record status; or updated date prior to created date

qa_l101_Images_missing_critical_info critical Missing image ID or event ID

qa_l101_Images_missing_critical_info critical Missing image ID or event ID

qa_l113_Locations_wo_images information Sampling locations with no images

qa_l113_Locations_wo_images information Sampling locations with no images

qa_l122_Images_missing_values warning Image records missing both image label and image 

description, or frame number, or image filename

qa_l122_Images_missing_values warning Image records missing both image label and image 

description, or frame number, or image filename

qa_n101_Task_list_missing_critical_info critical Missing task description, request date, or status; or the 

completed date is before the request date; or the 

completed date is filled in but the status is not 

'complete'

qa_n101_Task_list_missing_critical_info critical Missing task description, request date, or status; or the 

completed date is before the request date; or the 

completed date is filled in but the status is not 

'complete'

qa_n113_Task_list_summary information Summary of task list items

qa_n113_Task_list_summary information Summary of task list items

qa_p103_Snorkel_summary_data information Summary of snorkel survey data by location, date and 

observer

qa_p103_Snorkel_summary_data information Summary of snorkel survey data by location, date and 

observer

qa_p121_Snorkel_data_missing_critical_info critical Missing event ID, river section, observer, taxon, fork 

length code, or tally; or the taxon is not in the species 

lookup table or is not an active taxon

qa_p121_Snorkel_data_missing_critical_info critical Missing event ID, river section, observer, taxon, fork 

length code, or tally; or the taxon is not in the species 

lookup table or is not an active taxon
80 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Query name Type Returns records meeting the following criteria

qa_p132_Snorkel_data_duplicate_taxon_

obs

warning Duplicate records for event, river section, observer, 

fork length category, and taxon

qa_p132_Snorkel_data_duplicate_taxon_

obs

warning Duplicate records for event, river section, observer, 

fork length category, and taxon

qa_p142_Snorkel_data_values_not_in_

lookup

warning Observer name is not in the project crew lookup table, 

or the fork length category is not in the lookup table

qa_p142_Snorkel_data_values_not_in_

lookup

warning Observer name is not in the project crew lookup table, 

or the fork length category is not in the lookup table

qa_p153_Snorkel_data_maximum_tally information Maximum tally of individuals observed at once during 

snorkel surveys

qa_p153_Snorkel_data_maximum_tally information Maximum tally of individuals observed at once during 

snorkel surveys

qa_x101_Target_coord_errors critical For GIS review - target coordinates with incomplete 

UTMs, missing datum, or illogical created/updated 

dates

qa_x101_Target_coord_errors critical For GIS review - target coordinates with incomplete 

UTMs, missing datum, or illogical created/updated 

dates

qa_x112_Locations_without_target_coords warning For GIS review - locations missing target coordinate 

records

qa_x112_Locations_without_target_coords warning For GIS review - locations missing target coordinate 

records

qa_x203_Coordinates_distance_from_

target

information For GIS review - distance of field coordinates from 

target UTMs by sampling location 

qa_x203_Coordinates_distance_from_

target

information For GIS review - distance of field coordinates from 

target UTMs by sampling location

qa_x902_Locations_no_best_coord_

assigned

warning For GIS review - locations without best coordinates

qa_x902_Locations_no_best_coord_

assigned

warning For GIS review - locations without best coordinates

qa_x912_Coordinates_without_final_coords warning For GIS review - records missing final UTMs that 

incorporate post-processing and offsets

qa_x912_Coordinates_without_final_coords warning For GIS review - records missing final UTMs that 

incorporate post-processing and offsets

qa_x922_Locations_without_public_coords warning For GIS review - locations missing public coordinates

qa_x922_Locations_without_public_coords warning For GIS review - locations missing public coordinates

qa_x931_Coordinates_final_UTM_

inconsistencies

critical Final UTM coordinates are incomplete; or they are 

present and the coordinate type or datum is missing; 

or coord type or an estimated error value is present 

and the final coordinates are missing

qa_x931_Coordinates_final_UTM_

inconsistencies

critical Final UTM coordinates are incomplete; or they are 

present and the coordinate type or datum is missing; 

or coord type or an estimated error value is present 

and the final coordinates are missing

qa_x941_Coordinates_public_UTM_

inconsistencies

critical Public UTM coordinates are incomplete; or they are 

present and the public offset is missing; or public offset 

is present and the public coordinates are missing

qa_x941_Coordinates_public_UTM_

inconsistencies

critical Public UTM coordinates are incomplete; or they are 

present and the public offset is missing; or public offset 

is present and the public coordinates are missing

qa_x942_Coordinates_duplicates_on_final_UTMs warning Returns instances where multiple records have the 
SOP 3: Data Quality Review and Certification 81

Query name Type Returns records meeting the following criteria

same exact final UTMs

qa_x942_Coordinates_duplicates_on_final_UTMs warning Returns instances where multiple records have the 

same exact final UTMs

In addition to these automated checks, the person performing the quality review should remain 

vigilant for errors or omissions that may not be caught by the automated queries. Another task 

that cannot be automated is the process of making sure that all of the data for the current season 

are in fact entered into the database. This will often involve manual comparisons between field 

forms or other lists of the sites visited and the results of queries showing the sites for which data 

exist. The Data Manager also is available as needed to help construct new database queries or 

modify existing ones as needed. 
82 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Open the working copy of the database application and hit the button labeled “QA Checks”. 

This will open the quality review form. Upon opening, the quality review form automatically 

runs the validation queries and stores the results in a table built into the front-end database 

(tbl_QA_Results). Each time the queries results are refreshed, or the quality review form is reopened, the number of records returned and the run times are rewritten so that the most recent 

result set is always available; any remedy description and the user name for the person making 

the edits is retained between runs of the queries. These results form the basis of documentation in 

the certification report output as shown below. 

Using the Database Quality Review Tools

The first page of the quality review form has a results summary showing each query sorted by 

name, the number of records returned by the query, the most recent run time, and the description. 

There is also a button for refreshing the results, which may need to be done periodically as 

changes in one part of the data structure may change the number of records returned by other queries. 
SOP 3: Data Quality Review and Certification 83

Upon double-clicking a particular query name, the second page will open up to show the results 

from that query. 

In the upper-right is a switch that allows the user to put the form in either view mode (default) or 

edit mode. Upon changing to edit mode, the form changes color to provide a visual reminder that 

edits are possible. At this point the query results may be modified and the remedy details may be 

entered in the appropriate place. If certain records in a query result set are not to be fixed for 

whatever reason, this is also the place to document that. The user name is automatically filled in 

(if it was blank) once the user types in the remedy details.
84 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

The button labeled “Design view” also on this page will open the currently selected query in the 

design interface in Access. In this manner, the user can verify that the query is in fact filtering 

records appropriately. Note: Any desired changes to query structure or names should be 

discussed with the Data Manager prior to making these changes.

Certain queries, due to their structural complexity, cannot be edited directly. Other queries may 

not contain all of the fields the user may want to see in order to make the best decision about 

whether and how to edit a given record. In such cases, the user may opt to view and/or edit data 

directly in the data tables. To facilitate this process, the “Browse Data Tables” page on the form 

can be used to open the table directly for viewing and editing as needed. 

