National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center 

Salmonid Monitoring Protocol for the San Francisco 

Bay Area Network 

Narrative and Appendices - Version 4.0 

Natural Resource Report NPS/SFAN/NRR—2010/202
ON THE COVER 

From top left clockwise: adult coho salmon on John West Fork, Olema Creek (photograph by Greg Brown), 

juvenile coho salmon on Olema Creek (photograph by Sarah Carlisle), smolt coho salmon on Redwood Creek (photograph by 

Casey Del Real).
Salmonid Monitoring Protocol for the San Francisco 

Bay Area Network

Narrative and Appendices -Version 4.0 

Natural Resource Report NPS/SFAN/NRR—2010/202 

Michael L. Reichmuth (Fishery Biologist)1

Brannon J. Ketcham (Hydrologist)1

Darren Fong (Aquatic Ecologist)2

Sarah Carlisle (Fishery Technician)3

Erin Brown (Water Resources Intern)3

Marcus Koenen (I&M Program Manager)2

1

Point Reyes National Seashore 

Point Reyes Station, CA 94956 

2

Golden Gate National Recreation Area 

Fort Mason, Building 201 

San Francisco, CA 94123-0022 

3

Point Reyes National Seashore Association 

Point Reyes Station, CA 94956 

May 2010 

National Park Service 

Natural Resource Program Center 

1201 Oak Ridge Drive, Suite 150 

Fort Collins, Colorado 80525 
ii 

The National Park Service, Natural Resource Program Center publishes a range of reports that 

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Views, statements, findings, conclusions, recommendations, and data in this report are those of 

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This report is available from the San Francisco Bay Area I&M Network website 

(http://www.nature.nps.gov/im/units/SFAN) and the Natural Resource Publications Management 

website (http://www.nature.nps.gov/publications/NRPM). 

Please cite this publication as: 

Reichmuth, M., B.J. Ketcham, D. Fong, S. Carlisle, E. Brown, and M. Koenen. 2010. Salmonid 

monitoring protocol for the San Francisco Bay Area Network: narrative and appendices - version 

4.0. Natural Resource Report NPS/SFAN/NRR—2010/202. National Park Service, Fort Collins, 

Colorado. 

NPS 963/102568, May 2010 
iii 
iv 

Revision History Log 

Prev. 

Verersion 

Revision 

Date 

Author Changes Made Reason for Change New 

Version # 

1.00 4/05 Brannon 

Ketcham, 

Michael 

Reichmuth 

Multiple revisions 

while undergoing 

internal reviews. 

Development and 

addition to protocol. 

3.1 

3.1 1/07 Marcus Koenen Revised format, 

clarified content, 

revised objectives, 

moved details to SOP 

and moved overview 

information from SOP 

to this protocol 

narrative 

Address, peer 

review comments 

3.2 

3.3 5/08 Sarah Carlisle Making changes as 

suggested by MR 

 3.4 

 5/08 Erin Brown Mikes changes Permits, glossary 

3.4 7/08 Sarah Carlisle, 

Michael 

Reichmuth 

Table of Figures, 

Tables, Glossary, 

Appendixes, power 

analysis, updated 

formatting 

 3.5 

3.5 8/08 Brannon 

Ketcham, 

Michael 

Reichmuth, 

Marcus Koenen, 

Leigh Ann 

Starcevich 

Revisions to draft, 

Substantial changes to 

some sections 

Update based on 

feedback from 

Statisticians 

3.6 

3.6 8/08 Brannon 

Ketcham 

Minor revisions Additional review 

following MK 

incorporation of 

LAS comments 

3.61 

3.61 8/08 Dawn Adams NRTR formatting, 

minor edits 

Finalizing 3.62 

3.62 9/08 Michael 

Reichmuth 

Minor edits clarification 3.63 

3.63 11/08 Michael 

Reichmuth 

Minor Edits Incorporate Darren 

Fong comments 

3.64 

3.64 11/08 Michael 

Reichmuth 

Removed 

presence/non-detect 

from protocol 

Clarification 3.65 

3.65 11/08 D. Adams Formatting Finalizing for peer 

review 

3.66 

3.66 12/08 Michael 

Reichmuth 

Minor Edits For peer review 3.67 

3.67 2/10 Michael 

Reichmuth, 

Final edits for final 

submittal

Technical editing 

and response to 

4.0 
v 

Kris Freeman internal review 

comments

vii 

Contents 

Page 

Revision History Log ..................................................................................................................... iv 

Figures............................................................................................................................................ xi 

Tables ........................................................................................................................................... xiii 

Appendixes ................................................................................................................................... xv 

List of Acronyms ........................................................................................................................ xvii 

Executive Summary ..................................................................................................................... xix 

Acknowledgements ...................................................................................................................... xxi 

1 - Background and Objectives ....................................................................................................... 1 

1.1 Introduction and Purpose .................................................................................................. 1 

1.2 Life History ....................................................................................................................... 2 

1.3 Rationale for Selecting Resource for Monitoring ............................................................. 3 

1.4 Measurable Criteria and Desired Status ............................................................................ 5 

1.5 History of Monitoring ....................................................................................................... 5 

1.5.1 Monitoring in Marin County .................................................................................. 5 

1.5.2 Other Regional Monitoring Programs .................................................................... 7 

1.6 Monitoring Questions ....................................................................................................... 7 

1.7 Monitoring Objectives ...................................................................................................... 8 

1.8 Conceptual Model ............................................................................................................. 9 

1.9 Rationale for Objectives ................................................................................................. 11 

1.9.1 Juvenile Surveys (Basinwide GSS Method) ........................................................ 11 

1.9.2 Index Reach Method (Legacy Dataset) ................................................................ 11 

1.9.3 Spawner Surveys .................................................................................................. 11 

1.9.4 Smolt Surveys ...................................................................................................... 11 
viii 

1.10 Link to Management ..................................................................................................... 12 

1.10.1 NPS Management Objectives ............................................................................ 13 

1.11 Measurable Results and Deliverables ........................................................................... 13 

2 - Sampling Design...................................................................................................................... 15 

2.1 Study Area ...................................................................................................................... 15 

2.1.1 Overview of High Priority Streams ..................................................................... 17 

2.2 Sampling Design Overview ............................................................................................ 18 

2.2.1 Individual Level ................................................................................................... 18 

2.2.2 Population Level .................................................................................................. 18 

2.2.3 Community Level ................................................................................................ 18 

2.3 Seasonal Sampling Design .............................................................................................. 19 

2.3.1 Summer/Fall Sampling ........................................................................................ 19 

2.3.2 Winter Season ...................................................................................................... 21 

2.3.3 Spring Season ....................................................................................................... 25 

3 - Field Methods .......................................................................................................................... 27 

3.1 Basinwide GSS Juvenile Coho Surveys ......................................................................... 27 

3.2 Basinwide GSS Habitat Typing ...................................................................................... 27 

3.3 Basinwide GSS Surveys ................................................................................................. 27 

3.4 Index Reach Surveys (Legacy dataset) ........................................................................... 28 

3.5 Spring Surveys ................................................................................................................ 28 

3.6 Winter Surveys ................................................................................................................ 28 

4 - Data Management .................................................................................................................... 31 

4.1 Database Designs ............................................................................................................ 31 

4.1.1 Smolt Monitoring Database ................................................................................. 31 

4.1.2 Spawner Monitoring Database ............................................................................. 31 
ix 

4.1.3 Summer Monitoring Database ............................................................................. 32 

4.2 Annual Data Work Flow ................................................................................................. 33 

4.3 Quality Assurance and Quality Control .......................................................................... 33 

4.4 Version Control Guidelines and Database History ......................................................... 33 

4.5 Metadata Procedures ....................................................................................................... 34 

4.6 Data Storage and Archival Procedures ........................................................................... 35 

4.7 Data Distribution ............................................................................................................. 35 

5 - Data Analysis and Reporting ................................................................................................... 37 

5.1 Seasonal Updates ............................................................................................................ 37 

5.2 Seasonal Progress Reports .............................................................................................. 37

5.3 Annual Summary Reports ............................................................................................... 37 

5.3.1 Routine Data Analyses ......................................................................................... 37 

5.4 Analysis and Synthesis Reports ...................................................................................... 38 

5.5 Reporting Format ............................................................................................................ 38 

6 - Personnel ................................................................................................................................. 39 

6.1 Personnel Requirements .................................................................................................. 39 

6.1.1 Project Lead (Network) ........................................................................................ 39 

6.1.2 Hydrologist (PORE) ............................................................................................. 39 

6.1.3 Aquatic Ecologist (GOGA) .................................................................................. 39 

6.1.4 Data Manager (Network) ..................................................................................... 39 

6.1.5 Supporting Field Staff .......................................................................................... 39 

6.1.6 Community Volunteers ........................................................................................ 40 

6.2 Annual Workload and Field Schedule ............................................................................ 40 

6.2.1 Summer Surveys .................................................................................................. 40 

6.3 Qualifications .................................................................................................................. 41 
x 

6.4 Training ........................................................................................................................... 41 

6.4.1 Snorkeling ............................................................................................................ 41 

6.4.2 Electrofishing ....................................................................................................... 42

7 - Operational Requirements ....................................................................................................... 43 

7.1 Budget ............................................................................................................................. 43 

7.2 Budget Shortfalls ............................................................................................................ 43 

7.3 Facility and Equipment Needs ........................................................................................ 45 

7.4 Permitting Requirements ................................................................................................ 45

8 - Glossary ................................................................................................................................... 47 

9 - Literature Cited ........................................................................................................................ 51 
xi 

Figures 

Page 

Figure 1. San Francisco Bay Area Inventory and Monitoring Network ......................................... 1

Figure 2. The life cycle of coho salmon (Oncorhynchus kisutch). ................................................. 2

Figure 3. Key stressors to life cycle of coho salmon. ..................................................................... 6

Figure 4. Life cycle monitoring conceptual model. ...................................................................... 10

Figure 5. High and medium priority salmonid monitoring watersheds in Golden 

Gate National Recreation Area and Point Reyes National Seashore. ........................................... 16

Figure 6. Power test of trend for Peak Live Dead ......................................................................... 22

Figure 7. Power test of trend for redds per km ............................................................................. 23

Figure 8. Power test of trend for PLD for a single cohort. ........................................................... 24

Figure 9. Power test of trend for PLD for a single cohort. ........................................................... 24

Figure 10. Example of a three-year 10% decline for cohort 1 at all three creeks. ........................ 26

xiii 

Tables 

Page 

Table 1. Other regional salmonid monitoring efforts, including watershed, life stage, and 

methods used in monitoring. .................................................................................................... 7 

Table 2. Summary of survey type and metrics that contribute to individual, population, 

and community level metrics. ................................................................................................ 18 

Table 3. Power estimates based on number of sampling years (number of observations) 

and percent declines. .............................................................................................................. 25 

Table 4. Summary of metrics and sampling sites for each sampling season. ............................... 29 

Table 5. Annual field and reporting schedule. .............................................................................. 41

Table 6. Salmonid monitoring program budget: Annual estimated costs (FY2010). ................... 44 

Table 7. Priority monitoring efforts for salmonid monitoring protocol if match funding is 

reduced. .................................................................................................................................. 45 

xv 

Appendixes 

Page 

Appendix A. Fish and Stream Aquatic Assemblages ................................................................... 57 

Appendix B. CDFG Habitat Unit Types. ...................................................................................... 59 

Appendix C. Basinwide Habitat Survey Datasheet ...................................................................... 61 

Appendix D. Dive Datasheet ........................................................................................................ 63 

Appendix E. Index Reach Habitat Datasheets .............................................................................. 65 

Appendix F. Electrofishing Data Datasheet .................................................................................. 69

Appendix G. Basinwide Electrofishing Log ................................................................................. 71 

Appendix H. Index Reach Electrofishing Log .............................................................................. 75 

Appendix I. Pipe Trap Datasheet .................................................................................................. 77 

Appendix J. Spawner Survey Datasheet ....................................................................................... 81

Appendix K. Redd Survey Datasheet ........................................................................................... 85 

Appendix L. Monument Tag Locations ........................................................................................ 87 

Appendix M. Landowner Access Agreement ............................................................................... 97 

xvii 

List of Acronyms 

AUC Area Under the Curve 

CCCESU Central California Coast Evolutionarily Significant Unit 

CCNB Conservation Corps North Bay 

CDFG California Department of Fish and Game 

CESA California Endangered Species Act 

CSRP Coho and Steelhead Restoration Project 

CSMP Coho and Steelhead Monitoring Program 

DPS Distinct Population Segment 

EFH Essential Fish Habitat 

ENSO El Niño Southern Oscillation 

ESA Endangered Species Act 

EUON Eugene O’Neil National Historic Site 

FGDC Federal Geographic Data Committee 

FOPO Fort Point National Historic Site 

GOGA Golden Gate National Recreation Area 

GSS General Systematic Survey 

GUID Globally Unique Identifier 

I&M Inventory and Monitoring Program 

JOMU John Muir National Historic Site 

MCOSD Marin County Open Space District 

MMWD Marin Municipal Water District 

MUWO Muir Woods National Monument 

NMFS National Marine Fisheries Service 

NOAA National Oceanic and Atmospheric Administration 

NPS National Park Service 

NPS MTE National Park Service Metadata Tools and Editor Program 

NRDT Natural Resource Database Template 

ODFW Oregon Department of Fish and Wildlife 

PDO Pacific Decadal Oscillation 

PINN Pinnacles National Monument 

PLD Peak Live + Cumulative Dead 

PORE Point Reyes National Seashore 

PRSF Presidio of San Francisco 

QA/QC Quality Assurance/Quality Control 

RSCS Report of Specimens Collected or Salvaged 

SCP Scientific Collecting Permit 

SCWA Sonoma County Water Agency 

SFAN San Francisco Bay Area Network 

SJSU San Jose State University 

SPAWN Salmon Protection and Watershed Network 

USFWS U.S. Fish and Wildlife Service 

USGS U.S. Geological Survey 

YOY Young of the Year 

xix 

Executive Summary 

Within aquatic environments, biodiversity is being lost at rates greater than within terrestrial 

environments (Moyle et al. 1998). Through the San Francisco Bay Area Network (SFAN) 

Inventory and Monitoring planning process, the Threatened and Endangered Aquatic Species and 

Stream Fish Assemblages were identified as high priority indicators of ecological health of 

freshwater stream systems (Adams et al. 2006). In particular, steep declines of coho salmon 

(Oncorhynchus kisutch) in central California are a significant concern to park managers. 

This protocol documents the methodology used to monitor salmonids in freshwater streams 

annually at Golden Gate National Recreation Area and Point Reyes National Seashore. 

Although the sampling is designed to focus on the federally and state endangered coho salmon, 

data are also collected on federally threatened steelhead trout (O. mykiss) and any other species 

incidentally encountered during sampling. 

The protocol is divided into two parts. Part I is the protocol narrative and Appendixes. This 

provides the background information, justification, monitoring objectives, an overview of the 

sampling design, expected analyses and reports, and the operational budget. Part II covers the 

Standard Operating Procedures for all field work, data management, data analyses and reporting, 

and training and safety. 

The monitoring objectives addressed by this protocol include the following: 

1. Determine long-term trends in distribution and abundance, size (length) of spawning 

coho salmon by counting numbers of spawners, carcasses, and redds along reaches at 

Olema, Pine Gulch, Redwood, and Cheda Creeks. 

2. Determine long-term trends in abundance and condition of smolt coho salmon by 

conducting spring smolt trapping near mouths of Olema, Pine Gulch, and Redwood 

Creeks. 

3. Determine long-term trends in distribution and abundance and condition of juvenile coho 

salmon by conducting summer basinwide surveys (general systematic surveys [GSS]) at 

Olema, Pine Gulch, and Redwood Creeks. 

4. Determine long term trends in summer density, size, and age composition of coho salmon 

at preexisting index reaches at Olema, Pine Gulch, and Redwood Creeks. 

5. Identify gross changes in habitat (pool:riffle) in Olema, Pine Gulch, and Redwood Creeks 

during basinwide GSS surveys. 

Multiple life stage monitoring is conducted during: a. the winter to sample coho spawners and 

redds, b. the spring to sample smolt outmigration, and c. summer to sample juvenile population 

abundance. This approach has provided data for regional interpretation of coho trends in 

survivorship and is intended for use in further regional comparisons. 

This protocol builds on historic monitoring efforts that have focused on spawners at Redwood 

Creek since the 1940s. Much of the smolt and juvenile sampling has been conducted since the 
xx 

early to mid 1990s. Despite these long-term data sets, one of the challenges of sampling coho 

sampling is their 3-year life cycle. Adult coho generally do not return to a stream to spawn until 

their third year. As a result, there are three distinct year-classes. Although nine years of sampling 

exists for some creeks, it reflects only three data points for each coho year class. 

Preliminary analyses presented in SOP 10: Data Summaries and Analyses demonstrate that 

between 1994 and 2007, spawner populations of two year classes have remained relatively stable 

and one year class has shown an increase. Sampling during the last three years, however, 

indicate very few returning spawners across the Central California region (Miller 2010). 