Important: As with all edits performed during the quality review, these types of direct edits in 

the data tables should be made with extreme care as the validation checks that are built into the 

front-end data entry forms are not present in the tables themselves. It is possible, therefore, to 

make edits to the tables that may result in a loss of data integrity and quality. While the 

automated queries are intended to check for these, it is not possible to check for every possible 

error combination.

Note: Whenever making quality review edits – whether through a query or directly in a table – 

the user should remember to update the Updated_date and Updated_by fields to the current date 

and the current user name.

The first page of the quality review form has a button labeled “View summary report”. This 

button opens the formatted information for each query, the last run time, the number of records 

returned at last run time, a description and any remedy details that were typed in by the user. 

This report can be exported from the database and included as an attachment to the certification 

report by either hitting File > Export on the Access menu, or by right clicking on the report 

object and selecting Export. Select ‘Rich Text Format (*.rtf)’ to retain formatting to facilitate 

importing it into the certification report in Word. 

Generating Output for the Certification Report
SOP 3: Data Quality Review and Certification 85

Completing Data Certification 

Data certification is a benchmark in the project information management process that indicates 

that: (1) data are complete for the period of record; (2) they have undergone and passed the 

quality assurance checks; and (3) they are appropriately documented and in a condition for 

archiving, posting, and distribution as appropriate. Certification is not intended to imply that the 

data are completely free of errors or inconsistencies that may or may not have been detected 

during quality assurance reviews. 

To ensure that only quality data are included in reports and other project deliverables, the data 

certification step is an annual requirement for all tabular and spatial data. The Project Lead is 

primarily responsible for completing a NCCN Project Data Certification Form, available on the 

NCCN website. This brief form and the certified data should be submitted according to the 

timeline in Appendix H: Yearly Project Task List. Refer to the product delivery schedule in 

Section 6J - Product Delivery, Posting, and Distribution for delivery instructions. 
86 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

This page left intentionally blank 
Appendix A 87

Appendix A. Photographs of Fish Species Commonly Observed in NCCN Rivers. 

Photographs by Ernest Keeley used with permission. 

A. Cutthroat trout (OLYM files).

B. Bull trout (photo credit: Jason Dunham, USGS, 

Corvallis)

C. Sockeye salmon (photo credit: Ernest Keeley)

D. Coho salmon (photo credit: Ernest Keeley). 

E. Summer steelhead trout (photo credit: Ernest Keeley)

F. Chinook salmon (photo credit: Ernest Keeley)

G. Mountain whitefish (photo credit: Ernest Keeley)
88 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks 

Appendix B. Photographs and Locations of Reference Sites for the Eight Rivers in the Olympic National Park. 

®

Trail

Creek

Reference Site

Park Boundary

Flow

Bogachiel River (rkm 40.5-35.6)

Indian Creek
Appendix B 89

 

®

Trail

Road

Creek

Reference Site

Flow

Dosewallips River (rkm 25.9 – 23.5)

Pass 

Creek
90 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks 

®

Trail/Road

Unnamed Creek

Reference Site

Flow

North Fork Sol Duc River (rkm 7.1 – 3.6)
Appendix B 91

®

Trail/Road

Reference Site

Creek 

Flow

Sol Duc River (rkm 101.6 – 97.2)

Munden Creek
92 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks 

®

Road

Reference Site Flow

East Fork Quinault River (rkm 82.6 – 76.9)
Appendix B 93

®

Trail

Road

Reference Site

Flow

North Fork Quinault River (rkm 4.4 – 0.0)
94 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks 

®

Trail

Road

Park Boundary

Reference Site

Creek 

Flow

North Fork Skokomish River (rkm 48.1 – 45.5)

Slate Creek
Appendix B 95

®

Trail

Reference Site

Park Boundary

Flow

South Fork Hoh River (rkm 48.1–45.5)
96 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Appendix C. Power to Detect Regional Trends in Run Size Using the Maximum Count 

After T=5, 7, 10, and 15 Years of Multiple Annual Snorkel Surveys in Each of n=5 Rivers.

SACO, bull trout; PRWI, mountain whitefish; ONXX, cutthroat/rainbow trout; ONTS, Chinook 

salmon. Total percent change=(run size year 1 – run size year T )/(run size year 1). Equivalent 

annual percent changes are total percent change / T. Tick marks along the bottom axis in the plot 

area delineate the percent change detectable with 80 percent power after 10 years. Adopted from 

McDonald (2006). 0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

SACO Response="MAX.COUNT"; Mean=41.7; Residual StErr=19.86; CV=0.48; Auto 

Total Change (%)

(Assuming n=4 sites sampled each year)

5

7

10

Years=15

-88.9 88.9

East Fork Quinault, North Fork Quinault, North 

Fork Skokomish, and South Fork Hoh Rivers. 

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

PRWI

Response="MAX.COUNT"; Mean=222.1; Residual StErr=196.59; CV=0.89; Au 

Total Change (%)

(Assuming n=5 sites sampled each year)

5

7

10

Years=15

-102.3 102.3

Bogachiel, East Fork Quinault, North Fork Quinault, 

North Fork Skokomish, and South Fork Hoh Rivers. 

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

ONXX

Response="MAX.COUNT"; Mean=66.5; Residual StErr=51.78; CV=0.78; Auto 

Total Change (%)

(Assuming n=6 sites sampled each year)

5

7

10

Years=15

-89.7 89.7

Bogachiel, East Fork Quinault, North Fork 

Quinault, North Fork Skokomish, Sol Duc, and 

South Fork Hoh Rivers. 

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

ONTS

Response="MAX.COUNT"; Mean=3.6; Residual StErr=3.19; CV=0.88; Auto C 

Total Change (%)

(Assuming n=6 sites sampled each year)

5

7

10

Years=15

-99.1 99.1
Appendix D 97

Appendix D. Power to Detect Trends on Individual Rivers in Run Size Using the Maximum 

Count After T=5, 7, 10, and 15 Years of Multiple Annual Snorkel Surveys in a Single River. 

SACO, bull trout; PRWI, mountain whitefish; ONXX, cutthroat/rainbow trout; ONTS, Chinook 

salmon. Single river is the North Fork Skokomish River. Total percent change = (run size 

year 1 – run size year T )/(run size year 1). Equivalent annual percent changes are total percent 

change / T. Tick marks along the bottom axis in the plot area delineate the percent change 

detectable with 80 percent power after 10 years. Adopted from McDonald (2006). 0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

NFSkokomish SACO Response="MAX.COUNT"; Mean=53.1; Residual StErr=20.9; CV=0.39; Auto C 

Total Change (%)

(Assuming n=1 sites sampled each year)

5

7

10

Years=15

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

NFSkokomish PRWI

Response="MAX.COUNT"; Mean=277.1; Residual StErr=207.03; CV=0.75; Au 

Total Change (%)

(Assuming n=1 sites sampled each year)

5

7

10

Years=15

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

NFSkokomish ONXX

Response="MAX.COUNT"; Mean=84.1; Residual StErr=54.16; CV=0.64; Auto 

Total Change (%)

(Assuming n=1 sites sampled each year)

5

7

10

Years=15

0.0 0.2 0.4 0.6 0.8 1.0

-150 -100 -50 0 50 100 150

Power to Detect Change

NFSkokomish ONTS

Response="MAX.COUNT"; Mean=3.8; Residual StErr=3.37; CV=0.88; Auto C 

Total Change (%)

(Assuming n=1 sites sampled each year)

5

7

10

Years=15
98 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

 

Appendix E. Example of Snorkel Data Form Used in River Surveys. 