The state of California has strong interest in both the coho salmon and steelhead trout 

populations. Recent returns have been very low and both commercial and recreational salmon 

fishing along the California Coast was closed in 2008 and 2009. As a result of this concern, 

approximately half of the funding to conduct this monitoring program has come from the state 

through grants submitted to the Point Reyes National Seashore Association. 
xxi 

Acknowledgements 

We wish to thank the two anonymous reviewers who provided comments on previous drafts of 

this protocol. Jay Glase also provided comments to help improve this manuscript. Kirk 

Steinhorst, Leigh Ann Starcevich, and Kathy Irvine contributed greatly by conducting power 

analyses and augmenting the sampling design and analyses sections of the protocol. Kris 

Freeman provided editorial assistance including reformatting both the protocol narrative and 

associated SOPs to meet NRTR standards. Funding for this monitoring program is provided 

through the San Francisco Bay Area Network Inventory and Monitoring Program and has been 

augmented through grants by the Point Reyes National Seashore Association and the California 

Department of Fish and Game. The Marin Conservation Corps (now Conservation Corps North 

Bay) has also supported the program through staff assistance. We also thank the many volunteers 

who provide hundreds of hours of field assistance each year. 
1 

1 - Background and Objectives 

1.1 Introduction and Purpose 

The primary focus of this protocol is on tracking population trends, reproductive health, body 

condition, and habitat changes of anadromous salmon, with an emphasis on coho salmon 

(Oncorhynchus kisutch) found in the watersheds of the San Francisco Bay Area Network 

(SFAN) of national parks. These parks include: Golden Gate National Recreation Area (GOGA) 

including Muir Woods National Monument (MUWO) and Point Reyes National Seashore 

(PORE; figure 1). In addition, data are collected through the program will also help evaluate 

changes in the overall fish assemblages present in the streams of the San Francisco Bay Area 

Network. To complement this protocol, Inventory & Monitoring (I&M) water quality monitoring 

was initiated in fall 2006 (Cooprider and Carson 2006) and a streamflow monitoring program is 

under development (Fong et al. in prep.). 

Figure 1. San Francisco Bay Area Inventory and Monitoring Network. 
2 

1.2 Life History 

Monitoring salmonid populations is challenging because they maintain a certain amount of time 

in the freshwater and parts of their adult life in salt-water systems. Salmonids have five major 

life stages including egg, fry, juvenile, smolt, and adult (figure 2). Egg, fry, and juvenile life 

stages are restricted to freshwater systems. During the smolt and adult stages, salmonids spend 

time in both freshwater and ocean systems. Effective monitoring would have to focus on the 

species’ ability to survive in both of these areas. 

Coho salmon have a complex life history where an individual spends 14-16 months in their natal 

stream before leaving to the estuary and ocean. The individual typically does not return to its 

natal stream to spawn until 18 months after leaving it (PFMC 2000). As a result, in the SFAN 

streams there are three cohorts that have little influence on one another. In general, only one 

cohort will return to spawn during any given year and their offspring will return 3 years later to 

spawn, thus completing the coho life cycle. 

Figure 2. The life cycle of coho salmon (Oncorhynchus kisutch). 

Mature coho return from the ocean to their home 

streams to spawn, guided by their sense of smell. 

Spawning males turn brilliant red and grow hooked 

jaws and long teeth.

Life Cycle of 

Coho Salmon

Coho salmon spend 18 months 

in the ocean, feeding and 

growing and storing up energy 

for their journey back to their 

freshwater stream to spawn. 

After 16 months, the 

young salmon migrate to 

the ocean. At this stage 

they are known as smolts. 

Their physiology changes 

so that they can survive in 

saltwater. Their gills and 

kidneys change and they 

become silvery in color 

for better camouflage in 

the ocean. 

When all of the yolk has been absorbed, the young 

salmon come out of the gravel and feed on small prey in 

the stream. At this stage they are called fry. Spots and 

oval parr marks help them blend in to the stream 

environment. 

 After 4 to 6 weeks, the eggs 

hatch. The alevins remain under 

the gravel, living off the yolk sac 

until it is depleted. 

The female coho digs 

shallow nests, called redds, 

for her eggs in the gravel. 

The male fertilizes them. 

Coho salmon remain near 

their redds until they die. 
3 

The life history of winter run steelhead follows the same general life cycle pattern as coho 

salmon in that they hatch in freshwater, migrate to the ocean to mature, and return to freshwater 

to spawn. What varies between the two species life history is the variation in timing spent in each 

life stage for steelhead when compared to coho. Steelhead life strategies are far more variable 

than coho, including a wider spawning window (December to May) and freshwater residence 

time (1-3 years). In addition stealhead are iteoparous and may spawn multiple times before 

dying. 

1.3 Rationale for Selecting Resource for Monitoring 

Fisheries have long been of human concern mainly as a food supply and economic driver. 

Salmonids are a prime species that have come to represent the impacts that man can have on 

aquatic species and systems. Even within the National Park Service (NPS), records at MUWO 

document an interest and fascination with salmonids returning to spawn as early as the 1940s. 

Unfortunately, even into the 1980s, management activities that impaired the ability of these fish 

to thrive continued because of a lack of understanding with regard to salmonid habitat needs. 

The Magnuson-Stevens Fishery Conservation and Management Act, as amended by the 

Sustainable Fisheries Act of 1996 (PL 104-267), established new requirements for Essential Fish 

Habitat (EFH) for coho salmon and chinook salmon. Soon after, coho salmon (Federal Register 

1996) and steelhead trout (O. mykiss; Federal Register 1997) were listed as federally threatened. 

In response to continued depressed numbers in coho populations north of the San Francisco Bay, 

the California Department of Fish and Game (CDFG) completed listing of coho salmon as 

endangered through the California Endangered Species Act (CESA) in August 2004. 

Subsequently, the federal Endangered Species Act (ESA) status of coho salmon was downgraded 

to endangered in June 2005 (Federal Register 2005). Major causes for the decline include loss of 

habitat due to damming of streams, erosion and siltation of redd habitat, changes in stream 

temperature due to loss of canopy, nutrient influx as a result of agriculture and urbanization, 

overfishing, and channelization (figure 3). 

The National Marine Fisheries Service (NMFS) designated critical habitat for coho salmon to 

include all accessible reaches of rivers, including estuarine areas and their tributaries (Federal 

Register 1999). Through this designation, NMFS identified ten essential features of critical 

habitat including: substrate, water quality, water quantity, water temperature, water velocity, 

cover/shelter, food, riparian vegetation, space, and safe passage conditions. 

The original federal listing criteria stated that the Lagunitas/Olema Creek population accounted 

for more than 10% of the wild coho population (Brown et al. 1994) in the Central California 

Coast Evolutionarily Significant Unit (CCCESU). Recent research conducted by the NPS, Marin 

Municipal Water District (MMWD), and Salmon Protection and Watershed Network (SPAWN) 

has shown that the Lagunitas population likely represents up to 20% of the CCCESU population 

(Ketcham et al. 2004b). 

The NMFS Genetics Laboratory reports that the coho salmon from Redwood Creek (GOGA) 

represent a genetic outlier in the CCCESU with extreme genetic distance from all other samples 

collected within the CCCESU and the Southern Oregon-Northern California Coast ESU 

(Bjorkstedt et al. 2005). Genetic tests also indicate that coho which have returned to Pine Gulch 
4 

Creek after a thirty year absence were likely strays from Redwood Creek, representing a natural 

expansion of this genetically distinct and significant stock to a new watershed within PORE 

(Garza and Gilbert-Horvath 2003). Olema Creek was determined to be part of the Lagunitas 

Creek population, an independent population found within the coastal diversity strata of the 

CCCESU (Bjorkstedt et al. 2005). 

Threatened and endangered species are not generally considered effective indicators of habitat or 

environmental condition. This is not the case, however, for coho salmon and steelhead trout. 

Because coho salmon and steelhead trout live for more than a year in freshwater, and the 

conditions required to support wild coho and steelhead are highly restrictive, the species are 

susceptible to anthropogenic impacts to the stream and riparian systems. They demand yearround, high quality cold water, and complex instream and riparian habitat and structure to 

accommodate development from egg to smolt stage. Both coho and steelhead require these 

habitat conditions throughout the stream continuum and are thus important indicators of the 

aquatic ecosystem health throughout the watershed. 

The State of California Coho Recovery Strategy (CDFG 2004) stresses the need for monitoring 

of coho populations as well as the development of data/information system for compiling, 

analyzing, and distributing information on the status and trend of coho salmon and the status of 

coho salmon recovery (CA Recovery Strategy items RW-AM-03, RW-AM-05, RW-AM-06, 

RW-AM-07, BM-LA-05, and BM-LA-06 ). 

SFAN parks are actively initiating projects to improve habitat conditions for federally listed 

salmonids within park watersheds. It is vital for assuring taxpayer accountability, as well as 

assessing effectiveness of actions, to determine whether these habitat restoration actions 

measurably improved conditions for listed salmonids. The state also recognizes the importance 

of accountability and assessment in their recommendation for development, funding and 

implementation of effectiveness monitoring of restoration activities (CA Recovery Strategy 

items RW-AM-05, 09). 

This protocol is designed to intensively monitor the entire extent of usable coho habitat in three 

major watersheds found within the SFAN. The park realizes that this currently limits our ability 

to make inferences on the health of many of the other streams contained within the parks. 

However, this monitoring protocol does allow for direct relationships to park management 

activities surrounding the three major watersheds that are intensively monitored. If program 

funding increases it is anticipated that the Coho and Steelhead Monitoring Program (CSMP) will 

be expanded to increase coverage in non-coho bearing streams. 

In addition to freshwater conditions, coho salmon populations are highly responsive to ocean 

conditions. Research shows that salmonid populations observed in the freshwater systems are 

highly responsive to productivity of nearshore currents, El Niño Southern Oscillation (ENSO) 

events, and the Pacific Decadal Oscillation (PDO) events along the Pacific Coast (Pearcy 1997). 

Monitoring of these species at multiple life stages is valuable to the understanding of aquatic 

conditions and health of the watershed and of the sea. 
5 

1.4 Measurable Criteria and Desired Status 

Development of measurable criteria and desired status for coho bearing streams within NPS 

lands may occur in the future but is not currently part of this SFAN monitoring protocol. The 

State of California is in the process of drafting a Coastal Salmonid Monitoring Program, which 

would assign criteria and desired status for salmonids. In addition, NMFS anticipates release of 

the draft Recovery Plan for Central California Coast coho salmon in 2010 (Miller 2010). 

Recovery criteria will include numeric targets for adult returns and smolt outmigration at the 

watershed scale, including Lagunitas/Olema Creek, Pine Gulch Creek and Redwood Creek 

(NMFS, C. Ambrose, coho recovery coordinator, personal communication, 1 February 2010). 

This recovery plan will also include the maintenance of a coho salmon life-cycle monitoring 

station within the SFAN monitoring watersheds. Examples of potential Coastal Salmonid 

Program criteria or desired status may be based on criteria set forth by Oregon Department of 

Fish and Wildlife (ODFW) in their statewide coho conservation plan (ODFW 2007). The 

conservation plan outlines the following criteria: 

1. Abundance – the number of spawners. 

2. Persistence – the forecast likelihood that the population will persist in the future. 

3. Productivity – the number of recruits (progeny) produced per spawner (parent). 

4. Distribution – the distribution of spawners among habitats within a population’s home 

range. 

5. Habitat – the amount of available high quality habitat across all freshwater life stages. 

A sixth criterion, diversity, although not supported by current NPS activities will likely be 

measured by the NMFS genetics lab. Diversity is an index of genetic variability which is related 

to the population’s ability to respond to unpredictable natural variation in the environment. 

1.5 History of Monitoring 

1.5.1 Monitoring in Marin County 

Because adult salmon returning to the watersheds to spawn pique the interest of people, there is a 

long history of coho observations in the area. MUWO staff (within GOGA) staff began recording 

spawning in Redwood Creek in 1944. In the mid-1980s, local citizen groups began informally 

documenting wild coho spawning in Lagunitas and Olema Creeks. In 1994, GOGA and PORE 

biologists initiated more detailed surveys of Redwood Creek and assisted citizen groups with 

surveys on Olema Creek. 

The first complete surveys of Olema Creek were undertaken in the winter of 1995–1996 by the 

Tomales Bay Association and PORE. These surveys were expanded to Redwood Creek, Devil’s 

Gulch (a Lagunitas tributary) in 1997 through the NPS Coho and Steelhead Restoration Project 

(CSRP). These surveys have been conducted annually since 1997 by NPS staff and cooperators 

through funding from both the NPS and the CDFG. 

To increase the value of the information collected during spawning surveys and enable 

comparison of data from year to year, the NPS began efforts to standardize methods and test 

different survey methodologies. The NPS, in conjunction with MMWD and SPAWN have 

reported redd survey results to represent overall spawning densities and total coho smolt 
6 

production in the coastal Marin County watersheds. Additional monitoring results related to 

salmonid habitat use and distribution is well documented within PORE and GOGA watersheds 

(Ketcham et al. 2004a, 2004b, 2004c; Reichmuth et al. 2005, 2006a, 2006b). Through this 

protocol, the NPS will continue to advocate standardization of data collection techniques to 

improve countywide reporting practices. 

Figure 3. Key stressors to life cycle of coho salmon. 
7 

1.5.2 Other Regional Monitoring Programs 

Long-term monitoring programs for juvenile and adult salmonids have been established on 

Waddell and Scott Creeks in San Mateo County (Dr. Jerry Smith, San Jose State University 

[SJSU]), the Russian River drainage (Robert Coey, CDFG; David Manning, Sonoma County 

Water Agency [SCWA]; and University of California Cooperative Extension Program), the 

Lagunitas Creek watershed (MMWD and SPAWN), and the Noyo River drainage (Sean 

Gallagher and Scott Harris, CDFG; see table 1). The ability to use data from these sources for 

comparison depends on similarity in sampling techniques and coincidence of survey activities. 

Each of these programs is focused on answering somewhat different management questions. The 

proposed NPS protocol is most similar and comparable to the monitoring program described in 

the CDFG Interim Restoration Effectiveness and Validation Monitoring Protocols (Duffy 2005). 

Table 1. Other regional salmonid monitoring efforts, including watershed, life stage, and methods used in 

monitoring. 

Agency/ 

Group Watershed 

Life Stage 

(Season) Methods Used 

SJSU 

(Dr. Jerry 

Smith)/ 

NMFS 

Redwood Creek 

(Marin County) 

Juvenile (summer/fall) index reach electrofishing and 

snorkel counts 

Gazos Creek 

(San Mateo County) 

Waddell/Scott Creeks 

(Santa Cruz County) 

MMWD/ 

SPAWN 

Lagunitas Creek Juvenile (summer/fall) index reach electrofishing, snorkel 

counts 

Adult spawner (winter) visual spawner/carcass/redd 

counts 

Smolt (summer-fall) fyke/pipe downstream migrant 

traps 

SCWA/ 

CDFG 

Russian River Juvenile (summer/fall) 

Adult spawner (winter) 

Smolt (spring) 

various 

CDFG Noyo River Adult spawner (winter) 

Smolt (spring) 

visual spawner/carcass/redd 

counts 

fyke/pipe downstream migrant 

traps 

1.6 Monitoring Questions 

This protocol was developed to answer the following questions: 

• What habitat constraints exist in the parks that currently impede or limit salmon recovery 

efforts? 

• Are parks meeting resource protection mandates relative to salmonid habitat protection? 

• Is the condition (e.g., length, weight, presence of abnormalities) of coho salmon changing 

over time? 
8 

• What is the annual production of juvenile coho salmon outmigrants in Redwood, Olema, 

and Pine Gulch Creeks? 

• What is the annual escapement of returning adult coho salmon in Redwood, Olema, Pine 

Gulch, and Cheda Creeks? 

• What is the annual abundance of juvenile coho salmon rearing within Redwood, Olema, 

and Pine Gulch Creeks at summer base flow conditions? 

• What are the changes in salmonid densities at preexisting index reach locations on 

Redwood, Olema, and Pine Gulch Creeks? 

The following questions may be answered in part by this monitoring protocol but additional 

information will need to be gathered through park or partner efforts. 

• Where do non-native aquatic species (fish or crayfish) occur, and how do they affect 

native populations? 

• What are the fish populations and community assemblages within SFAN stream systems? 

• What are the distribution, condition, and health of non-salmonid fish within SFAN stream 

systems? 

• What is the population genetic structure and age-size relationship for salmonids? 

• What is the survivorship between life stages for each coho cohort within Redwood, 

Olema, and Pine Gulch Creeks? 

• How do population trends at GOGA and PORE compare with other watersheds in the 

region? 

• What are the changes in timing and distribution of salmonid spawning, adult sex ratios, 

and escapement estimates in select streams at PORE and GOGA? 

• What are the overall population trends of each coho salmon cohort within GOGA and 

PORE watersheds? 

1.7 Monitoring Objectives 

1. Determine long-term trends in distribution and abundance, size (length) of spawning 

coho salmon by counting numbers of spawners, carcasses, and redds along reaches at 

Olema, Pine Gulch, Redwood, and Cheda Creeks. 

2. Determine long-term trends in abundance and condition of smolt coho salmon by 

conducting spring smolt trapping near mouths of Olema, Pine Gulch, and Redwood 

Creeks. 

3. Determine long-term trends in distribution and abundance and condition of juvenile coho 

salmon by conducting summer basinwide surveys (general systematic surveys [GSS]) at 

Olema, Pine Gulch, and Redwood Creeks. 

4. Determine long term trends in summer density, size, and age composition of coho salmon 

at preexisting index reaches at Olema, Pine Gulch, and Redwood Creeks. 
9 

5. Identify gross changes in habitat (pool:riffle) in Olema, Pine Gulch, and Redwood Creeks 

during basinwide GSS surveys. 

1.8 Conceptual Model 

The purpose of the conceptual model (figure 4) is to provide an understanding of the causal 

relationships between coho salmon ecology, monitoring techniques, and management actions. 

While the measurable criterion stated previously will allow park staff to describe the state of the 

current coho populations, the conceptual model focuses on the habitat parameters associated with 

a healthy watershed. The model should be used to guide changes in survey techniques used, 

types of indicators to be measured, and support restoration activity initiatives. 

The flow of the model relates key life stages in the coho salmon life cycle to the related impacts 

known to impair watersheds and hamper species recovery. Each survey type will be used to 

measure key indicators. Although each indicator in itself may not be useful for making 

inferences on habitat constraints, the combined use of these indicators acquired through multiple 

life stage sampling will provide information on key population components. The population 

inferences can then be used to provide insight on critical habitat limitations such as food and 

refugia availability. The affected habitat is directly related to both natural and anthropogenic 

disturbances. Natural impacts may include such features as waterfalls, excessive rainfall, 

landslides, drought, and coastal upwelling. Human caused impacts may include diversions, 

culverts, armoring and other forms of stream degradation that are possible to rectify through 

well-informed management decisions.
10

 Life Cycle Survey Type Measured Indicator Population Inferences Affected Habitat Related Impact

FecunditySex Ratio# of Spawners# of Redds Attraction FlowsSpawning Distribution Migration BarriersSpawn Timing Migration Corridor Hazards# of Summer/Fall Juveniles Spawning Gravel QuantityJuvenile Summer/Fall Density Spawning Gravel QualityJuvenile Summer/Fall Size Substrate MobilityJuvenile Summer/Fall Condition Water Quality/QuantityJuvenile Summer/Fall Distribution Availability of Stream Margin & Off Cannel HabitatJuvenile Summer/Fall Habitat Census PredationWatershed Smolt Production Food AvailabilitySmolt emigration Timing Stream ConnectivitySmolt condition Availability of Estuarine habitatSmolt Size Ocean Conditions

X X X X Upstream Migration X X X X X 

X X Spawning Success X X X X X X X X 

X X X Incubation X X X X X X X X X X Fry emergence X X X 

X X X X X Spring Fry Rearing X X X X X 

X XXX X X Summer Juvenile Rearing X X X X X X X X 

X X X X Winter Juvenile Rearing X X X X X X X X X X 

X X Smolt Outmigration X X X X X X X 

X X X Estuary and Ocean Rearing X X X X X X X X X 

X X X 

X X 

X X 

X 

X - denotes an indicator that is esential in making the population 

inference in question.X - denotes an indicator that is not esential in making the population inference in question but can be used to support inferences in question.

Figure 4. Life cycle monitoring conceptual model. 
11 

1.9 Rationale for Objectives 

To ensure that population estimates are accurate and that management is appropriate and effective, 

monitoring needs to focus on multiple life stages. The multi-life stage monitoring include spawner 

surveys (winter), and smolt surveys (spring), juvenile basinwide (GSS) estimates (summer/fall), and 

continue monitoring legacy index reach monitoring (summer/fall). Each survey provides a snapshot 

of a major life stage within the salmon life cycle. These combined efforts will allow the NPS to 

explain the variability within the coho salmon population over time. 

1.9.1 Juvenile Surveys (Basinwide GSS Method) 

Monitoring juvenile salmonids during their freshwater residence phase provides useful 

information on overall population trends, particularly when combined with adult spawning data 

and smolt emigration data (Collins 2003), which are also part of our monitoring program. 

Sampling is most effective during summer and fall base flow conditions, when water clarity is 

greatest and conditions are more conducive to observation and capture of juvenile salmonids and 

other stream fish. 

Implementation of juvenile basinwide surveys (Dolloff et al. 1993) employs a variety of methods 

which are also conducive to monitoring other species of stream fish. While snorkeling is 

conducted on the target salmonid species (coho salmon), electrofishing on randomly selected 

calibration units will allow for the sampling of steelhead, as well as most other aquatic vertebrate 

species, as well as larger invertebrates (e.g., crustaceans). 

1.9.2 Index Reach Method (Legacy Dataset) 

Index reaches are maintained in the CSMP as legacy datasets. Because index reaches were not 

established using a probabilistic method, they cannot be used to make watershed statements. 

Index reach sampling contains the longest data set with over 9 years of continuous monitoring 

(more than 12 years in Redwood Creek). Juvenile salmonid index reach datasets have been used 

along with other indices, to determine the status of coho within California by regulatory agencies 

(CDFG 2002). Many of the longest salmonid datasets in the region are density estimates from 

established index reaches. Index reaches provide a snapshot of each individual index reach, 

which can be compared over time. These datasets have been used at the state and federal level 

for listing determinations of either endangered or threatened status. Time permitting SFAN plans 

to maintain monitoring index reaches at a reduced scale. 

1.9.3 Spawner Surveys 

Winter spawner surveys provide a measure of the overall spawning success and run size of each 

returning year class. When smolt survey data are available, escapement estimates may also be 

utilized to determine ocean survival. Coho redd counts are the only consistent metric used in all 

regional watersheds and are therefore an important indicator for regional comparisons of spawning 

success. 

1.9.4 Smolt Surveys 

Smolt surveys performed in conjunction with winter spawner surveys and summer juvenile surveys 

permit an evaluation of abundance during three of five distinct freshwater salmonid life history 

stages (egg, emergent fry, juvenile, smolt, adult). A significant body of literature has documented 

life stage bottlenecks and survival rates for salmonid populations. Many of these studies describe 
12 

how alterations to watershed connectivity and condition affect these species at these different 

freshwater life stages. At the time they smolt, most coho have spent one to two years in the 

watershed, while steelhead can be up to three years old (Pollard et al. 1997). Smolt production, 

therefore, is the best aggregate measure of watershed condition and productivity. The response of 

coho and steelhead populations to changes in habitat quality can not be properly assessed without a 

measure of smolt production. 

When evaluated as part of a comprehensive monitoring program, the smolt trap information can be 

compared with adult spawner indices to describe potential ocean productivity and survival, and with 

summer juvenile population estimates to assess rates of survival through the winter season. This 

type of comprehensive monitoring information is rare in the central California coast region, as most 

of this research has been focused in the Pacific Northwest. The habitat and climate supporting 

salmonids in this region have not been well studied, meaning that local adaptations by these species 

are not well understood. Smolt trap monitoring, in conjunction with other life stage monitoring 

activities allows the NPS to characterize aggregate watershed productivity for salmonids, and is a 

valuable resource for directing long-term management and restoration actions. Although smolt 

trapping is focused on salmonids, it also provides additional presence and size measurement data for 

other aquatic species during periods not covered by summer/fall monitoring activities. 

1.10 Link to Management 

In 1996, the NPS initiated a watershed restoration and monitoring project in Marin County in 

conjunction with the ESA listing of coho salmon and steelhead trout along the central California 

coast. The CSRP was a five-year NPS-funded cooperative effort between PORE, GOGA, and 

MUWO. The primary objective was to restore habitat. Monitoring juvenile fish abundance and 

habitat availability in Redwood Creek, Pine Gulch, Olema Creek, and Lagunitas Creek was used 

to evaluate the effectiveness of restoration activities. 

As a result of these initial efforts, and coordination among the region, the NPS monitoring 

program, now called the Coho and Steelhead Monitoring Program (CSMP), was recognized as a 

valuable resource and has subsequently been supported through CDFG matching funds since 

2002. The results of our monitoring efforts, have contributed greatly to the development of 

successful riparian, floodplain, and estuarine restoration projects to enhance habitat for coho 

salmon and steelhead at both GOGA and PORE. Program staff members have advised engineers 

on design to maximize habitat restoration value based upon information gathered through the 

monitoring efforts described in this protocol. 

Furthermore, park data are provided to non-governmental organizations as well as regulatory 

agencies responsible for coho salmon management and protection. These organizations and 

agencies have used park data to evaluate proposed management actions through Section 7 

consultations, status and review assessments, listing determinations, and recovery plan criteria. 

It is the intent of this monitoring program to use “early warning” signals about the yearly status 

of coho to trigger management discussions with regulatory agencies. Based on power analysis 

results, the long-term trend analyses approach described in this protocol would not provide parks 

and applicable agencies sufficient time to initiate management actions in response to catastrophic 

changes in the abundance of coho. At this time, NPS proposes that the absence or near absence 
13 

of coho from any life cycle monitoring station (basinwide GSS, smolt, and spawner) result in 

immediate discussions with NMFS and CDFG. Absence or near absence would be defined as a 

90% or greater reduction in abundance of any life stage from the prior cohort. 

This approach has already been tested with coho salmon in SFAN. In November 2007, an oil 

spill in the San Francisco Estuary resulted in bunker fuel oil reaching the outer coast shorelines 

of the parks.Winter spawner surveys indicated the absence of redds or coho adults from 

Redwood Creek, which drained to an oiled shoreline and lagoon. Presuming a cause-effect 

relationship, NPS contacted NMFS and CDFG staff for management advice. NMFS quickly 

initiated a region-wide assessment to determine the significance of this association. Their 

researchers concluded that poor oceanographic conditions likely caused catastrophic reductions 

of coho spawners region-wide, including Redwood Creek (MacFarlane et al. 2008). In this 

instance, “early warning data” from this program quickly relayed from the I&M program to Park 

managers and to regulatory agencies resulted in a timely assessment. 

1.10.1 NPS Management Objectives 

• Prevent the extinction of coho salmon from SFAN NPS managed lands. 

• Restore and maintain a healthy network of coho bearing watersheds within the SFAN 

NPS-managed lands. 

• Develop a coho population in Olema, Redwood, and Pine Gulch Creeks that is large 

enough to survive environmental variations and catastrophes. 

• Develop and maintain an integrated long term monitoring program. 

1.11 Measurable Results and Deliverables 

At the end of each monitoring season (summer, winter, and spring) data will be summarized into 

a progress report compiled by the fishery biologist and technicians. These reports will compile 

data that pertain to that individual monitoring season only. All three monitoring seasons will be 

compiled into a more comprehensive data summary annually by the fishery biologist and 

technicians. This annual report will include a summary of past data collected and estimated 

survival between life stages. Any annual dramatic decline in the coho population will also be 

provided in the annual report along with management recommendations. A trend report will be 

provided every nine to twelve years to conduct more intensive data analysis including 

comparison of data to relevant benchmarks (criteria, desired status, objectives, and questions). 

These reports will be provided to each park unit and the SFAN I&M Coordinator. In addition to 

the production of monitoring reports, a completed database will be provided to the I&M 

Coordinator after each monitoring season. 

15 

2 - Sampling Design 

2.1 Study Area 

The SFAN encompasses eight park units: (GOGA, FOPO, PRSF, MUWO, JOMU, EUON, 

PINN, and PORE). MUWO, FOPO, and PRSF are administered by GOGA (figure 5). Within the 

four parks are seven watersheds and 43 creeks (see SOP 9: Sampling Site Descriptions). 

However of these 43 creeks only 5 creeks have been documented to support coho salmon. 

Streams documented to support coho salmon habitat include Redwood Creek, Pine Gulch Creek, 

Olema Creek, Easkoot Creek, and Lagunitas Creek. Steelhead have been documented in many of 

the smaller GOGA, PORE and JOMU watersheds. Chalone Creek at PINN is a tributary of the 

Salinas River, and is the second largest drainage area in the Network, but the water regime and 

stream system are more directly linked to desert systems rather than coastal salmonid streams, 

and is not included in this monitoring protocol. The I&M program is developing an amphibian 

monitoring program to address PINN aquatic habitat. 

Since steelhead are more widespread than coho, surveys focus on streams where both species 

occur. As part of the summer monitoring efforts, the sampled population will include all fish 

species present in the sampling sites. 

High priority streams will be intensely monitored during all life stages using winter spawner 

surveys, spring smolt trapping, summer basinwide (GSS) surveys, and summer index reach 

surveys. Inferences will be limited to high priority streams. 

High priority streams are known to have coho and steelhead populations (Olema, Pine Gulch, 

Cheda, and Redwood Creeks; figure 5). Lagunitas Creek and Devils Gulch, high priority 

streams, are monitored through the MMWD. NPS staff members participate in monitoring plan 

development and efforts to coordinate data collection and quality. 

Medium priority streams will not be sampled as part of these monitoring protocols. It is 

anticipated that future monitoring of medium priority streams will occur as personnel and 

funding become available. Protocols for medium priority streams that will receive occasional site 

visits using low intensity monitoring techniques which will include presence/non-detect surveys 

only will be developed for peer review as staff and funding become available. Medium priority 

streams may contain salmonids (based on habitat) but populations have not been confirmed. 

These streams include all stream segments that are at least 500 m long that are contained within 

the SFAN NPS managed lands excluding PINN. Medium priority streams include watersheds 

that lie within GOGA, PORE and JOMU. 

Low priority streams will not be sampled as part of these monitoring protocols. Low priority 

streams are streams where coho and steelhead are not likely to occur or stream segments less 

than 500 m in length. 
16 

Figure 5. High and medium priority salmonid monitoring watersheds in Golden Gate National Recreation 

Area and Point Reyes National Seashore. 
17 

2.1.1 Overview of High Priority Streams 

2.1.1.1 Olema Creek: Olema Creek is the largest watershed in coastal Marin County, California 

and an important stream for coho salmon and steelhead within the CCCESU. The 15.9-km 

stream flows northwest through the Olema Valley, the landward expression of the San Andreas 

Fault Zone. Its confluence with Lagunitas Creek lies at the head of the ecologically significant 

Tomales Bay. Protected from development, the 37.6 km2

 (14.5 mi2) watershed is primarily 

contained within the boundaries of PORE and the GOGA North District. The watershed provides 

habitat to four federally protected aquatic species (California freshwater shrimp [Syncaris 

pacifica], endangered; coho salmon, endangered; steelhead, threatened; California red-legged 

frog [Rana aurora draytonii], threatened). Water quality and streamflow monitoring are also 

conducted in Olema Creek as part of the SFAN I&M Program. 

2.1.1.2 Cheda Creek: Cheda Creek is a small perennial tributary of the Lagunitas Creek 

watershed and provides critical habitat for steelhead trout and coho salmon. Past land-use within 

the Cheda Creek drainage has resulted in serious alterations to the natural hydrologic and 

riparian condition of the creek. These factors have negatively impacted salmonid populations, 

water quality, and the ability of the aquatic ecosystem to function properly. The construction of a 

fish passage structure in the fall of 2000 was part of an overall watershed restoration project 

initiated by the NPS to restore the system to a more natural and sustainable condition. The 

watershed provides habitat to coho salmon (endangered), steelhead (threatened), and the 

California red-legged frog (threatened), and California freshwater shrimp (endangered). 

2.1.1.3 Redwood Creek: Redwood Creek is an 23.1 km2 (8.9 mi2) coastal watershed in southern 

Marin County, California . Redwood Creek flows southwest from the flanks of Mt. Tamalpais, 

through MUWO, discharging to the Pacific Ocean through Big Lagoon at Muir Beach, CA. 

Protected from development, the watershed is primarily contained within the boundaries of Mt. 

Tamalpais State Park, GOGA and MUWO. The watershed provides habitat to coho salmon 

(endangered), steelhead (threatened), and the California red-legged frog (threatened). Water 

quality and streamflow monitoring are also conducted in Redwood Creek as part of the SFAN 

I&M Program. 

2.1.1.4 Pine Gulch Creek: Pine Gulch Creek drains a 19.4 km2

 (7.5 mi2) watershed in coastal 

Marin County, California, and is the primary freshwater input to Bolinas Lagoon. Pine Gulch 

Creek is located within the CCCESU where coho salmon and steelhead occur. The watershed 

supports a population of steelhead and it is generally accepted that it supported a native selfsustaining population of coho salmon into the 1970s. It is likely that the drought of the late 1970s 

coupled with in-stream damming during the same period severely depleted multiple year classes 

and led to unsuitable conditions for continued survival of the species within the Pine Gulch 

watershed. In 2001, NPS documented the return of coho salmon to the watershed beginning with 

the recovery of a coho carcass, and subsequent documentation of coho juveniles in the watershed 

the following summer (Brown and Ketcham 2002). The watershed provides habitat to coho 

salmon (endangered), steelhead (threatened), and the California red-legged frog (threatened). 

Water quality and streamflow monitoring are also conducted in Pine Gulch Creek as part of the 

SFAN I&M Program. 
18 

2.2 Sampling Design Overview 

This protocol presents a three tiered approach developed by Moyle et al. (1998) to monitor coho 

populations along with their habitat. This method includes analysis of fish at the individual level, 

population level and community level. This three tiered approach will use a combination of 

census, probabilistic, and judgmental study designs in order to gain information at all three levels 

of metrics. This sampling design is conducted year-round to assess population of all life stages 

including juvenile (summer/fall), spawners (winter), and smolt (spring); see Table 2. 