Olympic National Park Snorkel Survey Form

River /Creek:_________________________ Species: ___________ Date: ____/_____

WRIA #: __ __. __ __ __ __ Time of Survey: Begin _______ End _______

Survey Type: Index Supl. Other:________ Observer/s & Agency: _____________________

Flow: LOW MOD. LOW MOD. MOD. HIGH HIGH Water Temp (Co) = ______at ______

Water Visibility: EXC. V. GD. GOOD FAIR POOR

Location (river mile): _________ to ____________

Comments Summary

Species Mean FL Fork Length Species

(mm) Range Count

FISH COUNTS AND ESTIMATED LENGTHS

DIVER _______ DIVER _______

Sectio

(RM X –

Spe < 5 

(< 

5 – 1 

(2 

15 –

(6 –

30 –

(12 –

> 5 

(> 

Sp < 5 

(< 

5 – 1 

(2 

15 –

(6 –

30 –

(12 –

> 5 

(> 

Species Codes

ONK Coho salmon ON Unidentified salm CO Sculpin spp

ONTS Chinook salm SA Bull trout CA Longnose suc

ONMY Rainbow/Stealh SA Brook trout RH Longnose da

ONNE Sockeye/Kokan R Speckled dac

ONGO Pink salmon CA Largescale suc

PRW Mountain white LA River lampre

ONCL Cutthroat trou LA Pacific lampr

ONKE Chum salmon L Brook lampre
Appendix F 99 

Appendix F. Example of Electrofishing Data Form Used in River and Stream Surveys. 

 Page ____ of _____ 

Olympic National Park Electrofishing Survey Form

River /Creek:_________________________ Species: ___________ Date: ____/_____/____

WRIA #: __ __. __ __ __ __ Time of Survey: Begin _______ End _______

Survey Type: Index Supl. Other:________ Observer/s & Agency: _____________________

Survey Method: Walk Snorkel Air Boat Elect. Other: __________

Flow: LOW MOD. LOW MOD. MOD. HIGH HIGH Water Temp (Co) = ______at ______

Water Visibility: EXC. V. GD. GOOD FAIR POOR

Location (river mile): _________ to ____________

Shocker Settings and Information Summary

Shocker Setting: _________________ 

Species Mean FL Length Species

(mm) Range Count

Voltage Range: ________________

Time Counter Beginning: __________

Time Counter Ending: ___________

Conductivity (ms/cm): _____________

Species Fork

Length (mm) Weight (g) Species ForkLength (mm) Weight (g) Comments

Species Codes

ONKI Coho salmon ONXX Unidentified salmonid CACA Longnose sucker ONCL Cutthroat trout

ONTS Chinook salmon SACO Bull trout RHOS Speckled dace ONKE Chum salmon

ONMY Rainbow/Stealhead SAFO Brook trout RHCA Longnose dace

ONNE Sockeye/Kokanee SAMA Dolly Varden LARI Brook lamprey

ONGO Pink salmon COXX Sculpin spp. LAAY River Lamprey

PRWI Mountain whitefish RIBA Redside Shiner LATR Pacific Lamprey
100 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Appendix G. Existing Section 10A1a Permit Issued by NOAA Fisheries (cover letter) for 

Sampling in MORA That Is Valid Through December 31, 2011. 
Appendix H 101

Appendix H. Yearly Project Task List. 

This table identifies each task by project stage, indicates who is responsible, and establishes the 

timing for its execution. Protocol sections and SOPs are referred to as appropriate.

Project Stage Task Description Responsibility Timing

Preparation

(Chapter 6b) 

Notify Data Manager and GIS Specialist 

of needs (field maps, GPS support, 

training)

Project Lead by Dec 1

Initiate announcement for seasonal field 

crew positions

Project Lead Feb

Ensure all project compliance needs are 

completed for the coming season

Project Lead Mar

Hire seasonal field crew positions Project Lead by Mar 15

Inform GIS Specialist and Data Manager 

of specific needs for upcoming field 

season

Project Lead by Mar 31

Plan schedule and logistics, including 

ordering any needed equipment and 

supplies

Project Lead Apr

Update and load data dictionary and target 

coordinates into GPS units

GIS Specialist by Apr 15

Prepare and print field maps GIS Specialist by Apr 15

Purchase equipment (temp. loggers, 

snorkel gear, etc.)

Project Lead Apr

Ensure that project workspace is ready for 

use and GPS download software is loaded 

at each park

Project Lead, Data 

Manager and GIS 

Specialist

by May 1

Initiate computer access and key requests 

(may need park-specific dates)

Project Lead or Field Lead May

Provide field crew email addresses and 

user logins to Data Manager

Project Lead May

Generate pre-printed data forms Project Lead May

Implement working database copy Data Manager by May 15

Provide database/GPS training as needed Data Manager and GIS 

Specialist

May-June

Train field crew in fish identification, use 

of equipment, field sampling protocols, 

safety, vehicle use, and backcountry travel

Project Lead May-June

Data Acquisition

(Chapter 3a-e) 

Collect field data during field trips Technicians May-Sep

Review data forms after each day Technicians daily

Regular review of field forms for 

completeness and accuracy

Field Crew Lead weekly

De-brief crew on operations, field 

methods, gear needs

Project Lead weekly

Data Entry and

Processing

(Chapter 6d) 

Download GPS data and email files to GIS 

Specialist for correction

Technicians as soon as 

possible after 

data collection, 

usually in Sept

Download and process digital images Technicians as needed

Enter data into working copy of the 

database

Technicians weekly

Verification of accurate transcription as 

data are entered

Technicians weekly
102 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Project Stage Task Description Responsibility Timing

Periodic review of database entries for 

completeness and accuracy

Field Crew Lead weekly

Correct GPS data and send screen capture 

to Field Lead and Project Lead for review

GIS Specialist as needed, 

usually in Sept

Scan field forms as PDF documents Field Crew Lead by Sept 30

Merge, correct, and export GPS data. 

Upload processed and verified coordinates 

to database. Complete stream routing 

analysis, update reach lengths in database.

GIS Specialist Oct

Product 

Development

(Chapter 6i)

Complete field season report Field Crew Lead by Sept 30

Product Delivery

(Chapter 6j)

Send field season report to Project Lead, 

Data Manager, and GIS Specialist

Field Crew Lead by Sept 30

Quality Review

(Chapter 6e) 

Quality review and data validation using 

database tools

Project Lead Oct-Nov

Prepare coordinate summaries and/or GIS 

layers and data sets as needed for spatial 

data review

GIS Specialist by Oct 15

Joint quality review of GIS data, 

determine best coordinates for subsequent 

mapping and field work

Project Lead and GIS 

Specialist

late Oct

Metadata

(Chapter 6f) 

Identify any sensitive information 

contained in the data set (see Section 6i, 

Reporting and Product Development for 

a definition)

Project Lead by Nov 30

Update the project metadata interview 

form

Project Lead by Nov 30

Data Certification 

and Delivery

(Chapter 6g) 

Certify the season’s data and complete the 

certification report

Project Lead Nov

Deliver certification report, certified data, 

and updated metadata interview form to 

Data Manager (and GIS Specialist as 

applicable)