2.2.1 Individual Level 

Assessment at the individual level tracks changes in the condition and health of each fish 

encountered. Measurements of weight and length are used to evaluate for comparative metrics 

including individual condition factors (e.g., Fulton’s K) and weight-length relationships for all 

fish species. Fish are also observed for abnormalities including obvious stunted growth, lesions, 

parasites, etc. 

2.2.2 Population Level 

Evaluation at the population level is limited to the high priority streams and includes distribution 

and overall abundance of each species encountered. Metrics of evaluation include length 

histograms to determine presence of multiple age or size classes as well as estimates of density 

and/or population size. Evaluation of fish size and condition is also used for evaluation of health 

at the population level, by looking at the overall range in weight-length relationships within 

species and age-class. 

2.2.3 Community Level 

Information collected on non-target species may be used in the future to evaluate community 

level changes and to provide data to regional efforts on status and trends. Inferences, however, 

will be strictly limited without adding sampling methods to target other species across 

monitoring locations. 

Table 2. Summary of survey type and metrics that contribute to individual, population, and community 

level metrics. 

Level Juvenile Salmonid Data Winter: Spawner Data 

Spring: Smolt 

Trapping Data 

Individual Level • length-weight; 

• condition factors/ 

• abnormalities 

• sex 

• length-weight 

condition 

factors/abnormalities 

• genetic samples 

(carcasses) 

• length-weight 

• condition factors/ 

abnormalities 

Population Level • size distribution 

• size/age-classes 

• population size and 

relative abundance 

• spatial distribution 

• spawner population size 

and relative abundance 

• sex ratio 

• spawning timing 

• size distribution 

• size/age-class 

• number of smolt 

Community Level • species diversity • species diversity 
19 

2.3 Seasonal Sampling Design 

Because of the varying behavior of coho salmon throughout the year, a separate sample design is 

required to assess each life stage. During the summer, basinwide surveys are conducted to assess 

the abundance of juvenile populations. During the winter, spawner surveys are conducted along 

reaches. During the spring, smolts are trapped at the mouths of creeks. A power analysis was 

conducted using data from each sampling scheme to determine duration of effort in order to 

detect change. The 3-year life cycle of coho salmon results in the necessity to conduct analysis 

on cohort year, rather than calendar year. Therefore, true replication on a specific cohort occurs 

every three years rather than annually within a stream. Power to detect trend will require longer 

monitoring periods to account for this life cycle characteristic. 

Annual trend represents the change in each three-year cohort cycle. Therefore, a net trend over 

12 years represents the total trend from 4 cohort-cycle measurements. The NPS expects power of 

at least 77% to detect a net change of 75% using the updated basinwide survey design during 

at least three cohort cycles. Power to detect trend in escapement PLD estimates is uniformly less 

than 60% regardless of survey length or annual decrease for the examined ranges. Power for 

trend tests of redds per km is less than 40% unless the population declines drastically. Power to 

detect trend in PLD and redds per km may be improved if trends of single cohorts are examined, 

thus eliminating variation among cohorts. By implementing the current smolt trapping design, 

the NPS expects to exceed 80% power to detect an overall net change of 76% with six 

observations per cohort and a three year change of 25%. 

2.3.1 Summer/Fall Sampling 

The current survey design for juvenile coho salmon uses a basinwide estimate based on a GSS of 

snorkeled pools. The basinwide surveys will be the primary survey type for juvenile coho 

sampling. In addition, long-term index reach density surveys are conducted to maintain this 

established legacy dataset. 

2.3.1.1 Basinwide General Systematic Surveys: Basinwide GSS surveys based on Dolloff et al. 

(1993) are conducted in each of the three core watersheds (Olema, Pine Gulch, and Redwood 

Creeks) to determine juvenile population abundance during each summer/fall sampling period. 

As part of the basinwide GSS surveys, a random start pool is chosen and every fifth pool is 

surveyed by snorkeling the pool in a single pass. Sampling effort is focused on pool habitats to 

decrease sampling time. Data from legacy index reaches on Redwood, Pine Gulch, and Olema 

Creeks since 1997 indicates that over 90% of the coho captured during summer juvenile surveys 

were occupying pool habitat units (Carlisle et al. 2009). 

Habitat data are collected annually during these basinwide GSS surveys to describe the physical 

attributes of individual habitat units (e.g., pools) within each creek. Surveys start at the bottom of 

the survey area and move upstream. Every fifth pool unit is flagged for basinwide GSS 

snorkeling and several measured widths are taken for the purpose of calibrating the estimated 

width. In addition several measured widths are taken for every 10th flatwater and riffle for the 

purpose of calibrating the estimated width. Side channel and backwater features are also 

recorded. 
20 

For each creek, one of the first five pools inventoried on the downstream end is randomly 

selected for sampling. From there, every fifth pool upstream is sampled by snorkeling. Because 

the basinwide survey sites focus on pool habitats, inferences are limited to populations of coho in 

pool units throughout each watershed. Locations and details for the basinwide survey sites are 

found in SOP 9. 

Basinwide estimates of juvenile population in pools for all three watersheds are needed for 

monitoring. However, single-pass snorkel surveys have been shown to be biased low, accounting 

for only 40% of the true number of fish present (Rodgers et al. 1992). The methods of Hankin 

and Reeves (1988) use a ratio estimator that exploits a more accurate method of detection as the 

basis for calibration. In past basinwide monitoring efforts, the Hankin and Reeves (1988) method 

was applied by using the electrofishing results from index reaches to adjust single-pass snorkel 

survey counts of the systematically chosen sites. However, the use of index sites as the 

calibration data set does not meet the requirement of sampling independence. 

Based on additional review of our methods, the protocol will implement standard calibration 

methods where 20% of dive pools will be electrofished for calibration, as described in Dolloff et 

al. (1993). 

2.3.1.2 Power Analysis: Starcevich and Irvine (2008) conducted a power analysis using the 

basinwide abundance estimates. The basinwide estimates were computed from an untested 

calibration method used with a non-random subset of pools. Starcevich and Irvine (2008) 

recommend that basinwide GSS data be collected using a true subsample of the systematic sites 

for calibration. Based on this feedback, the protocols now include calibration techniques 

consistent with Dolloff et al. (1993). Given the basinwide sampling design the NPS expects to 

detect three year change of 75% with a power of over 75%. The number of years required to 

reach this level of power depends on the three year rate of return. Once data are available, the 

power analysis should be conducted again and the sampling design refined as appropriate. 

2.3.1.3 Index Reaches: Index reaches are approximately 100 m in length (roughly 30 wetted 

widths). Index reaches are located in Olema, Redwood, and Pine Gulch Creeks. Sampling along 

the reaches provides estimates of juvenile salmonid density, species diversity data, and 

individual fish biotics for the index reaches. The reaches were established in the 1990s, have 

been monitored annually and have been the only means of providing consistent data on the entire 

fish community. The index reach electrofishing efforts will be maintained as a legacy dataset. 

Because stream habitat conditions change dramatically year to year due to differing flow 

conditions and habitat adjustments to sediment and woody debris influences, habitat units within 

the index reaches are variable. The start and stop points of the index reaches are fixed stream 

lengths and may only be adjusted slightly to capture entire habitat units, and not cut them off in 

the middle. Survey length was determined based on the number of sample units that could be 

adequately sampled by a five-person crew in one day. There are 16 index reaches in the network 

(tables 23–25 and figs. 49–51 in SOP 9: Sampling Site Descriptions). The number of index 

reaches sampled each year and the level of data collected may be reduced depending on budget 

constraints. Monitoring along the same index reaches provide detailed information on that stream 

segment in a particular portion of the stream. 
21 

The limitations of index reach surveys are well known. Sample site selection is not systematic, 

sample size is small relative to the overall number of habitat units, and distribution of fish 

throughout stream reaches is not necessarily consistent. The fish and habitat parameters collected 

via index reach surveys can be very accurate for the sampled area, but are not necessarily 

applicable to the rest of the stream or watershed. Index reach population results are no longer 

used for any other watershed level population estimates. 

2.3.2 Winter Season 

2.3.2.1 Spawner Reaches: Spawner reaches are used to estimate escapement for a variety of 

salmonids throughout the Pacific Northwest (Johnston et al. 1987; Irvine et al. 1992; Anderson 

and McGuire 1994; Downie and Peterson – undated). The surveys focus on coho salmon because 

their spawning behavior is more predictable than steelhead, and individual and redd counts can 

be conducted more accurately. Field crews will indentify steelhead redds, live fish, and carcasses 

when possible but will not have the available resources to perform surveys during the entire 

steelhead spawning period (December through May). 

Escapement surveys are usually conducted between November and January and depend on 

environmental conditions conducive to spawning. Monitoring is conducted on mainstem habitat 

within Olema, Pine Gulch, Redwood, and Cheda Creeks. The length of the creek is broken into 

2- to 4-km survey reaches to allow multiple survey crews to complete surveys in a single day 

(typically 10–14 km of stream habitat are surveyed in a single day). Reaches within these 

watersheds represent nearly the entire documented spawning habitat within each watershed. The 

results of escapement and redd surveys are restricted to the survey area completed in a single 

day. The scope of inference for estimated trends is restricted to the entirety of the survey reach 

within each watershed. 

SFAN personnel census creek main stems and some selected tributaries. Watersheds are visited 

once a week or less if water is high or turbid. Observer efficiency (ability to see fish and redds) is 

affected by streamflow conditions and visibility into the water. Surveys are timed with flow 

patterns to maximize visibility into the water. Teams of two to four observers walk upstream and 

count live fish, carcasses, and redds. Live fish are measured visually and sex and species is 

recorded. Carcasses are measured, sex identified, and a clip is taken to mark the carcass to 

prevent double counting. The clip is preserved for submittal to the NMFS genetics lab per the 

NPS research and collection permit #1046. Redds are flagged and length and width 

measurements are recorded. From these data, estimates of Area Under the Curve (AUC), Peak 

Live Cumulative Dead (PLD), and redd counts and density may be obtained (See SOP 10). 

As with many biological resources, detection error can affect an observer’s ability to census a 

population. In streams in northern California, more accurate counts of adult coho salmon using 

weir counts have been used to estimate the bias in adult escapement estimates from visual 

surveys such as ours. Where possible, SFAN would solicit assistance by universities or other 

agencies (e.g., CDFG, NMFS) to help determine bias in total adult coho escapement. If detection 

probabilities do not differ dramatically over time, then the ability to detect trend over time for 

these four watersheds may not be compromised by detection error. 
22 

2.3.2.2 Power Analysis: A power analysis was conducted by Starcevich (2008) using pilot data 

from escapement surveys conducted from the 1997–1998 to the 2006–2007 spawner season in 

Olema, Pine Gulch, and Redwood Creeks. Reaches were visited between one and ten times 

within a season. Since redds are flagged and are unlikely to be double-counted, observed redds 

were totaled to watershed level and density estimates were calculated using the total stream 

length surveyed annually within a watershed. Redds recorded as “definite” redds were used for 

coho only. 

The Olema Creek watershed is extensive and has typically not been surveyed in a single day. 

PLD estimates are time-dependent, so these estimates were calculated for tributaries surveyed 

during the same day. Olema Creek mainstem, John West Fork, and a group of four tributaries 

(Boundary Gulch, Giacomini Creek, Horse Camp Creek, and Quarry Gulch) each have separate 

PLD measurements. A weighted average of Olema Creek mainstem, John West Fork, and the 

four smaller tributaries was computed to summarize PLD at the watershed level and to avoid 

double-counting errors. The weighted mean is a conservative summary of PLD because it is 

always less than the maximum PLD measurement. 

The results of the power for tests of trend for PLD and redds per km (figures 6 and 7, 

respectively) indicate that both outcomes are highly variable and require drastic population 

declines before obtaining the power to detect change with any reliability. For example, the 

monitoring program has a less than 50% power for detecting a 75% decline of PLD over 10 

years (3 cohort returns, figure 6). Similarly, there is a less than 30% power for detecting a 50% 

decline of number of redds over 10 years (3 cohort returns, figure 7). Additional environmental 

covariates may explain some of the variation in cohorts or watersheds or the random unexplained 

variation. 

Figure 6. Power test of trend for Peak Live Dead (PLD; from Starcevich 2008). 
23 

Figure 7. Power test of trend for redds per km (from Starcevich 2008). 

A power analysis that focused on just one cohort was used to determine if the power to detect 

linear trends in escapement parameters would be greater without the additional sources of 

variation among cohorts and cohort-watershed interactions. The results of the cohort power 

analyses for PLD and redds per km are provided in figures 8 and 9, respectively. The power to 

detect linear trend in escapement parameters is improved by examining a single cohort, 

especially for redds per km. The analysis demonstrates that the monitoring program has 60% 

power for detecting a 75% decline of PLD over 10 years (3 cohort returns) when analyzing data 

for a single cohort (figure 8). Likewise, there is 60% power for detecting a 50% decline in the 

number of redds (figure 9). 
24 

Figure 8. Power test of trend for PLD for a single cohort. 

Figure 9. Power test of trend for PLD for a single cohort. 
25 

2.3.3 Spring Season 

2.3.3.1 Smolt Traps: Smolt traps document the abundance of juvenile coho salmon migrating 

from their natal streams to the ocean. Although targeted at salmonids, smolt trapping also 

provides information on other fish and aquatic species. Smolt traps are placed at the downstream 

ends of Olema, Pine Gulch, and Redwood Creeks. Trap site locations are chosen based on 

accessibility, stream gradient, and location within the watershed. In general the site should be 

located in a relatively straight section of stream channel that contains a pool unit at the top of the 

site that leads to a straight relatively straight riffle unit. Cheda Creek is not included in smolt 

trapping because it is a tributary to Lagunitas Creek. Traps would not be able to differentiate 

between smolt originating in Cheda Creek from those originating in other areas of the Lagunitas 

watershed. 

2.3.3.2 Power Analysis: A power analysis using pilot smolt data was conducted by Irvine (2008) 

using DARR estimates (figure 10; Bjorkstedt 2000). At the time of the analysis, however, only 

one cohort at Olema and Pine Gulch Creeks had two observations (2004 and 2007). Based on the 

power analysis, for the proposed sampling design of smolts (Olema, Redwood, and Pine Gulch 

Creeks) to achieve 80% power would require greater than 12 observations for each cohort at all 

three creeks in order to detect a 10% three-year decline. Because of the three-year return cycle 

for smolts this would mean greater than 35 years of annual sampling. Table 3 displays an 

example of a three-year 10% decline for cohort 1 at all three creeks. Because of limited data 

available, these models should be reproduced as more data become available. 

 

Table 3. Power estimates based on number of sampling years (number of observations) and percent 

declines. 

Power Years Sampled (number of observations) % Decline Every 3 Years 

0.102 2005–2016 (4 per cohort) 2.5 

0.114 2005–2028 (8 per cohort) 2.5 

0.146 2005–2040 (12 per cohort) 2.5 

0.454 2005–2052 (16 per cohort) 2.5 

0.127 2005–2016 (4 per cohort) 10.0 

0.322 2005–2028 (8 per cohort) 10.0 

0.703 2005–2040 (12 per cohort) 10.0 

0.957 2005–2052 (16 per cohort) 10.0 
26 

Figure 10. Example of a three-year 10% decline for cohort 1 at all three creeks. 
27 

3 - Field Methods 

The field component includes three major monitoring components conducted at different times 

of the year: summer/fall surveys for juvenile salmonids and other fish and aquatic species; winter 

surveys for spawning adult salmonids; and spring salmonid smolt trapping (see table 4). Field 

techniques are largely consistant with the CDFG Interim Restoration Effectiveness and 

Validation Monitoring Protocols (Duffy 2005) and the Coho Broodstock Recovery Program in 

the Russian River basin. All aspects related to field methods and implementation are discussed in 

the Standard Operating Procedures: 

SOP 1: Basinwide GSS Juvenile Coho and Habitat Surveys 

SOP 2: Index Reach Surveys 

SOP 3: Specialized Field Methods 

SOP 4: Spring Outmigrant Smolt Trapping 

SOP 5: Winter Adult Spawner Surveys 

3.1 Basinwide GSS Juvenile Coho Surveys 

Summer surveys will provide data about: 

a. fish habitat including geomorphic features on specific areas within each watershed, 

b. fish abundance and distribution data, and 

c. individual and population condition within each watershed. 

3.2 Basinwide GSS Habitat Typing 

For each survey area, the field crew classifies the habitat, measures the length, depth, and 

estimates the average width of each habitat unit. Units are classified as pool (scour pool, 

backwater pool, plunge pool, or mid-channel pool), flatwater, or riffle. The width of each habitat 

unit is estimated visually (see SOP 1). 

3.3 Basinwide GSS Surveys 

Field crews collect fish abundance and distribution data by snorkeling, seining, and 

electrofishing. The sampling can be performed in relatively short periods of time and is preferred 

over other approaches that rely on electrofishing or trapping techniques alone (Dolloff et al. 

1993, Williams et al. 2004). 

Snorkel counts are conducted in each of the pools identified for sampling during the habitat 

surveys. Divers use a dive light to search under vegetation, woody debris, and undercut banks. 

Multiple snorkel passes may be necessary depending on the size and complexity of the unit. All 

target species (coho) are counted. Presence of non-target species is documented, as well as cover, 

habitat complexity, and general survey conditions are noted. Snorkelers record or call out (to an 

on-shore assistant) their observations and transfer the information immediately to field sheets 

once they complete a pool unit. A subsample of the snorkeled pool units are calibrated using 

multiple pass electrofishing as described in Dolloff et al. (1993). Field methods are detailed in 

SOPs 1 and 3. 
28 

3.4 Index Reach Surveys (Legacy dataset) 

Index reach surveys are performed during the fall following the completion of Basinwide GSS 

surveys. Index reaches are separated into a series of sampling units, which are used collectively 

to describe each index reach. Index reach units are determined each season by delineating each 

habitat type contained within the index reach. Each unit within the reach is isolated using block 

nets upstream and downstream. The units are then sampled individually with an electrofisher or 

seine net, using a multiple pass depletion technique. A subsample of fish is measured for 

individual and population purposes (length and weight). After the fish sampling is completed, 

habitat measurements and assessments will be made by the field crew for the purposes of historic 

site description in case a drastic change in stream condition occurs. Field methods are detailed in 

SOPs 2 and 3. 

3.5 Spring Surveys 

Spring smolt surveys include capture and handling of juvenile salmonids and other fish with 

downstream migrant traps. Smolts are captured using pipe/fyke net traps. Traps are designed to 

minimize impingement under high flows and in-trap predation of fry by larger juvenile 

salmonids and other fish. A subsample of fish is measured for individual and population 

purposes (length and weight). Mark and recapture techniques are used on smolt to determine 

trapping efficiency, which is necessary to estimate outmigration rates. Field methods are detailed 

in SOP 4. 

3.6 Winter Surveys 

Coho salmon spawner surveys involve observation of live fish and measurement of carcasses and 

redds. The surveys are conducted annually between November and February in the Olema, Pine 

Gulch, Cheda and Redwood Creek watersheds. Surveys are conducted by trained volunteers and 

PORE/GOGA staff approximately every 1–2 weeks during favorable weather and stream flow 

conditions, with less frequent surveys during less favorable conditions. 

Typically, teams of 2 to 3 people survey reaches of 2- to 4-km in length, walking upstream along 

creek margins and banks where possible and looking for redds, carcasses, and live fish. Start and 

end locations for reaches are based on known access points. Occasional steelhead adults and 

redds are observed and counted incidental to coho observations. Locations of all live fish, 

carcasses and redds are recorded in reference to permanent tags that mark every 100 m of stream 

length. Redds are targeted as they are stationary and can be monitored over time to determine 

spawning success. Field methods are detailed in SOP 5. 
29 

Table 4. Summary of metrics and sampling sites for each sampling season. 

Sampling Season 

Summer/Fall 

(July–Oct) 

Winter 

(Early Nov–Feb) 

Spring 

(Late March–May) 

Life Stage Sampled Juvenile Spawner Smolt 

Sampling Design Used 1. Basinwide GSS 

2. Index reach 

Spawner survey Smolt trap 

Field Methods Snorkeling, seining, 

electrofishing in 

basinwide survey units 

and 100-m index 

reaches 

Count live and dead fish, 

and redds along 2- to 4-

km reaches 

Pipe/fyke net traps placed 

near mouth of streams 

Data Gathered 1. Habitat typing 

2. Coho salmon 

abundance 

3. Species diversity 

1. Abundance 

2. Carcass sex and length

3. Redd count 

1. Abundance 

2. Fish weight and length 

3. Species diversity 

 

Sampling Sites High priority streams 

(Olema, Pine Gulch, 

Redwood, and Cheda 

Creeks) 

High priority streams High priority streams 

(Cheda Creek not 

included) 

Sampling Frequency Sampling is performed 

on one creek at a time 

with each creek taking 

approx. one month to 

complete 

If stream conditions allow, 

each stream is surveyed 

weekly

Smolt traps are checked 

one to two times per day 

31 

4 - Data Management 

This chapter briefly describes how the salmonid monitoring protocol meets established I&M data 

management objectives through data entry specifications, database design, quality assurance and 

control measures, metadata development, data maintenance, data storage, and data archiving. 

SOP 8: Data Management describes in more detail the data management procedures for all the 

components of the protocol. 

4.1 Database Designs 

4.1.1 Smolt Monitoring Database 

The SFAN staff has continued to use a relational Microsoft Access database for the smolt 

monitoring program originally designed in 1999. The database has undergone some fundamental 

design modifications since the SFAN I&M program began its oversight of the program, but the 

basic data fields stored in the database have remained relatively unchanged. The last significant 

changes to the database occurred in the winter of 2005 when the SFAN data management staff 

performed a thorough review and clean-up of all legacy data stored in the database and modified 

the table design to its current form. The database is titled Smolt_MasterXP.mdb. 

The data in the smolt database are simply organized around field events, where a different event 

represents each day and each smolt trap that is checked by the field staff. The survey or event 

data are related to the counts of fish species collected in the trap on that day, fish measurements 

(weight and fork length), and the list of field staff present on the survey. A table within the 

database stores UTM coordinates and a descriptive location of each smolt trap installed during 

the course of the monitoring project. Linking the survey records to the correct trap location 

provides a spatial reference to the smolt data. 

4.1.2 Spawner Monitoring Database 

The SFAN staff has continued to use a relational Microsoft Access database for the smolt 

monitoring program originally designed in 1997. The database has undergone some fundamental 

design modifications since the SFAN I&M program began its oversight of the program, but the 

basic data fields stored in the database have remained relatively unchanged. The last significant 

changes to the database occurred in the winter of 2005 when the SFAN data management staff 

performed a thorough review and clean-up of all legacy data stored in the database and modified 

the table design to its current form. The database is titled Spawner_MasterXP.mdb. 

The data in the spawner database are simply organized around field events, where a different 

event is represented for each survey of a particular stream reach performed by the field staff and 

volunteers. The survey or event data are related to the observations of spawning coho salmon or 

steelhead trout and the measurements of redds encountered during the survey. 

The location of each fish or redd observed during a spawner survey is referenced to the nearest 

downstream 100-m section tag. Each tag, usually placed on a tree along the stream bank, 

represents the beginning of a 100-m stream section. Within the spawner database, stream tag 

locations are stored in a separate locations table with corresponding UTM coordinates. Linking 
32 

the fish and redd observation records to the correct stream tag location records provides a spatial 

reference to the data. 

4.1.3 Summer Monitoring Database 

The SFAN staff has continued to use a relational Microsoft Access database for summer 

salmonid monitoring activities (Basinwide GSS and Index Reach) since the program began in 

1997. Although, the core database has undergone several fundamental design modifications over 

the years, the core data elements stored in the database have not changed significantly. The 

current database design was completed in 2005 under the guidance of the SFAN I&M program 

just prior to the start of the 2005 summer monitoring season. The last significant changes to the 

database occurred in the winter of 2006 when the SFAN data management staff completed 

reporting tools for basinwide habitat and fish population summaries. The database is titled 

Summer_MasterXP.mdb. 

The data in the summer database are organized around field events, where a different event 

represents each summer monitoring activity, including habitat typing, snorkeling, and 

electrofishing. Habitat typing event records exist for each day that a particular stream is habitat 

typed, with the related data records being the stream units measured and cataloged during that 

survey. Separate event records are maintained for each stream unit that is snorkeled, with snorkel 

pass information and fish species counts for each pass related to each snorkel event record. 

Finally, separate event records are created for each stream unit that is electrofished, with pass 

information, fish counts, fish measurements, and fish population estimate data related to each 

electrofishing event record. The summer database also houses data related to index reach habitat 

assessments, which is not a primary I&M monitoring activity. 

The location of each stream habitat unit cataloged during habitat typing surveys and 

subsequently snorkeled and/or electrofished is referenced to the nearest downstream 100-m 

section tag. Each tag, usually placed on a tree along the stream bank, represents the beginning of 

a 100-m stream section. Within the summer database, stream tag locations are stored in a 

separate locations table with corresponding UTM coordinates. Linking the summer monitoring 

surveys to the correct stream tag location records provides a spatial reference to the data. 

During habitat typing surveys, each stream habitat unit is assigned a sequential basinwide habitat 

unit code representing the stream location, unit number, and year. The basinwide unit code is 

again recorded if and when the unit is revisited during the season for electrofishing or snorkeling. 

Standardized documentation of basinwide unit codes allows the SFAN staff to easily create 

queries to compare fish counts between snorkel surveys and electrofish surveys or compare unit 

measurements (length, width, depth) recorded during separate field events. 

A series of queries have been developed within the summer database that follows the guidelines 

developed by Dolloff et al. (1993) for calculating basinwide habitat and fish population 

estimates. The queries and a simple user interface, developed by the SFAN I&M program, allow 

the database user to easily generate core summary statistics for use in annual reports and longterm trend analyses. Correct documentation of basinwide unit codes between corresponding 

habitat typing, electrofish, and snorkeling records is essential to calculating the basinwide 

estimates. 
33 

4.2 Annual Data Work Flow 

The master monitoring databases contain or will contain all smolt, spawner, and summer 

monitoring data collected to date in the SFAN parks. The SFAN I&M program is still in the 

process of converting legacy summer monitoring data from the previous to the current database 

format. The SFAN Data Manager is responsible for managing the master databases and assisting 

the Project Lead and field staff with any database issues. 

Rather than enter monitoring data directly into the master databases, satellite databases are 

created at the beginning of each monitoring season that parallel the structure of the master 

databases. The SFAN Data Manager prepares separate databases for the smolt, spawner, and 

summer field seasons and provides them to the field staff based at PORE. The satellite data 

tables are blank in each of the databases, but the look-up tables are populated and ready for use. 

The databases are provided in MS Access XP format. 

At the end of each season, the salmonid field staff is responsible for proofing the data entry 

records for all satellite databases against the paper datasheets completed in the field. When 

complete, the satellite databases are sent or provided to the SFAN Data Manager for additional 

review and certification. Once certified, the Data Manager imports the satellite data into the 

master database, appends the data to the appropriate tables, and archives the satellite. 

4.3 Quality Assurance and Quality Control 

The success of the salmonid monitoring program is dependent on the quality of the data it 

collects, manages, and disseminates. Analyses performed to detect ecological trends or patterns 

require data that are recorded properly and have acceptable precision, accuracy, and minimal 

bias. Poor-quality data can limit detection of subtle changes in ecosystem patterns and processes, 

can lead to incorrect interpretations and conclusions, and can greatly compromise the credibility 

of the program managing it. 

Quality assurance (QA) can be defined as an integrated system of management activities 

involving planning, implementation, documentation, assessment, reporting, and quality 

improvement to ensure that a process, item, or service is of the type and quality needed and 

expected by the consumer. Quality control (QC) is a system of technical activities that measure 

the attributes and performance of a process, item, or service relative to defined standards (Palmer 

2003). While QA procedures maintain quality throughout all stages of data development, QC 

procedures monitor or evaluate the resulting data products. 

To ensure that the salmonid monitoring program produces and maintains data of the highest 

possible quality, QA/QC procedures are implemented to identify and minimize errors at each 

project stage associated with the data life cycle. SOP 8: Data Management outlines specific 

QA/QC guidelines and procedures to be followed during data entry, data collection, data 

verification, and data validation. 

4.4 Version Control Guidelines and Database History 

Version control guidelines for the salmonid monitoring databases will follow those presented in 

the SFAN Data Management Plan (Press 2005). Prior to any major changes to the database 

design, a back-up copy of the database should be made. Once the database design changes are 
34 

complete, the database should be assigned the next incremental version number. The final copy 

of the previous database version should be archived with the version closing date incorporated 

into the database title. Version numbers should increase incrementally by hundredths (e.g., 

version 1_01, version 1_02, etc.) for minor changes. Major revisions should be designated with 

the next whole number (e.g., version 2_0, 3_0, 4_0, etc.). Significant database re-design may 

require approval by the project manager, review by other data management staff, and revisions to 

the data management SOP. The database version number should be included in the file title of 

the database, for example, Smolt_MasterXP_v1_00. 

The Data Manager maintains history logs of each of the salmonid monitoring databases. Within 

the smolt and spawner master monitoring databases, the history log is incorporated directly into 

the database as table tblEditLog. The history log for the summer monitoring database is in a 

separate Microsoft Word document titled Summer_Database_Log. 

All design modifications to the databases are tracked within the history logs and are referenced 

to changes in database version numbers. Design modifications include changes to the table 

structure, user interface, or underlying macros and Visual Basic Code. Major changes to the data 

themselves are also noted in this document, such as when a new set of annual data are uploaded. 

It is especially important to note edits to the data that will result in changes to final data 

summaries previously published in annual reports or other media. This will prove invaluable to 

data users attempting to understand differences in data between years. 

4.5 Metadata Procedures 

The NPS GIS Committee requires all NPS GIS data layers to be described with the NPS 

Metadata Profile, which combines the Federal Geographic Data Committee (FGDC) standard, 

elements of the ESRI metadata profile, the Biological Data Profile, and NPS-specific elements. 

Although no standard has been applied to natural resource databases and spreadsheets, the SFAN 

will complete the NPS Metadata Profile to the greatest extent possible to document the master 

salmonid monitoring databases. Because the annual datasets are uploaded into the master 

databases without alteration, the SFAN will not create separate metadata records each satellite 

database. 

Complete metadata records for the SFAN salmonid monitoring databases will be generated in 

compliance with current NPS standards by the Network Data Manager. Because the location data 

for this project is stored as UTM coordinates within the MS Access databases, there are no 

spatial data products associated with this protocol that require metadata records. 

When completed, metadata records, but not the data, will be posted to the NPS Data Store for 

public discovery and consumption. Contact information within the metadata records will direct 

interested parties to the Network Data Manager for further inquiries. Master database metadata 

records posted to the NPS Data Store will be updated annually after the annual data has been 

uploaded or following database revision to a new version whole number (i.e., v1_3 to v2_0, but 

not v2_0 to v2_1). 
35 

4.6 Data Storage and Archival Procedures 

All master data files for the salmonid monitoring project are housed at GOGA. The SFAN I&M 

Program office and the SFAN Data Manager are stationed at GOGA. The master databases, 

reside in a separate folder directory from archived seasonal satellite databases and previous 

master database versions. The database directory is located at: 

Inpgogamahe1\Divisions\Network I&M\Individual Vital Signs\Streamfish Assemblages\ 

data\databases 

The salmonid field office, field staff, and the Project Lead are all based at PORE. Following 

error-checking and proofing, all field datasheets are organized in folders or binders and cataloged 

according to stream name and monitoring activity (smolt trap checks, spawner surveys, habitat 

typing, etc.). The datasheets are kept in the salmonid field office at PORE. In time, all datasheets 

will be submitted to the PORE Curatorial Manager for long-term storage.

At PORE, digital data files are housed at: 

Inppore05\Resources\Natural\_Fish\Databases 

Within this directory, separate folders store active satellite databases and copies of the master 

databases. 

4.7 Data Distribution 

Guidance documents, reports, and data must be easily discoverable and obtainable for the 

salmonid monitoring program to inform park management and to enable sharing program 

information with other organizations and the general public. The main mechanism for 

distribution of the salmonid monitoring documents and data will be the internet. The salmonid 

monitoring protocol, accompanying SOPs, and all annual reports will be made available for 

download at the SFAN website: http://science.nature.nps.gov/im/units/sfan/

As previously mentioned, the salmonid monitoring database will not be posted for public 

download, but metadata records for the master databases will be maintained at the NPS Data 

Store. The metadata records will direct interested parties to the SFAN Data Manager for further 

inquiries. 

In addition to the NPS Data Store, the NPS I&M Program maintains an on-line natural resource 

bibliographic database known as NatureBib. NatureBib records will be created for all of the 

salmonid monitoring documents, including the protocol, annual reports, and any resulting 

publications. 

37 

5 - Data Analysis and Reporting 

Reporting results is a critical component of long-term vital signs monitoring to ensure that 

information generated through the program is available to all levels of park management 

including planning, interpretation, maintenance, and law enforcement. The overall strategy 

includes development of 1) seasonal updates 2) seasonal progress reports 3) annual summary 

reports and 4) analysis and synthesis reports. 

5.1 Seasonal Updates 

Seasonal updates will be provided to all park staff, program volunteers, and all interested parties 

at the end of each field season. Seasonal updates will provide a subjective summary of each field 

season using raw data sources only. These updates are produced with the intent of providing real 

time information to park interpretive staff, program volunteers, and resource managers. 

Providing real time information not only allows managers to be proactive on major resource 

issues that may be impacting NPS fisheries, but it also increases public awareness and keeps 

program volunteers involved in the program. 

5.2 Seasonal Progress Reports 

Seasonal progress reports are designed as a summary of finalized (QA/QC) data for each field 

season. Population estimates will be calculated and provided in each progress report. Seasonal 

progress reports will also provide an account of the events that occurred throughout each season. 

Summary reports are provided for both park resource managers and the CDFG as a final 

synopsis of each field season. 

5.3 Annual Summary Reports 

Annual summary reports are provided as a more comprehensive report including regional 

comparisons, life stage comparisons, and multiyear summaries that will be prepared annually. 

Salmonid annual reports will also include summaries of winter adult escapement surveys, spring 

smolt out migration studies, and summer juvenile fish density and population estimates for each 

watershed, as well as comparisons between years. Annual summary reports are designed as a 

compilation of the three seasonal reports placed in context with historic and regional data. The 

intent of the annual report is to provide summarized data with a comparative analysis for each 

year compared to the historic average and regional trend to resource managers. Annual reports 

may allow resource managers to observe trends or anomalies before a synthesis report is 

produced. 