Project Lead by Nov 30

Update project GIS data sets, layers and 

associated metadata records

GIS Specialist Dec-Jan

Upload certified data into master project 

database, store data files in NCCN Digital 

Library1

Data Manager Dec-Jan

Submit certified water temperature data 

WRD for merging with WRD STORET2

and EPA STORET2

Data Manager Dec-Jan

Notify Project Lead of uploaded data 

ready for analysis and reporting

Data Manager by Jan 15

Finalize and parse metadata records, store 

in NCCN Digital Library1

Data Manager and GIS 

Specialist

by Mar 15

Data Analysis

(Chapter 6h)

To be decided after analysis SOPs are 

written

Data Analyst Jan-Feb

Reporting and

Product 

Development

(Chapter 6i) 

Export automated summary queries and 

reports from database

Data Analyst Jan-Feb

Generate report-quality map output for 

reports

GIS Specialist Feb-Mar, as 

needed

Acquire the proper report template from 

the NPS website, create annual report

Data Analyst and Project 

Lead

Feb-Apr

Screen all reports and data products for 

sensitive information

Project Lead Feb-Apr
Appendix H 103

Project Stage Task Description Responsibility Timing

Prepare draft report Project Lead Feb-Apr

Product Delivery

(Chapter 6j) 

Submit draft I&M report to Network 

Coordinator for review

Project Lead by May 1

Review report for formatting and 

completeness, notify Project Lead of 

approval or need for changes

Network Coordinator May

Upload completed report to NCCN Digital 

Library1 submissions folder, notify Data 

Manager

Project Lead upon approval

Deliver other products according to the 

delivery schedule and instructions

Project Lead upon 

completion

Product check-in Data Manager upon receipt

Posting and

Distribution

(Chapter 6j) 

Submit metadata to NPS Data Store3 Data Manager by Mar 15

Create NatureBib4 record, post reports to 

NPS clearinghouse

Data Manager upon receipt

Update NPSpecies5 records according to 

data observations

Data Manager Jan-Mar

Submit certified data and GIS data sets to 

NPS Data Store3

Data Manager Jun (after 2-

year hold)

Archival and

Records 

Management

(Chapter 6k) 

Store finished products in NCCN Digital 

Library1

Data Manager upon receipt

Review, clean up and store and/or dispose 

of project files according to NPS 

Director’s Order #196

Project Lead Jan

Move hard-copy data forms to park 

collections

Project Lead Jan

Season Close-out

(Chapter 6l) 

Inventory equipment and supplies, store 

gear for winter

Field Crew Lead by Sept 30

De-brief field crew concerning safety, 

logistics, and data concerns

Project Lead, Technicians by Sept 30

Meet to discuss the recent field season, 

and document any needed changes to field 

sampling protocols or the working 

database

Project Lead, Data 

Manager, and GIS 

Specialist

by Nov 30 of 

the same year

Discuss and document needed changes to 

analysis and reporting procedures

Project Lead, Data 

Analyst, and Data 

Manager

by Mar 31

1 The NCCN Digital Library is a hierarchical digital filing system stored on the NCCN file servers (Boetsch and 

others, 2005). Network users have read-only access to these files, except where information sensitivity may 

preclude general access.

2

 NPSTORET (http://www.nature.nps.gov/water/infoanddata) and EPA STORET (http://www.epa.gov/storet/) are, 

respectively, the NPS and national enterprise data warehouses for water quality data. NPSTORET is maintained by 

NPS-Water Resources Division (WRD) and is synchronized with EPA STORET on a regular basis.

3 NPS Data Store is a clearinghouse for natural resource data and metadata (http://science.nature.nps.gov/nrdata). 

Only non-sensitive information is posted to NPS Data Store. Refer to the section on sensitive information in 

Section 6J, Product Delivery, Posting, and Distribution for details.

4 NatureBib is the NPS bibliographic database (http://www.nature.nps.gov/nrbib/index.htm). This application has 

the capability of storing and providing public access to image data (for example, PDF files) associated with each 

record.

5 NPSpecies is the NPS database and application for maintaining park-specific species lists and observation data 

(http://science.nature.nps.gov/im/apps/npspp/index.htm).

6 NPS Director’s Order 19 provides a schedule indicating the amount of time that the various kinds of records should 

be retained. Available at: http://data2.itc.nps.gov/npspolicy/DOrders.cfm. 
104 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

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Appendix I 105

Appendix I. Database Documentation. 

The database for this project consists of three types of tables: core tables describing the “who, 

where, and when” of data collection, project-specific tables, and lookup tables that contain 

domain constraints for other tables. Although core tables are based on NCCN standards, they 

may contain fields, domains, or descriptions that have been added or altered to meet project 

objectives. 

The database includes the following standard tables:

tbl_Locations Sample locations – river reaches and temperature data 

observation points 

tbl_Target_Coords Target coordinates for sample locations

tbl_Events Data collection event for a given location 

tbl_Coordinates Coordinate data collected during sampling events

tbl_GPS_Info GPS information associated with sampling event coordinates

tbl_Observers Observers for each sampling event

tbl_Task_List Checklist of tasks to be completed at sampling locations

tbl_Images Images associated with sampling events

tbl_QA_Results Quality assurance query results for the working data set

tbl_Edit_Log Edit log for changes made to data after certification

The following are project-specific data tables:

tbl_Electro_Data Electroshocking survey observation data

tbl_Snorkel_Data Snorkel survey observation data

tbl_Temp_Data Temperature data from data loggers

tbl_Temp_Files Temperature data log files

The following are a few of the more prominent, standard lookup tables: 

tlu_Project_Crew List of personnel associated with a project

tlu_Project_Taxa List of species associated with project observations

tlu_Park_Taxa Park-specific attributes for taxa
106 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Figure I1. Entity relationship diagram of the project database. Relationships between tables are represented by lines. Dark green 

tables represent core standard tables; light green represents extended standard tables; light brown are standard lookup tables. 

Project-specific tables are unshaded.
Appendix I 107

Data Dictionary 

Note: Required fields are denoted with an asterisk (*). 

File name: Fish_Assemblages_FIa10.DM1

Model name: Physical

Platform: Microsoft Access

Report date: 1/10/2008 11:45:53 AM 

tbl_Coordinates - Coordinate data collected during sampling events

 Coord_label Coord_label 

Index Index columns

 Coord_type Coord_type 

 Coord_updated Coord_updated 

Datum Datum

 Event_ID Event_ID 

 Field_coord_source Field_coord_source 

 GIS_loc_ID GIS_loc_ID 

 pk_tbl_Coordinates (primary) Coord_ID 

Field name Index/key Data type Description

Coord_ID primary * text (50) Unique identifier for each coordinate 

record

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now()) 

GIS_loc_ID indexed text (50) GIS feature ID for each set of 

coordinates, to link with geospatial 

layers

Event_ID indexed 

(FK)

text (50) Sampling event of coordinate data 

collection

Coord_label indexed text (25) Name of the coordinate feature (for 

example, plot center, NW corner)

Is_best bit Indicates whether this set of coordinates 

is the best available for this location

UTM_east decimal (9,3) Final UTM easting (zone 10N, meters), 

including any offsets and corrections

UTM_north decimal (10,3) Final UTM northing (zone 10N, meters), 

including any offsets and corrections

Coord_type indexed text (20) Coordinate type stored in UTM_east and 

UTM_north: target, field, post-processed

Datum indexed text (5) Datum of UTM_east and UTM_north

Default: "NAD83"