5.3.1 Routine Data Analyses 

Detailed description and documentation of routine analyses are included in SOP 10. Refer to 

Carlisle et al. (2009) for an example of the types of analyses that will be conducted. Results will 

be presented separately for each watershed and each of the three year classes. 

5.3.1.1 Juvenile Population Estimates: Calibrated snorkel counts are used for basinwide 

population estimates, using survey techniques developed by Hankin and Reeves (Dolloff et al. 

1993). Fish densities, fork length frequencies, fish condition, and habitat composition are 

calculated from the collected juvenile data. 
38 

5.3.1.2 Winter Spawner Data: Because coho return to spawn over a one- to three-month period 

November through January (weather dependent) and residence time on the spawning grounds is 

variable, live fish may be double counted during repeated surveys. Reported spawning estimates 

are made using the PLD (Peak Live + Cumulative Dead) index. This index is derived by adding 

the peak number of live fish observed during a single survey to the number of carcasses 

recovered on or prior to that date and is considered a minimum estimate of the population. 

Carcass information is also used to calibrate observer length and sex estimates. Redd counts are 

used to describe spawning density and spatial distribution. Where survey frequency is adequate, 

reporting will include escapement estimates using the AUC method (Irvine et al. 1992). 

5.3.1.3 Smolt Population Estimates: Trapping results can be compared with previous annual 

results. Results will also be examined temporally to determine when the bulk of smolt and fry 

migration occurs; and environmental conditions such as rainfall and temperature are gathered to 

detect influences on migratory timeframes. The collection of weight and length allows analysis 

of individual and population condition metrics. Fish population estimates and standard error are 

calculated using the computer software program DARR for stratified mark/recapture data. 

5.4 Analysis and Synthesis Reports 

Analysis and synthesis reports are produced on a nine-year cycle with the intent of evaluating the 

success in answering the key monitoring questions and current status of coho salmon relative to 

the desired status. Analysis and synthesis reports are intended to provide a benchmark for park 

management in the mission to preserve and protect the stream resources for future generations. 

Methods for long-term trend analysis are described in SOP 10. In general, the salmonid 

monitoring protocol will report results by year, and synthesize long-term regional results within 

these documents. This report will differ from the annual report by providing statistics to describe 

trends over the long-term. 

Due to the cohort structure of coho salmon, a modified mixed linear model of VanLeeuwen et al. 

(1996) and Piepho and Ogutu (2002) will be used to determine population trends. Covariate 

information (e.g., fish K factors, local rainfall, and habitat data) will be incorporated into the 

trend analysis to explain temporal and spatial variation and more precisely measure trend. Model 

selection for mixed models analyzed with restricted maximum likelihood will be selected using 

Bayes Information Criterion (Schwarz 1978, Gurka 2006). 

5.5 Reporting Format 

Formats of the seasonal, annual, and long-term trend reports will follow the templates of the 

Natural Resource Publications Management 

(http://www.nature.nps.gov/publications/nrpm/index.cfm). 
39 

6 - Personnel 

The salmonid monitoring program is a full-time commitment for a minimum crew of three to 

four staff, including the project leader and two to three field staff. Volunteers will be necessary 

during specific times when additional personnel are required, particularly for winter spawner 

surveys and summer index reach electrofishing surveys. Volunteers will be utilized for nonsensitive tasks such as recording data, dip netting for fish, and as additional observers during 

spawner surveys. All staff should review the fisheries job hazard analysis before starting field 

monitoring. It is the responsibility of the field crew leader to review critical field safety points 

with volunteers prior to starting each survey. 

6.1 Personnel Requirements 

6.1.1 Project Lead (Network) 

Implementation of year-round surveys and reporting is conducted by a GS-9 Fishery Biologist. 

The Fishery Biologist is required to have extensive experience in fishery science. Approximately 

50% of their time is for fieldwork and 50% for data management, data analysis and reporting 

working closely with the Network Data Manager. The Fishery Biologist schedules, oversees, 

provides training to, and works closely with cooperators and volunteers. 

6.1.2 Hydrologist (PORE) 

The Hydrologist at PORE supervises the Fishery Biologist/Project Lead, hires new staff, 

provides programmatic and budget oversight, handles contracts or cooperative agreements, and 

reviews all documents produced by the Biologist. The Hydrologist is also responsible for 

submitting grant requests and ensuring that permit requirements are met. The Hydrologist 

represents the NPS at a variety of local and regional salmonid-related forums. 

6.1.3 Aquatic Ecologist (GOGA) 

The GOGA Aquatic Ecologist provides technical assistance, guidance, and permit compliance 

throughout the project. The Ecologist may also represent the NPS at a variety of local and 

regional salmonid-related forums. 

6.1.4 Data Manager (Network) 

The Network Data Manager provides support for managing the project database including the 

development of queries, analyses, and reports. The Data Manager is ultimately responsible for 

building proper QA/QC procedures into the database management system and that appropriate 

data handling procedures are followed. The Data Manager is also responsible for archiving 

electronic data, data security, and facilitating software upgrades as necessary. The Data Manager, 

in collaboration with the Project Lead/Fishery Biologist, will develop and modify data entry 

forms, queries, and reports as necessary. 

6.1.5 Supporting Field Staff 

Supporting field staff members have been funded through the CDFG grants with staff hired 

through Point Reyes National Seashore Association and/or Conservation Corps North Bay 

(CCNB). One full-time and two seasonal assistants are needed to implement the program. The 

full-time staff member will serve as the crew leader in the field. Field staff may include 
40 

volunteers, interns, seasonal staff, or cooperators. The field staff should expect to be conducting 

field work 75% of the time, with approximately 25% of their time in the office to transfer and 

manage field collected data during the months when field operations are being performed (table 

5). In late fall (October–November) and late winter (February), field staff commits 80% of their 

time to data entry, data summaries, data analysis and reporting (table 5). Field staff may also 

help coordinate community volunteers. 

6.1.6 Community Volunteers 

Community volunteers provide more than 1,200 hours per year in volunteer support to the 

program annually. Over the years, a core group of well-trained volunteers has been established. 

New volunteer participants are solicited as needed. Hands-on training is provided by assisting in 

the field with experienced field staff. 

6.2 Annual Workload and Field Schedule 

Surveys are conducted year round as presented in table 5. 

6.2.1 Summer Surveys 

6.2.1.1 Basinwide Surveys: Basinwide surveys are conducted from July to mid October and 

require a crew of four staff members. Snorkel surveys require two trained and qualified staff to 

perform coho dive counts. All staff members must have at least one full season of snorkeling 

experience before they can be utilized for snorkel surveys. Basinwide habitat censuses are 

performed using two trained and qualified staff members. Staff members will be trained by the 

program lead (I&M Fishery Biologist) prior to each field season. 

6.2.1.2 Index Reach Surveys: Index reach monitoring is conducted annually after the completion 

of Basinwide GSS surveys. Index reach monitoring requires at minimum a crew of three, though 

five is preferable. The crew should include at least two trained and qualified staff, one to operate 

the electrofishing unit and the other to process (weigh and measure) captured fish. Other park 

staff or volunteers may be recruited as needed. 

6.2.1.3 Winter Spawner Surveys: Spawner surveys are conducted between late November and 

early February. The surveys require 5–10 volunteers. Each team is led by a trained program staff 

member or an experienced volunteer team leader. Volunteer team leaders will be determined by 

the Program Lead (I&M Fishery Biologist), but in general the volunteer should have at least 2 

years of experience. Volunteer team leaders must be able to properly identify adult salmonids 

and redds without the aid of a program staff member. The program lead must ensure that both 

program staff and volunteer leaders are proficient at both data collection and fish processing 

techniques prior to each field season. 

6.2.1.4 Spring Smolt Surveys: Spring smolt surveys occur between March and early June. Traps 

must be checked on a daily basis (including weekends and holidays) and requires the availability 

of two to three experienced people to conduct the work. Because this involves handling of 

threatened and endangered species, only qualified personnel can operate the traps. Volunteers 

may only be used for transcribing data onto datasheets, assisting in trap construction, and 

assisting in trap maintenance. 
41 

Table 5. Annual field and reporting schedule. 

Field Task 

(# of staff) Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec 

Summer Habitat 

Surveys (2) 

 X X X X X 

Summer Basinwide 

Survey (4) 

 X X X X X 

Summer Index Reach 

Surveys (3-5) 

 X X 

Summer Progress 

Report 

 X X 

Winter Spawner 

Surveys (2–3) 

X X X X 

Winter Progress 

Report 

 X X 

Spring Smolt Trapping 

(2–3) 

 X X X X 

Spring Progress 

Report 

 X X 

Annual Report X X 

Permit Report X X X 

6.3 Qualifications 

The program requires observation and handling of threatened and endangered species. 

Appropriate handling and care associated with these species is developed through training and 

field experience. The aquatic species list is short enough that field staff, without local 

experience, may learn the identification skills quickly (within a week of field experience). What 

is most important is an interest in and respect for the fish species that are handled through this 

program. The project leader should have a strong background in fisheries monitoring and 

analysis techniques, and should be an effective teacher of field skills. The project leader will also 

oversee field staff to insure that they are capable of safely handling the fish species. All I&M 

Fisheries staff are included in the federal and state ESA research and collection permits. 

6.4 Training 

Personnel should review Training and Safety SOP #11 and associated protocols, supporting 

documents, and field datasheets for each survey type. 

Other specific tasks such as operating a backpack electrofisher will also require specialized 

training. 

6.4.1 Snorkeling 

Snorkel surveys require highly skilled observers with at least one field season or 300 hours of 

snorkeling experience (Hillman et al. 1992). 
42 

6.4.2 Electrofishing 

If new personnel are being trained, several days should be scheduled to practice electrofishing. 

All filed staff operating electrofishing units must posses a valid CPR training certification card. 

Only staff should operate electrofishing equipment. Pregnant women or any individual with a 

surgically implanted electronic device such as a pacemaker must not participate in electrofishing 

activities but may assist in fish processing.
43 

7 - Operational Requirements 

7.1 Budget 

This protocol assumes a project staffing level of three to four staff, including the project leader, 

field crew leader, AmeriCorps member, and field technician. The fieldwork is accomplished with 

the assistance of volunteers, particularly during winter surveys and summer electrofishing 

surveys. Program funding currently comes from the SFAN I&M Program and is supplemented 

by grants from CDFG Competitive Grant Program through FY2013 (table 6). 

7.2 Budget Shortfalls 

The current budget is augmented by grants through FY2013. The CSMP has received funding 

from the CDFG competitive grants program since 2002. Given the past and current level of 

funding, combined with the current status of the CCC ESU coho populations, CDFG will likely 

continue their support of the CSMP. In case grant or match funds are not available, the 

monitoring program would be reduced to cover only the higher priority monitoring components, 

as outlined in table 7. Some expenses such as equipment costs may vary per year. In addition, the 

number of monitored watersheds and/or sites would be reduced to a manageable level based on 

existing staff and volunteer availability. Field support for monitoring is currently augmented, but 

may be achieved with student interns and volunteers. The minimum cost for each survey type 

proposed in table 7 assumes the maximum use of volunteer effort. It should also be noted that 

minimum costs in table 7 were developed separate from the combined budget presented in table 

6 since some costs such as vehicle and equipment are reduced when annually performing 

multiple survey types. Qualified student interns from the Pacific Coast Learning Center have 

provided additional summer field assistance since 2004 and it is anticipated that this program 

will continue in FY2011 and beyond. 
44 

Table 6. Salmonid monitoring program budget: Annual estimated costs (FY2010). 

Funding Source/ 

Expense Categories 

Description Amount 

I&M Program $90,700 

CDFG (through FY2013) $102,000 

 Total Available Funds $192,700 

Expenses 

 Spawner Surveys – I&M Project Leader (8 pp) $25,000 

 Smolt Trapping – I&M Project Leader (5 pp) $15,000 

 Basinwide Surveys – I&M Project Leader (8 pp) $25,000 

 Index Reach Surveys – I&M Project Leader (2 pp) $ 6,000 

I&M Project Leader Total GS-9 – Subject-to-furlough (23 pp) $71,000 

I&M Data Manager GS-11 (approx. 2 pp) $ 7,500 

NPS Labor Total $78,500 

Network Travel & Training $ 700 

 Spawner Surveys – DFG Grant Field Crew Leader (8 pp) $18,000 

 Smolt Trapping – DFG Grant Field Crew Leader (5 pp) $13,000 

 Basinwide Surveys – DFG Grant Field Crew Leader (9 pp) $20,000 

 Index Reach Surveys – DFG Grant Field Crew Leader (2 pp) $ 4,500 

DFG Grant Crew Leader Total Cooperative Agreement or GS-7 equivalent (25 pp) $55,500 

 Smolt Trapping - DFG Grant Field Technician (5 pp) $ 9,000 

 Basinwide Surveys - DFG Grant Field Technician (8 pp) $14,500 

 Index Reach Surveys - DFG Grant Field Technician (2 pp) $ 3,500 

DFG Grant Field Technician Total Cooperative Agreement or GS-5 (15pp) $27,000 

Field Crew CCNB/AmeriCorps (20 pp fixed per year) $18,000 

DFG Grant Labor $100,500 

 Spawner Survey Equipment Maintenance & Replacement $ 500 

 Smolt Trapping Equipment Maintenance & Replacement $ 4,000 

Summer Index Reach & Basinwide Equipment Maintenance & 

Replacement (Both surveys require similar equipment) $ 3,000 

Equipment Total Cooperative Agreement ($1,500) and I&M Program ($6,000) $ 7,500 

Vehicle Fixed cost per year $ 5,000 

Total Expenses $192,700 

 Balance -0- 
45 

Table 7. Priority monitoring efforts for salmonid monitoring protocol if match funding is reduced. 

Rank/ 

Priority 

Monitoring 

Component 

Min. 

Cost 

# Sites/Time 

Commitment 

Min.

Staff 

Min. 

Volunteer Pros/Cons 

1 Spawner 

surveys 

$50,000 3 watersheds (Olema, 

Pine Gulch, Redwood) 

(3 months total) 

2–3 2–5 Specific to salmonids; existing 

dataset since 1997; can involve 

many volunteers; valuable to 

regional salmonid recovery; 

CCCESU Recovery Goal 

2 Smolt trapping $62,000 3 sites 

(3 months total) 

3–4 1–4 Focused on salmonids but also 

yield info for some other spp; 

existing dataset since 1998; 

requires 7 day/week 

commitment; CCCESU 

Recovery Goal 

3 Basinwide 

surveys 

$70,000 3 watersheds x 3–4 

weeks per watershed 

(3 months total) 

3–4 0–4 Best for salmonids but can be 

used for some other spp; yields 

population estimate for target 

spp; existing datasets since 

2001 (Pine Gulch Creek), 2003 

(Olema Creek) & 2004 

(Redwood Creek) 

4 Index reach 

surveys 

$16,000 5–6 sites (1–2 weeks) 

per watershed x 3 

watersheds (1.5 

months total) 

2–3 2–3 Focused on specific stream 

reaches; samples stream 

habitat and entire vertebrate 

community; existing dataset 

since 1999 

7.3 Facility and Equipment Needs 

The fish monitoring program is housed at PORE, where appropriate office space and equipment 

storage is available. Complete equipment lists specific to each of the monitoring components are 

given in the respective SOPs. Most of the equipment required to implement this monitoring 

protocol has been acquired although there is a continuing need for equipment maintenance and 

replacement. The equipment and materials (dry suits, wet suits, electrofisher, nets, scales and 

other equipment) required for monitoring are subject to extensive wear and tear, and require 

repair or replacement on a regular basis. 

7.4 Permitting Requirements 

All of the proposed monitoring will be conducted under research and collection permits from the 

CDFG and NMFS. Various reporting requirements are associated with the permits and are 

outlined in SOP 6. 

NPS is authorized under NMFS permit #1046 modification #2 until February 2012 to take adult 

and juvenile federally endangered coho salmon, threatened steelhead, and chinook salmon (O. 

tshawytscha) associated with fish population and habitat studies in drainages on, and proximate 

to, NPS lands in Marin County, California within the central California coast ESU/Distinct 

Population Segment (ESU/DPS). Types of studies for which federal ESA listed fish are 

authorized to be taken include: 1) salmonid smolt outmigration monitoring, 2) juvenile salmonid 

diet composition, 3) adult salmonid spawner monitoring, 4) summer/fall juvenile salmonid 

distribution, population abundance, and habitat monitoring 5) juvenile salmonid winter habitat 
46 

utilization, 6) adult salmonid spawner escapement monitoring, and 7) juvenile salmonid rescue 

and relocation. 

Field work also falls within the scope of CDFG Scientific Collection Permit 2081 (b). This 

permit applies to NPS research and monitoring activities in drainages proximate to NPS lands in 

Marin County, San Francisco County, San Benito County, Contra Costa County, and Monterey 

County, California. Stream segments on non-federal lands in Marin County on which NPS 

research and monitoring activities may occur include: 

• Devil’s Gulch (tributary to Lagunitas Creek) within Samuel P. Taylor State Park 

• Redwood Creek and tributaries within Mt. Tamalpais State Park 

• Pine Gulch and tributaries on private and Marin County Open Space District (MCOSD) 

land 

• Easkoot Creek and other Bolinas Lagoon tributaries on private and local government 

lands 

• Tomales Bay tributaries on state, local government, and private lands. 
47 

8 - Glossary 

Adipose fin: A small fleshy fin with no rays, located between the dorsal and caudal fins. 

Age: The number of years of life completed, here indicated by an Arabic numeral, followed by a 

plus sign if there is any possibility of ambiguity (age 5, age 5+). 

Age class: A group of individuals of a certain species that have the same age. 

Alevin: The developmental life stage of young salmonids and trout that are between the egg and 

fry stage. The alevin has not absorbed its yolk sac and has not emerged from the spawning 

gravels. 

Anadromous: Fish that hatch rear in fresh water, migrate to the ocean (salt water) to grow and 

mature, and migrate back to fresh water to spawn and reproduce. 

Anal fin: The fin located on the ventral median line and behind the anus. 

Assemblage: a group or aggregate of things gathered or collected. 

Basinwide survey: A survey which provides a statistically accurate estimate of stream habitat 

and/or a population of a particular fish species for a broad area or entire stream. 

Evolutionarily Significant Unit (ESU): A population of organisms that is considered distinct for 

purposes of conservation. 

California Central Coast Evolutionarily Significant Unit (CCCESU): The distinct population of 

all naturally spawning populations of coho salmon from Punta Gorda in northern California 

south to and including the San Lorenzo River in central California, as well as populations in 

tributaries to San Francisco Bay, excluding the Sacramento–San Joaquin River system. 

Caudal fin: The tail fin. 

Cohort: See year class. 

Community: An assemblage of interacting populations occupying a particular area. 

Condition factor: A ratio relating fish length to fish weight and measuring the relative plumpness 

of a fish. 

Critical size: The average size of the fish in a year-class at the time when the instantaneous rate 

of natural mortality equals the instantaneous rate of growth in weight for the year-class as a 

whole. Also called optimum size. 
48 

Egg-to-smolt survival: The numerical difference between the number of fertilized eggs produced 

by a group of fish and the number of smolts resulting from those eggs. 

Electrofishing: The use of electricity to capture fish 

Emergence: The process during which fry leave their gravel spawning nest and enter the water 

column. 

Emigration: Referring to the movement of organisms out of an area. See immigration and 

migrating. 

Escapement: The quantity of sexually mature adult salmon (typically measured by number or 

biomass) that successfully passes through a fishery to reach the spawning grounds. 

Falcate: Hooked or curved like a sickle. 

Fecundity: The reproductive capacity of an individual, usually measured as the total number of 

eggs produced by a female fish. 

Fin ray: A soft or hard cartilaginous rod in fins. 

Fingerling: Refers to a young fish in its first or second year of life. 

Fork length: The length of a fish from the most anterior part of the body to the tip of the medial 

caudal fin ray. 

Fry: A stage of development in young salmon or trout. During this stage the fry is usually less 

than one year old, has absorbed its yolk sac, is rearing in the stream, and is between the alevin 

and parr stage of development. 

Habitat unit: Stream morphology classification unit, such as a pool (scour pool, backwater pool, 

plunge pool, or mid-channel pool), flatwater, or riffle. 

Immigration: Referring to the movement of organisms into an area. See emigration and 

migrating. 

Index reach survey: Established stream reaches approximately 100 m in length, sampled during 

summer/fall base flow periods to assess fish abundance and distribution. 

Iteroparous: The ability to reproduce more than once in a lifetime. 

Jack salmon: A young male salmon that matures precociously (earlier than other fish in its ageclass). 

Juvenile: Fish from one year of age until sexual maturity. 
49 

Krill: Small abundant crustaceans that form an important part of the food chain in Antarctic 

waters. 

Kype: The distinctive hooked jaw that male salmon develop during spawning. 

Lateral line: A series of sensory pores opening to the exterior and along the side of fish. 

Length frequency: An arrangement of recorded lengths which indicates the number of times each 

length or length interval occurs. 

Live box: A container filled with water and often equipped with accessories such as aeration 

equipment that is used to hold and transport live fish. 

Milt: The sperm of fishes. 

Natal stream: Stream of birth. 

Naturally spawning populations: Populations of fish that have completed their entire life cycle in 

the natural environment without human intervention. 

Outmigration: The migration of fish down the river system to the ocean. 

Parr: The developmental life stage of salmon and trout between alevin and smolt, when the 

young have developed parr marks and are actively feeding in fresh water. 

Parr marks: Distinctive vertical bars on the sides of young salmonids 

Pre-smolt: A juvenile salmon or steelhead that has not yet reached the physiological state known 

as a smolt. 

Pre-spawning mortality: Generally refers to non-fishery mortality of adult salmon and steelhead 

between the time the fish enter the stream and the completion of spawning. 

Precocious: Fish that have matured more quickly, or faster than the remaining fish of the ageclass. 

Ray: One of the supports of a fin. 

Rearing: Refers to the amount of time that juvenile fish spend feeding in nursery areas of rivers, 

lakes, streams and estuaries before migration. 

Redd: A nest of fish eggs consisting of gravel, typically formed by digging motion performed by 

an adult female salmon. 

Relative abundance: An estimate of actual or absolute abundance; usually stated as an index; for 

example, as bottom trawl survey stratified mean catch per tow. 
50 

Reproduce: To produce offspring. 

Resident species: Species of fish which spend their entire lives in freshwater. 

Roe: The eggs of fishes. 

Salmonid: Fish of the family Salmonidae that includes salmon and steelhead. 

Seine: A length of netting with weights at the bottom and floats at the top that is pulled from the 

ends through the water to sample fishes. 

Semelparous: Species that reproduce only once during their lifetime. 

Smolt: Refers to the salmonid or trout developmental life stage between parr and adult, when the 

juvenile is at least one year old and has adapted to the marine environment. 

Smoltification: Refers to the physiological changes anadromous salmonids and trouts undergo in 

freshwater while migrating toward saltwater that allow them to live in the ocean. 

Spawn: The act of reproduction of fishes. The mixing of the sperm of a male fish and the eggs of 

a female fish. 

Stock: A specific population of fish spawning in a particular stream during a particular season. 

Straying: A natural phenomena of adult spawners not returning to their natal stream, but entering 

and spawning in some other stream. 

Thalweg: The line defining the lowest points along the length of a river bed or valley. 

Upwelling: The movement of nutrient rich waters from the bottom of the ocean to the surface. 

Year class: Fish in a stock born in the same year. Synonymous with cohort. 

Yearling: A one-year old fish. 
51 

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Ketcham, B. J., G. G. Brown, and O. G. Wolff, 2004c. Long-term coho salmon and steelhead 

trout monitoring program in coastal Marin County – summer 2003 monitoring progress 

report. Report to California Department of Fish and Game, contract #P0130434, Point Reyes 

National Seashore, California. 

MacFarlane, R. B., B. Wells, and S. A. Hayes. 2008. Coho and Chinook salmon decline in 

California during the spawning seasons of 2007/08. NOAA National Marine Fisheries 

Service, Southwest Fisheries Science Center, Fisheries Ecology Division, Santa Cruz, 

California.
54 

Miller, G. 2010. In central California, coho salmon are on the brink. Science 237: 512-513. 

Moyle, P. B., M. P. Marchetti, J. Balrige, and T. L. Taylor. 1998. Fish health and diversity: 

Justifying flows for a California stream. Fisheries 23(7):6–16. 

Oregon Department of Fish and Wildlife (ODFW). 2007. Oregon coast coho conservation plan 

for the state of Oregon. Oregon Department of Fish and Wildlife, Salem, Oregon. 

Palmer, C. J. 2003. Approaches to quality assurance and information management for regional 

ecological monitoring programs. Pages 211–225 in D. E. Busch, and J. C. Trexler, editors. 

Monitoring ecosystems: Interdisciplinary approaches for evaluating ecoregional initiatives. 

Island Press, Washington, D.C. 

Pacific Fishery Management Council (PFMC). 2000. Pacific coast salmon management plan, 

appendix 14. Pacific Fishery Management Council, Portland, Oregon. Online. 

(www.pcouncil.org/salmon/salfmp/a14/99efh2.pdf). Accessed August 2004. 

Pearcy, W. G. 1997. Salmon production in changing ocean domains. Pages 331–352 in D. J. 

Stouder, P. A. Bisson, and R. J. Naiman, editors. Pacific salmon and their ecosystems. 

Chapman & Hall, New York. 

Piepho, H.-P. and J. O. Ogutu. 2002. A simple mixed model for trend analysis in wildlife 

populations. Journal of Agricultural, Biological, and Environmental Statistics 7(3):350–360. 

Pollard, W. R., C. Groot, and G. F. Hartman. 1997. Field identification of coastal juvenile 

salmonids. Harbour Publishing Company, Madeira Park, British Columbia. 

Press, D. T. 2005. Data management plan for the San Francisco Bay Area Network Inventory 

and Monitoring Program. USDI National Park Service, San Francisco, CA. 

Reichmuth, M., B. J. Ketcham, D. Fong. 2005. Adult escapement monitoring program summary 

2004–2005. PORE/NR/WR/06-01. Point Reyes National Seashore, Point Reyes, CA.–

Reichmuth, M., C. Del Real, and B. J. Ketcham. 2006a. Smolt trapping program summary – 

Olema Creek, Pine Gulch, and Redwood Creek, Marin County, CA. 2006. Report to Pacific 

States Marine Fisheries Commission – California Adaptive Watershed Improvement Grant # 

ADWI-CE-15. PORE/NR/WR/07-01. Point Reyes National Seashore, Point Reyes, CA. 

Reichmuth, M., B. J. Ketcham, K. Leising, and B. Craig. 2006b. Olema Creek watershed 

summary monitoring report, Marin County, CA. 1997–2005. PORE/NR/WR/06-02. Point 

Reyes National Seashore, Point Reyes, CA. 

Rodgers, J. D., M. F. Solazzi, S. L. Johnso, and M. A. Buckman. 1992. Comparison of three 

techniques to estimate juvenile Coho salmon populations in small streams. North American 

Journal of Fisheries Management 12:79–86. 
55 

Schwarz, G. 1978. Estimating the dimension of a model. The Annals of Statistics 6: 461–464. 

Starcevich, L. A. 2008. Power analysis of escapement trends for the Coho salmon protocol. San 

Francisco Bay Area Inventory and Monitoring Program Unpublished Report, Sausalito, CA. 

Starcevich, L. A., and K. Irvine. 2008. Estimates of status and trend for the SFAN juvenile Coho 

salmon. San Francisco Bay Area Inventory and Monitoring Program Unpublished Report, 

Sausalito, CA. 

VanLeeuwen, D. M., L. W. Murray, and N. S. Urquhart. 1996. A mixed model with both fixed 

and random trend components across time. Journal of Agricultural, Biological, and 

Environmental Statistics 1(4):435–453. 

Williams, L. R., M. L. Warren, Jr., S. B. Adams, J. L. Arvai, and C. M. Taylor. 2004. Basin 

visual estimation technique (BVET) and representative reach approaches to wadeable stream 

surveys: methodological limitations and future directions. American Fisheries Society: 

Fisheries 29(8):12–22. 

57 

Appendix A. Fish and Stream Aquatic Assemblages 

While juvenile coho and steelhead are likely to be the most frequently captured aquatic species, 

there are several others that may be encountered. Because salmonid surveys will likely be the 

primary long-term stream fish monitoring program supported by the parks, collected data will be 

important for not only documenting the status and trends of juvenile salmonids, but other species 

as well. Equal care in field sampling and consistency in identification is required. 

Common name Scientific name Life stage Code 

Coho salmon Oncorhynchus kisutch young of year CO 

Steelhead/Rainbow trout Oncorhynchus mykiss young of year SH 

Unknown salmonid Salmonid 

Sculpin spp. Cottus spp. SCU 

Prickly sculpin Cottus asper PS 

Coastrange sculpin Cottus aleuticus CRS 

Riffle sculpin** Cottus gulosus RS 

Pacific staghorn sculpin Leptocottus armatus PSS 

Threespine stickleback Gasterosteus aculeatus STK 

California roach Hesperoleucus symmetricus RO 

Sacramento sucker Catostomus occidentalis SUC 

*Golden Shiner Notemigonus crysoleucas 

Lamprey spp. Lampetra spp. ammocete LAM 

Pacific lamprey Lampetra tridentata smolt/adult PL 

Pacific brook lamprey Lampetra pacifica adult PBL 

River lamprey Lampetra ayresi adult RL 

*Green sunfish Lepomis cyanellus GSF 

Other Aquatic Vertebrates 

California giant salamander Dicamptodon ensatus larva CGS 

California newt Taricha torosa adult CAN 

Rough-skinned newt Taricha granulosa adult RSN 

California red-legged frog Rana aurora draytonii adult RLF 

*Bullfrog Rana catesbeiana adult BF 

Foothill yellow-legged frog Rana boylii YLF 

Pacific treefrog Hyla regilla adult PTF 

Western pond turtle Clemmys marmorata WPT 

*Red-eared slider Pseudemys scripta elegans RES 

Invertebrates 

California freshwater shrimp Syncaris pacifica CFS 

*Signal crayfish Pacifastacus leniusculus Cray 

*Swamp crayfish Procambarus clarkii SWC 

*non-native 

59 

Appendix B. CDFG Habitat Unit Types. 

From Flosi et al. 1998. 

Level III Level IV 

Type Code Type Code 

Riffle R 

Low Gradient Riffle LGR 

High Gradient Riffle HGR 

Cascade C 

Cascade CAS 

Bedrock Sheet BRS 

Flatwater FW 

Pocket Water POW 

Glide GLD 

Run RUN 

Step Run SRN 

Edgewater EDW 

Main Channel Pool MC 

Trench Pool TRP 

Mid-Channel Pool MCP 

Channel Confluence Pool CCP 

Step Pool STP 

Scour Pool SC 

Corner Pool CRP 

Lateral Scour Pool - Log Enhanced LSL 

L. Scour Pool - Root Wad Enhanced LSR 

L. Scour Pool - Bedrock Formed LSBk 

L. Scour Pool - Boulder Formed LSBo 

Plunge Pool PLP 

Backwater Pools BW 

Secondary Channel Pool SCP 

Backwater Pool - Boulder Formed BPB 

Backwater Pool - Root Wad Formed BPR 

Backwater Pool - Log Formed BPL 

Dammed Pool DPL 

Dry DR Dry DRY 

Culvert CU Culvert CUL 

Not Surveyed NS Not Surveyed NS 

Not Surveyed due to a marsh MAR 

61 

Appendix C. Basinwide Habitat Survey Datasheet 
62 

Instructions for Basinwide Habitat Survey Datasheet 

Stream: Stream name. 

Watershed: Watershed name. 

Date: mm/dd/yy. 

Location: Name of reach covered by that page or description of location on stream. 

Crew: Names of all personnel. (First, Last) 

BW Unit #: Numbered sequentially moving upstream, starting with 1 at beginning 

(downstream end) of survey area. 

Section Number: Record the nearest downstream monument tag to be used as a reference 

point and approximate distance from tag. Not applicable for side channel 

and basinwide habitats. 

Unit Type: Using CDFG level III classification system. Note primary and secondary 

types if unit consists of more than one type. 

Side Channel: Check box if the habitat unit lies within a side channel. 

Len. (m): Length of habitat unit, measured along thalweg, to the nearest 0.1 m

Est. Width (m): Visually estimated average width of habitat unit. 

Measured Widths: Up to five widths measured to the nearest 0.1 m for predetermined 

calibration units. 

Tran Length (m): Record distance between transects to the nearest meter. 

Max Depth (m): Record the maximum depth of all pools and flatwater unit types to the 

nearest 0.1 m. 

Crest Depth (m): Record crest depth to nearest 0.01 m for all pool and flatwater units. 

Comments : Record monument tag #’s and locations, split channels, and other notable 

landmarks in comments section. If split channel indicate left bank (LB) or 

right bank (RB) unit. 
63 

Appendix D. Dive Datasheet 
64 

Instructions for Dive Datasheet 

Stream: Stream name. 

Watershed: Watershed name. 

Location: Name of reach covered by that page or description of 

 location on stream. 

Date: mm/dd/yy. 

Divers: Names of all personnel. (First, Last) 

Recorder: Name of person recording data. (First, Last) 

BW Unit # / Type: BW Unit # and type of preselected dive unit. Should match BW

Unit # and Unit Type from Basinwide Habitat Survey datasheet. 

Section #/Location: Nearest downstream monument tag for locational reference and 

approximate distance from tag. Should match Section # and 

Location from Basinwide Habitat Survey datasheet. 

Index Reach #/Index Unit #:If applicable the name or number of the index reach, and number 

of the unit within the index reach, starting at 1 from the 

downstream end. 

Diver Initials: Initial of diver or divers snorkeling each unit. 

Pass #: Fill out separate line for each snorkeling pass. 

Pass Time:Start/End: Start time and end time of snorkel pass in minutes. 

Species: CO (coho), SH (steelhead), or other species observed. 

Age: YOY (young of year) or 1+ if applicable. 

Number: Number of coho counted per pass or P (present) for all other 

species observed. 

Visibility: Estimate of underwater visibility distance (in meters). 

Comments: General notes including habitat unit complexity or obstructions, 

undercut banks, presence of non target species. 
65 

Appendix E. Index Reach Habitat Datasheets 
66 
67 

Instructions for Index Reach Habitat Datasheet 

Stream: Stream name. 