Est_horiz_error decimal (9,3) Estimated horizontal error (meters) of 

UTM_east and UTM_north

Field_UTME decimal (9,3) UTM easting (zone 10N) as recorded in 

the field
108 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Field_UTMN decimal (10,3) UTM northing (zone 10N) as recorded in 

the field

Field_datum text (5) Datum of field coordinates

Field_horiz_error decimal (9,3) Field coordinate horizontal error (m)

Field_offset_m decimal (6,2) Distance (meters) from the field 

coordinates to the target

Constraint: Is Null Or >=0

Field_offset_azimuth smallint Azimuth (degrees, declination corrected) 

from the coordinates to the target

Constraint: Is Null Or (>=0 And <=360)

Field_coord_source indexed text (12) Field coordinate data source

GPS_file_name text (50) GPS rover file used for data downloads

GPS_model text (25) Make and model of GPS unit used to 

collect field coordinates

Source_map_scale text (16) Approximate scale of the source map

Source_citation text (250) Name and date of the source map

Coordinate_notes memo Notes about this set of coordinates

Coord_created_date datetime Time stamp for record creation

Default: Now()

Coord_updated indexed datetime Date of the last update to this record

Coord_updated_by text (50) Person who made the most recent edits

 
Appendix I 109

tbl_Edit_Log - Edit log for changes made to data after certification

 Edit_date Edit_date 

Index Index columns

 Edit_type Edit_type 

pk_tbl_Edit_Log (primary) Data_edit_ID

 Project_code Project_code 

Table_affected Table_affected

User_name User_name

Field name Index/key Data type Description

Data_edit_ID primary * text (50) Unique identifier for each data edit record

Default: =Format(Now(),"yyyymmddhhnnss") & '-' &

1000000000*Rnd(Now())

Project_code indexed * text (10) Project code, for linking information with 

other data sets and applications

Default: "FIa10"

Edit_date indexed * datetime Date on which the edits took place

Default: Date()

Edit_type indexed * text (12) Type of edits made: deletion, update, 

append, reformat, tbl design

Edit_reason text (100) Brief description of the reason for edits

User_name indexed text (50) Name of the person making data edits

Table_affected indexed text (50) Table affected by edits

Fields_affected text (200) Description of the fields affected

Records_affected text (200) Description of the records affected

Data_edit_notes memo Comments about the data edits
110 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tbl_Electro_Data - Electroshocking survey observation data

 Condition Condition 

Index Index columns

 Event_ID Event_ID 

 pk_tbl_Electro_Data (primary) Observation_ID 

River_section River_section

 Taxon_ID Taxon_ID 

Field name Index/key Data type Description

Observation_ID primary * int Unique identifier for each record

Event_ID indexed (FK)* text (50) Sampling event

River_section indexed * text (10) Section of the river to which the 

observation applies ('index' indicates the 

entire reach)

Default: "index"

Taxon_ID indexed (FK)* text (50) Taxon observed

Fork_length_mm smallint Measured fork length, in millimeters

Constraint: >=10 And <=900

Condition indexed * text (1) Condition observed

Default: "U"

Mark_type text (10) Type of marking observed (for example,

adipose clip) 

Obs_notes text (50) Comments about the observation
Appendix I 111

tbl_Events - Data collection event for a given location

Constraints: : [Counter_end] Is Null Or [Counter_end] Is Null Or 

[Counter_end]>=[Counter_start] 

Certified_date Certified_date

Index Index columns

 Entered_date Entered_date 

 Location_ID Location_ID 

 pk_tbl_Events (primary) Event_ID 

Start_date Start_date

 Survey_type Survey_type 

 Temp_file (unique) Temp_file

 Updated_date Updated_date 

Verified_date Verified_date

Field name Index/key Data type Description

Temp_file unique (FK) text (25) Name of the temperature data log file

Event_ID primary * text (50) Unique identifier for each sampling event

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now())

Location_ID indexed (FK)* text (50) Sampling location for this event

Project_code * text (10) Project code, for linking information with 

other data sets and applications 

Default: "FIa10"

Start_date indexed * datetime Start date of the sampling event

Start_time datetime Start time of the sampling event

End_date datetime End date of the sampling event (optional)

End_time datetime End time of the sampling event

Survey_type indexed * text (25) Survey method

Survey_extent text (25) Description of the extent of the reach 

surveyed

Km_surveyed decimal (6,3) Number of kilometers surveyed, updated 

from GIS after routing GPS data

Constraint: Is Null Or (>=0 And <=6)

Target_species text (20) Target species code, if applicable

Water_temp_C single Water temperature observed, in Celsius

Constraint: Is Null Or (>=0 And <=25)

Water_obs_time datetime Time at which the water temperature was 

observed

Flow_est text (10) Flow conditions during the survey

Visibility text (10) Water visibility conditions during the 

survey 

Weather text (10) Weather conditions during the survey

Shocker_setting text (25) Shocker setting

Voltage_range text (25) Shocker voltage range used

Counter_start smallint Shocker counter start value

Constraint: Is Null Or (>=0 And <=10000)
112 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Counter_end smallint Shocker counter end value (indicator of 

the number of seconds the shocker was 

used)

Constraint: Is Null Or (>=0 And <=10000)

Conductivity_mscm text (25) Conductivity setting, in ms/cm

Event_notes memo Comments about the sampling event

Entered_by text (50) Person who entered the data for this event

Entered_date indexed datetime Date on which data entry occurred

Default: Now()

Updated_by text (50) Person who made the most recent updates

Updated_date indexed datetime Date of the most recent edits

Verified_by text (50) Person who verified accurate data 

transcription

Verified_date indexed datetime Date on which data were verified

Certified_by text (50) Person who certified data for accuracy 

and completeness

Certified_date indexed datetime Date on which data were certified

QA_notes memo Quality assurance comments for the 

selected sampling event
Appendix I 113

tbl_GPS_Info - GPS information associated with sampling event coordinates

 Coord_ID Coord_ID 

Index Index columns

 Corr_type Corr_type 

Datum GPS_datum 

Feat_name Feat_name

 Feat_type Feat_type 

GPS_date GPS_date

GPS_file GPS_file

 Location_ID Location_ID 

 pk_tbl_GPS_Info (primary) GPS_ID

Field name Index/key Data type Description

GPS_ID primary * text (50) Unique identifier for the GPS record

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now()) 

Coord_ID indexed (FK) text (50) Coordinate identifier

Location_ID indexed text (50) Sample location, used for temporary 

links

Feat_type indexed text (20) Feature type (point, line, or polygon) 

collected with GPS 

Data_dict_name text (50) Data dictionary name used to collect 

feature

Feat_name indexed text (50) Feature name in data dictionary

GPS_file indexed text (50) GPS file name

GPS_date indexed datetime Date GPS file was collected

GPS_time datetime Time GPS file was collected

AM_or_PM text (2) Ante-meridian or post-meridian (a.m. or 

p.m.) if a 12 hour clock was used

Corr_type indexed text (50) GPS file correction type

GPS_UTME decimal (9,3) UTM easting in GPS unit

GPS_UTMN decimal 

(10,3)

UTM northing in GPS unit

UTM_zone text (5) UTM projection system zone

Default: "10N"

GPS_datum indexed text (5) Datum of GPS coordinates

Elev_m decimal (9,3) Elevation (meters) in GPS unit

Num_sat int Number of satellites tracked by GPS unit 

during data collection

GPS_duration text (25) Length of time GPS file was open

Filt_pos int Number of GPS positions exported from 

GPS file

PDOP decimal (9,3) Position dilution of precision scale

HDOP decimal (9,3) Horizontal dilution of precision scale

H_err_m decimal (9,3) Horizontal error (meters)

V_err_m decimal (9,3) Vertical error (meters)

Std_dev_m decimal (9,3) Standard deviation (meters)

GPS_process_notes text (255) GPS file processing notes
114 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tbl_Images - Images associated with sampling events

 Event_ID Event_ID 

Index Index columns

Image_label Image_label

 Image_quality Image_quality 

 Image_type Image_type 

pk_tbl_Images (primary) Image_ID

Field name Index/key Data type Description

Image_ID primary * text (50) Unique identifier for each image record

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now()) 

Event_ID indexed (FK)* text (50) Sampling event

Image_type indexed text (20) Type of image

Default: "ground photo"

Image_label indexed text (25) Image caption or label

Image_desc text (255) Brief description of the image bearing, 

perspective, etc.

Frame_number text (10) Frame number for photographic images

Image_date datetime Date on which the image was created, if 

different from the sampling event date 

Image_source text (50) Name of the person or organization that 

created the image

Image_quality indexed tinyint Quality of the image

Is_edited_version bit Indicates whether this version of the 

image is the edited (originals = False)

Object_format text (20) Format of the image

Orig_format text (20) Format of the original image

Image_edit_notes text (200) Comments about the editing or 

processing performed on the image

Image_is_active bit Indicates whether the image is still 

being used for navigation or 

interpretation

Default: True

Image_root_path text (100) Drive space location of the main project 

folder or image library

Image_project_path text (100) Location of the image from the main 

project folder or image library

Default: "images\"

Image_filename text (100) Name of the image including extention 

(.jpg) but without the image path 

Image_notes memo Comments about the image 

Sort_order indexed * int Sort order for displaying records in the 

order they were entered
Appendix I 115

tbl_Locations - Sample locations - river reaches and temperature data observation points

Constraints: : [Upstream_km] Is Null Or [Downstream_km] Is Null Or 

[Upstream_km]>[Downstream_km] 

 Loc_updated Loc_updated 

Index Index columns

 Location_code Location_code 

 Location_status Location_status 

 Location_type Location_type 

 Park_code Park_code 

 pk_tbl_Locations (primary) Location_ID 

 Public_offset Public_offset 

 udx_tbl_Locations Location_code 

Watercourse_type Watercourse_type

Watershed_name Watershed_name

Field name Index/key Data type Description

Location_ID primary * text (50) Unique identifier for each sample 

location

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now()) 

Park_code indexed * text (4) Park code

 Default: "OLYM"

Watershed_name indexed * text (50) Watershed in which the sample 

location is found

Location_code indexed * text (10) Alphanumeric code for the sample 

location

Location_type indexed * text (20) Indicates the type of sample 

location

Watercourse_type indexed * text (10) Type of watercourse (stream, river)

Location_name text (50) Brief colloquial name of the 

sample location (optional) 

Upstream_km single Kilometer mark associated with the 

upstream boundary of the reach

 Constraint: Is Null Or (>0 And <=120)

Downstream_km single Kilometer mark associated with the 

downstream boundary of the reach 

 Constraint: Is Null Or (0 And <=120)

WRIA_code text (50) Water Resource Inventory Area 

code associated with the reach

UTME_public decimal (9,3) UTM easting (zone 10N, meters). 

Note: in addition to any 

measurement error, these 

coordinates may have been offset 

up to 2 km from their actual 

position. 
116 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

UTMN_public decimal (10,3) UTM northing (zone 10N, meters). 

Note: In addition to any 

measurement error, these 

coordinates may have been offset 

up to 2 km from their actual 

position.

Public_offset indexed text (50) Type of processing performed to 

make coordinates publishable

Location_status indexed text (10) Status of the sample location

Travel_notes memo Directions for relocating the 

sample location

Location_notes memo Other notes about the sample 

location

Loc_established datetime Date the sample location was 

established

Loc_discontinued datetime Date the sample location was 

discontinued 

Loc_created_date datetime Time stamp for record creation

 Default: Now()

Loc_updated indexed datetime Date of the last update to this record

Loc_updated_by text (50) Person who made the most recent edits

tbl_Observers - Observers for each sampling event

Contact_ID Contact_ID

Index Index columns

 Event_ID Event_ID 

 Observer_role Observer_role 

 pk_tbl_Observers (primary) Event_ID, Contact_ID 

Field name Index/key Data type Description

Event_ID primary (FK)* text (50) Sampling event identifier

Contact_ID primary (FK)* text (50) Observer identifier

Observer_role indexed text (25) Role of the observer during data 

collection (optional)

Observer_notes text (200) Comments about the observer specific 

to this sampling event
Appendix I 117

tbl_QA_Results - Quality assurance query results for the working data set

 pk_tbl_QA_Results (primary) Query_name, Time_frame

Index Index columns

 Query_name Query_name 

 Query_result Query_result 

 Query_type Query_type 

Time_frame Time_frame

Field name Index/key Data type Description

Query_name primary * text (100) Name of the quality assurance query

Time_frame primary * text (30) Field season year or range of dates for 

the data being passed through quality 

assurance checks

Query_type indexed text (20) Severity of data errors being trapped: 

1=critical, 2=warning, 3=information

Query_result indexed text (50) Query result as the number of records 

returned the last time the query was run

Query_run_time datetime Run time of the query results

Query_description memo Description of the query

Query_expression memo Evaluation expression built into the 

query 

Remedy_desc memo Details about actions taken and/or not 

taken to resolve errors

Remedy_date datetime When the remedy description was last 

edited

QA_user text (50) Name of the person doing quality 

assurance

Is_done * bit Temporary flag to indicate that the user 

is done reviewing this query even if 

some records remain
118 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tbl_Snorkel_Data - Snorkel survey observation data

 Event_ID Event_ID 

Index Index columns

 Observer Observer 

 pk_tbl_Snorkel_Data (primary) Event_ID, River_section, Observer, Taxon_ID, 

Fork_length_code 

River_section River_section

Field name Index/key Data type Description

Event_ID primary (FK)* text (50) Sampling event

River_section primary * text (10) Section of the river for which the 

species tally applies ('index' indicates 

the entire reach)

 Default: "index"

Observer primary * text (50) Observer name

Taxon_ID primary (FK)* text (50) Taxon observed

Fork_length_code primary * text (10) Fork length category

Tally * smallint Number of individuals observed

 Constraint: >0 And <=500

tbl_Target_Coords - Target coordinates for sample locations

 Location_ID Location_ID 

Index Index columns

 pk_tbl_Target_Coords (primary) Location_ID, Target_type 

Target_updated Target_updated

Field name Index/key Data type Description

Location_ID primary (FK)* text (50) Sample location

Target_type primary * text (10) Type of target (e.g., upstream or 

downstream boundary)

Target_UTME decimal (9,3) Target UTM easting (zone 10N)

Target_UTMN decimal 

(10,3)

Target UTM northing (zone 10N)

Target_datum text (5) Target coordinate datum

Default: "NAD83"

Target_notes memo Notes about the target coordinates

Target_created_date datetime Time stamp for record creation

Default: Now()

Target_updated indexed datetime Date of the last update to this record

Target_updated_by text (50) Person who made the most recent edits
Appendix I 119

tbl_Task_List - Checklist of tasks to be completed at sampling locations

 Task_status Task_status 

Index Index columns

Date_completed Date_completed

 pk_tbl_Task_List (primary) Location_ID, Request_date, Task_desc 

Field name Index/key Data type Description

Location_ID primary (FK)* text (50) Sampling location

Request_date primary * datetime Date of the task request

Default: Now()

Task_desc primary * text (100) Brief description of the task

Requested_by text (50) Name of the person making the initial 

request

Task_status indexed text (50) Status of the task

Default: "active"

Date_completed indexed datetime Date the task was completed

Followup_by text (50) Name of the person following up on or 

completing the task

Task_notes memo Notes about the task

Followup_notes memo Comments regarding what was done to 

follow-up on or complete this task 

tbl_Temp_Data - Temperature data from data loggers

 pk_tbl_Temp_Data (primary) Log_date, Log_time, Temp_file

Index Index columns

Temp_file Temp_file

Field name Index/key Data type Description

Log_date primary * datetime Start date of the log file

Log_time primary * datetime End date of the log file

Temp_C single Temperature in Celsius

QA_flag text (3) Data quality flag

Temp_file primary (FK)* text (25) Name of the temperature data log file

Field name

tbl_Temp_Files - Temperature data log files

Index/key Data type Description

Temp_file primary * text (25) Name of the temperature data log file

Log_start_date * datetime Start date of the log file

Log_end_date datetime End date of the log file

File_path text (100) Path and file name of the log file

File_notes text (200) Comments about this log file
120 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

Field name

tlu_Condition_Code - List of fish condition codes

Index/key Data type Description

Condition_code primary * text (1)

Condition_desc text (100)

Sort_order tinyint

tlu_Coord_Label - List of project-specific coordinate labels (template)

Field name Index/key Data type Description

Coord_label primary * text (25)

Coord_label_desc text (100)

Sort_order tinyint

tlu_Coord_Source - List of coordinate data sources (standard)

Field name Index/key Data type Description

Coord_source primary * text (12)

Coord_source_desc text (100)

Sort_order tinyint

tlu_Coord_Type - List of coordinate types (standard)

Field name Index/key Data type Description

Coord_type primary * text (20)

Coord_type_desc text (100)

Sort_order tinyint

tlu_Datum - List of coordinate datum codes (standard)

Field name Index/key Data type Description

Datum primary * text (5)

Datum_desc text (50)

Sort_order tinyint

 

tlu_Edit_Type - List of the types of post-certification edits made to data (standard)

Field name Index/key Data type Description

Edit_type primary * text (12)

Edit_type_desc text (100)

Sort_order tinyint

 
Appendix I 121

tlu_Flow_Code - List of water flow condition codes

Field name Index/key Data type Description

Flow_code primary * text (10)

Flow_desc text (100)

Sort_order tinyint

 

tlu_Fork_Length_Code - List of fork length observation categories

Constraints: : [Length_min_cm]<[Length_max_cm]

Field name Index/key Data type Description

Fork_length_code primary * text (10)

Midpoint_cm single

Length_min_cm tinyint

Length_max_cm tinyint

Sort_order tinyint

 

tlu_GPS_Model - List of GPS devices used to collect coordinate data (template)

Field name Index/key Data type Description

GPS_model primary * text (25)

Sort_order tinyint

tlu_Image_Format - List of image, map, and photographic formats (template)

Field name Index/key Data type Description

Image_format primary * text (12)

Image_format_desc text (100)

Sort_order tinyint

tlu_Image_Quality - List of quality ranks for images (template)

Field name Index/key Data type Description

Quality_code primary * tinyint

Image_quality * text (20)

Image_quality_desc text (100)
122 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tlu_Image_Type - List of image types (template)

Field name Index/key Data type Description

Image_type primary * text (12)

Image_type_desc text (100)

Sort_order tinyint

tlu_Location_Type - List of location type codes (template)

Field name Index/key Data type Description

Location_type primary * text (20)

Loc_type_desc text (200)

Sort_order tinyint

tlu_Observer_Role - List of observer role assignments (template)

Field name Index/key Data type Description

Observer_role primary * text (25)

Role_desc text (100)

Sort_order tinyint

tlu_Origin_Code - List of origin codes for park taxa (standard)

Field name Index/key Data type Description

Origin_code primary * text (16)

Origin_desc text (100)

NPSpp_ID smallint

Sort_order tinyint

 

tlu_Parks - List of NCCN parks and park codes (standard)

Field name Index/key Data type Description

Park_code primary * text (4)

Park_name text (50)
Appendix I 123

tlu_Park_Taxa - Park-specific attributes for taxa (template)

 Park_origin Park_origin 

Index Index columns

 Park_status Park_status 

 pk_tlu_Park_Taxa (primary) Taxon_ID, Park_code 

 Record_status Record_status 

Field name Index/key Data type Description

Taxon_ID primary (FK)* text (50) Taxon identifier

Park_code primary * text (4) Park code

Park_status indexed text (16) Status of the taxon in this park (from 

NPSpecies)

Default: "unknown"

Park_origin indexed text (16) Origin of the taxon in this park (from 

NPSpecies)

Default: "unspecified"

Local_list bit Indicates that the taxon is the preferred 

one for use at the park (from 

NPSpecies)

Local_accepted_TSN int Taxonomic serial number of the local 

preferred taxon (from NPSpecies)

Preferred_sci_name text (255) Preferred scientific name of the taxon at 

the park (from NPSpecies)

Park_taxon_notes memo Comments about the taxon specific to 

this park

Record_status indexed text (16) Indicates the status of the record in 

terms of synchrony with master 

databases

Default: "new record"

Created_date datetime Time stamp for record creation

Default: Now()

Updated_date datetime Date of the last update to this record

Updated_by text (50) Person who made the most recent edits

tlu_Park_Taxon_Status - List of codes for park species occurrence (standard)

Field name Index/key Data type Description

Taxon_status_code primary * text (16)

Taxon_status_desc text (250)

NPSpp_ID smallint

Sort_order tinyint

 
124 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tlu_Project_Crew - List of personnel associated with a project (template)

 Contact_location Contact_location 

Index Index columns

 Contact_updated Contact_updated

First_name First_name

Last_name Last_name

Organization Organization

 pk_tlu_Project_Crew (primary) Contact_ID

 Project_code Project_code 

Field name Index/key Data type Description

Contact_ID primary * text (50) Unique identifier for the individual 

(Lastname_Firstname_MI)

Project_code indexed * text (10) Project code, for linking information 

with other data sets and applications

Last_name indexed * text (24) Last name

First_name indexed text (20) First name

Middle_init text (4) Middle initials

Organization indexed text (50) Employer (for example, NPS-MORA)

Position_title text (50) Position title held by the individual

Email text (50) Email address

Work_voice text (25) Work phone number

Work_ext text (5) Work extension number

Mobile_voice text (25) Mobile phone number

Home_voice text (25) Home phone number

Fax text (25) Fax number

Contact_location indexed text (255) Where the individual is located

NPS_login text (50) NPS network login

Contact_notes memo Notes about the contact

Contact_created datetime Time stamp for record creation

Default: Now()

Contact_updated indexed datetime Date of the last update to this record

Contact_updated_by text (50) Person who made the most recent edits

Contact_is_active bit Indicates that the contact record is 

currently available for data entry pick 

lists

Default: True
Appendix I 125

tlu_Project_Taxa - List of species associated with project observations (template)

 Subcategory Subcategory 

Index Index columns

Accepted_TSN Accepted_TSN

Category Category 

 pk_tlu_Project_Taxa (primary) Taxon_ID 

 Project_code Project_code 

 Record_status Record_status 

 Scientific_name (unique) Scientific_name

Species_code (unique) Species_code

 Taxon_type Taxon_type 

TSN TSN

Field name Index/key Data type Description

Taxon_ID primary * text (50) Unique identifier for each taxon

Default: =Format(Now(),"yyyymmddhhnnss") & '-' & 

1000000000*Rnd(Now()) 

Project_code indexed * text (10) Project code, for linking information 

with other data sets and applications

Default: "FIa10"

Species_code unique * text (20) Unique field code for each project 

taxon

Scientific_name unique * text (100) Scientific name of the taxon (from 

ITIS/NPSpecies)

Common_name text (100) Common name for the taxon (from 

ITIS/NPSpecies)

Pref_com_name text (100) Preferred common name for this project

TSN indexed int ITIS taxonomic serial number or a 

provisional number (from NPSpecies)

Accepted_TSN indexed int ITIS taxonomic serial number of the 

accepted name for this taxon (from 

NPSpecies)

Category indexed text (20) General category of the taxon (from 

NPSpecies)

Default: "unspecified"

Subcategory indexed text (20) Subcategory specific to the needs of 

each taxonomic discipline (from 

NPSpecies)

Authority text (60) Taxonomic authority (from ITIS)

Authority_subsp text (60) Taxonomic authority for subspecific 

taxa (from ITIS)

Family text (60) Taxonomic family (from ITIS)

Taxon_type indexed text (12) Indicates the taxonomic resolution and 

certainty represented by this record

 Default: "specific"

Taxon_notes memo General notes about the taxon

Created_date datetime Time stamp for record creation
126 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

 Default: Now()

Updated_date datetime Date of the last update to this record

Updated_by text (50) Person who made the most recent edits

Taxon_is_active bit Indicates that the record is currently 

available for data entry pick lists

 Default: True

Record_status indexed text (16) Indicates the status of the record in 

terms of synchrony with master 

databases

 Default: "new record"

Rec_status_notes text (255) Notes about the disposition of the 

record

Project_taxon_notes memo Project-specific comments about the 

taxon

tlu_QA_Flag - List of temperature data quality flag codes

Field name Index/key Data type Description

QA_flag primary * text (3)

Flag_desc text (100)

Sort_order tinyint

tlu_Site_Status - List of status codes for sampling stations (standard)

Field name Index/key Data type Description

Site_status primary * text (10)

Site_status_desc text (200)

Sort_order tinyint

 

tlu_Source_Scale - List of common map scales associated with maps and imagery (standard)

Field name Index/key Data type Description

Source_scale primary * text (16)

Source_scale_desc text (100)

Sort_order tinyint

 

tlu_Survey_Type - List of survey method types

Field name Index/key Data type Description

Survey_type primary * text (25)

Survey_desc text (100)

Sort_order tinyint

 
Appendix I 127

tlu_Taxon_Category - List of taxonomic categories (standard)

Field name Index/key Data type Description

Category primary * text (20)

Category_desc text (100)

NPSpp_ID smallint

Sort_order tinyint

 

tlu_Taxon_Rec_Status - List of status codes for taxon records (standard)

Field name Index/key Data type Description

Record_status_code primary * text (16)

Record_status_desc text (200)

Sort_order tinyint

tlu_Taxon_Type - List of taxon resolution codes (standard)

Field name Index/key Data type Description

Taxon_type primary * text (12)

Taxon_type_desc text (200)

Sort_order tinyint

tlu_Visibility_Code - List of water visibility condition codes

Field name Index/key Data type Description

Visibility_code primary * text (10)

Visibility_desc text (100)

Sort_order tinyint

 

tlu_Watercourse_Type - List of watercourse types

Field name Index/key Data type Description

Watercourse_type primary * text (10)

Type_desc text (100)

Sort_order tinyint
128 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

tlu_Watersheds - List of major watersheds

Constraints: : [Total_length_km] Is Null Or [Park_length_km] Is Null Or 

[Total_length_km]>=[Park_length_km] 

Has_hatchery Has_hatchery

Index Index columns

 Has_anadromous_fish Has_anadromous_fish 

 Park_code Park_code 

 pk_tlu_Watersheds (primary) Watershed_name

Watershed_GIS Watershed_GIS

Watershed_name Watershed_name

WRIAID WRIA_ID

Field name Index/key Data type Description

Watershed_name primary * text (25) Name of the watershed

Park_code indexed * text (4) Park in which the watershed is found

Default: "OLYM"

Area_ha int Watershed area, in hectares

Constraint: Is Null Or >0 And <1000000

Percent_in_park smallint Percent of the watershed found within 

the NPS boundary 

Constraint: Is Null Or (>=0 And <=100)

Elev_boundary_m smallint Elevation at the park boundary, in 

meters

Constraint: Is Null Or (>=0 And <10000)

Elev_headwaters_m smallint Elevation at the headwaters, in meters

Constraint: Is Null Or (>=0 And <10000)

Total_length_km decimal (5,2) Total length, in kilometers

Constraint: Is Null Or (>0 And <=100)

Park_length_km decimal (5,2) Length within the NPS boundary, in 

kilometers

Constraint: Is Null Or (>0 And <=100)

Gradient_perc text (25) River gradient, percent

Summer_flow_cms text (50) Estimated mean summer flow, in cubic 

meters per second

Max_safe_flow_cms text (50) Maximum flow for safe sampling, in 

cubic meters per second

Has_anadromous_fish indexed text (3) Indicates whether or not anadromous 

fish are known for this watershed

Has_hatchery indexed text (1) Whether or not a hatchery is present 

inside this watershed

Drains_to text (50) The watershed into which this 

watershed drains

Larger_basin text (25) The larger watershed basin in which 

this watershed is found

Huc4_basin text (25) Crosslink field for the Hydrologic 

Universal Code 4th field names 
Appendix I 129

WRIA_ID indexed smallint Crosslink field for the Water Resource 

Inventory Area number of the 

watershed

On_park_list bit Indicates that the watershed is normally 

part of the park pick list

Is_grouped bit Indicates that the watershed represents 

a grouping of natural watersheds, 

typically of small coastal streams that 

drain to salt water

Watershed_notes text (255) Comments regarding this watershed 

record

Watershed_GIS indexed smallint GIS ID code for the watershed

tlu_Weather_Code - List of weather condition codes

Field name Index/key Data type Description

Weather_code primary * text (10)

Weather_desc text (100)

Sort_order tinyint
130 Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks

This page left intentionally blank 
Prepared by the USGS Publishing Network, 

Bill Gibbs 

Linda Rogers

Sharon Wahlstrom

For more information concerning the research in this report, contact the 

Director, Forest and Rangeland Ecosystem Science Center

U.S. Geological Survey, 777 NW 9th Street

Corvallis, Oregon 97330

http://fresc.usgs.gov
Brenkman and others— Protocol for Monitoring Fish Assemblages in Pacific Northwest National Parks—Techniques and Methods 2–A7