Date: mm/dd/yy. 

Index Reach #: Number of established sample site.

Location: Description of location on stream--site name if at index reach or other 

established location. 

Crew: Names (First, Last) of all personnel. 

Recorder: Name of person (First, Last) recording data. 

Bank Vegetative: Visually estimate cover of the overstory (%OS), understory (%US), and 

Cover ground cover (%FG) for the index reach and circle the percentage 

category. 

Dry Bed: Visually estimate the amount of dry bed along thalweg of index reach if 

flow in main channel is disconnected and circle the percentage category. 

Isolated Pools: Indicate if isolated pools exist in the index reach, either backwater/side 

units or along thalweg. 

Woody Debris: Tally each type or size class of woody debris in the index reach within the 

Tally bankfull channel. 

Bank Erosion: Visually estimate the extent of bank erosion in the index reach and circle 

the percentage category for each bank. 

water temp *C: Water temperature in Celsius from YSI 85, YSI 30, or thermometer. 

DO%: Dissolved oxygen % from YSI 85. 

mg/l: Dissolved oxygen mg/l from YSI 85. 

conductivity: Conductivity from YSI 85 or YSI 30. 

sp. cond.: Specific conductance from YSI 85 or YSI 30.

salinity: Salinity from YSI 85 or YSI 30. 

Instream Shelter: Visually estimate the amount and type of instream shelter for each habitat 

unit and record the percentage of habitat unit covered by each type. 

Comments: General notes or comments for the index reach. 

(Instructions for Page 2) 

Unit #: Numbered sequentially moving upstream, starting with 1 at downstream 

end. Should match Unit # from Index Reach Electrofishing Log. 
68 

Unit type: Using CDFG level III classification system. Note primary and secondary 

types if unit consists of more than one type. Should match Habitat Type

from Index Reach Electrofishing Log. 

Length: Length of habitat unit, measured along thalweg, to the nearest 0.1 m. 

Max depth: Depth measured to the nearest 0.01 m at the deepest point of pool or 

flatwater unit (not needed for riffle units). 

Crest depth: Depth measured to the nearest 0.01 m at the crest of flatwater or pool 

tailout (not needed for riffle units). 

For each transect, measure the wetted channel width to the nearest 0.1 m and record under Total 

width. 
69 

Appendix F. Electrofishing Data Datasheet 
70 

Instructions for Electrofishing Datasheet 

Stream: Stream name. 

Location: Description of location on stream--# and/or name of index reach or site 

 name if at other established location. 

Date: mm/dd/yy. 

Crew: Names (First, Last) of all personnel. 

Gear Type: Model/type of electrofisher or type of seine used. 

Unit #: Basinwide habitat unit number for GSS calibration pools. For Index 

 Reaches enter the Index Reach number followed by the unit number. 

 Index Reach unit numbers are numbered sequentially moving upstream, 

 starting with 1 at downstream end of index reach. 

Unit Description: Habitat type using CDFG level III classification system. Note primary and 

secondary types if unit consists of more than one type. Should match 

Habitat Type from Index Reach Electrofishing Log or Basinwide Habitat 

Datasheet.

Pass #: Electrofishing pass number in which fish was captured, or “seine” if seine 

capture. 

Species: Species (and age class of steelhead) using codes at bottom of sheet. For 

steelhead young of year use SH, for age 1+ steelhead use SH 1+. 

Fork Length (mm): Fork length measured to the nearest mm (=total length for sculpin and 

stickleback). 

Bag+fish wt. (g): Gross weight to the nearest 0.01 g of fish in weighing bag (rezero scale 

before weighing each fish). 

Bag post wt. (g): Residual weight of bag after fish is removed (can be positive or negative 

#). 

Fish condition: Indicate B for burn, I for other injury, or M for mortality or probable 

mortality. 

Comments: General notes or comments. 

 
71 

Appendix G. Basinwide Electrofishing Log 
72 

Instructions for Basinwide Electrofishing Log 

Stream: Stream name. 

Date: mm/dd/yy. 

Subproject: Project associated with the survey (Efish Index, Efish Basin, Fish Rescue, 

Restoration, Other). 

Gear Type: Model/type of electrofisher or type of seine used. 

Recorder: Name (First, Last) of person recording data 

Crew: Names (First, Last) of all personnel. 

. 

Section #: Record the nearest downstream monument tag to be used as a reference 

 point and approximate distance from tag. 

Unit Type: Using CDFG level III classification system. Note primary and secondary 

types if unit consists of more than one type

BW Unit #: Numbered sequentially moving upstream, starting with 1 at downstream 

end. 

Seine or E-fish: Enter either seine or E-fish (electrofishing) for the sampling type used. 

Time: Time readout (seconds) from electrofisher for each pass. 

Volts: Electrofisher volts setting for each pass (should be same for all passes on a 

unit). 

Setting: Electrofisher current/frequency setting for each pass; unpulsed DC is 

setting used most often (same setting should be used for all passes). 

H2O Temp: Enter the water temperature in oC. 

DO%: Enter the percent of dissolved oxygen. 

DO mg/l: Enter the dissolved oxygen in milligrams per litter. 

Cond: Enter the conductivity in micromhos per centimeter. 

Spec Cond: Enter the specific conductivity in micromhos per centimeter. 

Salinity: Enter the salinity in parts per thousand. 

For each species/age class, record the # captured in each pass: 

CO: Coho 

SH YOY: Steelhead young of year 

SH 1+: Steelhead age 1+ 

AM: Lamprey ammocetes (Field identification keys are not yet adequate to 

determine species) 

RO: California roach 

STK: Three spine stickleback 

SCU: Sculpin (Field identification keys are not yet adequate to determine 

species) 

Other: Other species captured or comments specific to each pass. 

Total Catch: Total catch per species for all passes. 

Mortality: Mortalities (if any) for each species/age class (include injured individuals if likely 

 mortality) 
73 

Pass type: Enter the pass type, either E-fish or seine pass. 

Comments: General comments for each unit, including any mortalities or injuries. 

75 

Appendix H. Index Reach Electrofishing Log 
76 

Instructions for Index Reach Electrofishing Log 

Stream: Stream name. 

Index Reach #: Number of established sample site 

Date: mm/dd/yy. 

Subproject: Project associated with the survey (Efish Index, Efish Basin, Fish Rescue, 

Restoration, Other). 

Gear Type: Model/type of electrofisher or type of seine used. 

Recorder: Name (First, Last) of person recording data 

Crew: Names (First, Last) of all personnel. 

Section #: Record the nearest downstream monument tag to be used as a reference 

point and approximate distance from tag. 

Index Reach Unit #: Numbered sequentially moving upstream, starting with 1 at downstream 

 end of index reach.

Unit Type: Using CDFG level III classification system. Note primary and secondary 

types if unit consists of more than one type

BW Unit #: Numbered sequentially moving upstream, starting with 1 at downstream 

end. 

Time: Time readout (seconds) from electrofisher for each pass. 

Volts: Electrofisher volts setting for each pass (should be same for all passes on a 

unit). 

Setting: Electrofisher current/frequency setting for each pass; unpulsed DC is 

setting used most often (same setting should be used for all passes). 

For each species/age class, record the # captured in each pass: 

CO: Coho 

SH YOY: Steelhead young of year 

SH 1+: Steelhead age 1+ 

AM: Lamprey ammocetes (Field identification keys are not yet adequate to 

determine species) 

RO: California roach 

STK: Three spine stickleback 

SCU: Sculpin (Field identification keys are not yet adequate to determine 

species) 

Other: Other species captured or comments specific to each pass. 

Total Catch: Total catch per species for all passes. 

Mortality: Mortalities (if any) for each species/age class (include injured individuals 

if likely mortality)

Comments: General comments for each unit, including any mortalities or injuries. 
77

Appendix I. Pipe Trap Datasheet Sheet # ____of____ Date _____/_____/_____ 

NATIONAL PARK SERVICE COHO SALMON AND STEELHEAD TROUT MONITORING PROGRAM

STREAM:_____________________ CREW:__________________ H2O TEMP:_______________ ARRIVAL TIME:________________ DEPARTURE TIME:_________ WEATHER:________________ 

STAGE HEIGHT:________________ CIRCLE THIS WEEKS MARK TYPE: PANJET: ANAL (A) LOWER CAUDAL (LC) 

 PINK (P) BLUE (B) ORANGE (O) 

COMMENTS:

______________________________________________________

CLIP OR NOTCH TYPE:

________________________________________________________________

FIN CLIP (C) FIN NOTCH (N) 

________________________________________________________________ ANAL (A) UPPER CAUDAL (UC) 

________________________________________________________________ 

LOWER CAUDAL (LC) 

TRAP IS: WORKING PARTIALLY WORKING NOT WORKING

Fish 

# 

Species 

CO, 

SH, 

etc. 

Fry / Parr 

Presmolt / Smolt 

Adult 

Fork 

Length 

(mm) 

Fish 

Weight (g)

Bag 

Weight (g)

New Mark/Recap (NUCAN, NLCAN, NA, RUC, RLC, RA, etc.) 

Mark Color 

Dead 

Injured 

cS

Tissue Envelope ID Comments 

1 2 3 4 5 6 7 8 9 

10 11 12 13 14 15 16 
78

17 18 19 20 

Recap Code 

UN Notch 

LC Notch/A Clip 

Anal Notch 

LC Notch 

UC Clip 

LC Clip 

Anal Clip 

Blue Clip 

Pink Lower Caudal 

Orange Lower Caudal 

Pink Anal 

Total Daily Trap Summary (Recap Summary on back) Species Total Live TOTALDEAD # NEW # MARKED # RECAP COMMENTSCOHO SMOLTSCOHO PRESMOLTSSTEELHEAD SMOLTSSH PRESMOLTSSH PARRCOHO FRYSH FRYSCULPIN (SCU) ROACH (RO) STICKLEBACK (STK) OTHERRECAP TALLY: 

SPECIES CODE COMMON NAME 

AMMA spotted salamander BF Bullfrog BUAM eastern american toad CAN California newt CFS California freshwater shrimp CGS California giant salamander CH Chinook CO Coho salmon 
79

CRAY Signal crayfish SWC Swamp crayfish CRS Coastrange sculpin GSF Green sunfish GSH Golden shiner LAM Lamprey spp. PBL Pacific brook lamprey PL Pacific lamprey PS Prickly sculpin PSS Pacific staghorn sculpin PTF Pacific treefrog RES *Red-eared slider RL River lamprey RLF California red-legged frog RO California roach RS Riffle sculpin RSN Rough-skinned newt SAL Unknown salamander/newt Salmonid Unknown salmonid SCU Sculpin spp. SH Steelhead/Rainbow trout STK Threespine stickleback SUC Sacramento sucker UNK Species Unknown WPT Western pond turtle YLF Foothill yellow-legged frog 

81 

Appendix J. Spawner Survey Datasheet 
82 

Instructions for Spawner Survey Datasheet 

The Spawner Survey Datasheet contains the following fields for recording information at the 

beginning and end of each survey reach. All information must be written in pencil on waterproof 

copies of the datasheet provided by the park staff. Please write legibly. 

Stream: Record the full name of the stream you are surveying. 

Reach: Record the reach number. 

Date: Enter the survey date in Month / Day / Year format. 

Weather: Record the weather conditions at the time of the survey. 

Start Time: Enter the time at the beginning of the survey. 

End Time: Enter the time at the end of the survey. 

Observers: Enter the first initial and last name of all crew members. 

Recorder: Enter the name (first, last) of the person who is writing the data. 

Tel: Enter the telephone number of the recorder (datasheets can become 

illegible). 

Water Temp: Record the water temperature in either Celsius (C) or Fahrenheit (F) using 

thermometers provided by the park staff. 

Water Clarity: Measure water clarity in a pool by noting the depth at which the bottom of 

the marked survey rod is no longer visible (to the nearest 10 cm). 

Stage: Some stream reaches have staff gauges (graduated plates) to measure 

water level. If you encounter a gage on your survey, record the water level 

to the nearest one hundredth of a foot and the time of your observation. 

Location: Record the nearest downstream monument tag and the estimated distance 

between the monument tag and the location of the fish sighting.

Species: Check the box for the fish species (coho, steelhead, or unknown).

Live Fish: For live fish, give the sex (male, female, unknown) and estimated length 

in cm.

Carcasses: For any carcasses, give the sex (male, female, unknown) and the length in 

cm. If it is a new carcass, write down the mark code used on the fish. If it 

is a recaptured carcass, record the code taken from the fish. If scales and 

tissue are taken, mark the appropriate boxes.
83 

Comments: Record any comments relative to the fish sighting- fish condition, fish 

spawning, etc. 

85 

Appendix K. Redd Survey Datasheet 

Instructions for the Redd Survey Datasheet 

The Redd Survey Datasheet contains the following fields for recording information at the 

beginning and end of each survey reach. All information must be written in pencil on waterproof 

copies of the datasheet provided by the Park staff. Please write legibly. 

Stream: Record the full name of the stream you are surveying. 

Reach: Record the reach number. 

Date: Enter the survey date in Month / Day / Year format. 

Weather: Record the weather conditions at the time of the survey. 

Start Time: Enter the time at the beginning of the survey. 

End Time: Enter the time at the end of the survey. 

Observers: Enter the first initial and last name of all crew members. 

Recorder: Enter the name (first,last) of the person who is writing the data. 

Tel: Enter the telephone number of the recorder (datasheets can become 

illegible). 
86 

Water Temp: Record the water temperature in either Celsius (C) or Fahrenheit (F) using 

thermometers provided by the park staff. 

Water Clarity: Measure water clarity in a pool by noting the depth at which the bottom of 

the marked survey rod is no longer visible (to the nearest 10 cm). 

Stage: Some stream reaches have staff gages (graduated plates) to measure water 

level. If you encounter a gage on your survey, record the water level to the 

nearest one hundredth of a foot and the time of your observation. 

Specific Location: Tag # Downstream Nearest downstream monument tag 

Tag Dist (m) Estimated distance between monument tag and red 

location 

Bank Redd location along bank (Left bank, Right bank, or 

Main Channel) 

New Redd: Check box if the redd is a new redd with no previous history recorded on 

it

New Data: Check box if the redd is a previously recorded redd but the data taken on it 

is new

Redd Description: Species Record the species that created the redd 

Def Record the confidence level of that ID 

Len (m) Record the length of the redd in meters 

Wid (M) Record the width of the redd in meters 

 Fish on Redd: 

 Species Record the species of any fish located on redd 

 # Record the number of any fish located on redd 

Comments: Record any information related to the redd such as fish located near redd, 

carcasses located near the redd, fish spawning near the redd, etc. 
 

87 

Appendix L. Monument Tag Locations 

Table L-1. Location information for monument tags on Olema Creek mainstem. 

Table L-1. Location information for monument tags on Olema Creek mainstem (continued). 

tag # 

25–150 

Bank 

side Location information Y Coordinate X Coordinate 

25 LB Dead Tree 

26 LB Dead Alder 

27 RB Willow 

28 LB Willow 

29 LB Willow 

30 LB Alder 

31 LB Willow upstream of Bear Valley Bridge 4210474.582 518449.107 

32 LB Alder 4210415.108 518469.482 

33 RB Willow 4210313.477 518535.143 

34 LB Alder 4210248.064 518561.182 

35 RB Alder 4210216.606 518599.383 

36 RB Alder 4210209.158 518726.027 

37 RB 

Alder, more then 100 from tag 36, above bird 

coop 4210045.126 518831.850 

38 RB Alder 4209982.166 518888.955 

39 LB Alder 4209928.116 518937.568 

40 LB Alder 4209810.380 518986.799 

41 RB Alder, just upstream of Quarry Gulch 4209744.939 519000.133 

42 RB Alder 4209650.182 518948.569 

43 LB Alder, next to cemetery pasture 4209553.186 518957.739 

44 LB Alder 4209481.642 518906.120 

45 RB Alder 4209422.530 518825.283 

46 RB Alder 4209360.595 518810.361 

47 RB Bay 4209323.010 518772.314 

48 RB Alder, 10 m downstream of car wall 4209239.143 518796.988 

49 RB Alder, new tag placed in old tag spot 4209161.829 518824.002 

50 LB Alder high on bank 4209100.117 518905.592 

51 LB Alder, in clump of alders 4209034.247 518990.488 

52 RB Alder 4208920.626 519017.118 

53 LB Alder across from barb wire fence 4208851.608 519028.107 

54 RB Alder bellow large down fir in creek 4208807.133 519098.833 

55 RB Fir tree upon bank from rock face 4208691.644 519090.158 

56 LB Alder 4208680.487 519155.157 

57 LB 

Alder across from eroded bank, new tag inline w/ 

old 4208635.921 519186.336 
 

88 

Table L-1. Location information for monument tags on Olema Creek mainstem (continued). 

tag # 

25–150 

Bank 

side Location information Y Coordinate X Coordinate 

58 LB Alder 4208535.905 519177.155 

59 LB Alder 4208431.792 519197.174 

60 RB Alder 4208418.337 519296.552 

61 LB Alder across from rock wall 4208394.763 519395.013 

62 RB Alder at bottom of index #4 4208373.959 519406.833 

63 RB Alder at top of index #4 4208334.168 519443.654 

64 LB Alder 4208245.016 519497.542 

65 LB Alder 4208213.599 519551.294 

66 LB Alder across from sand stone wall 4208264.462 519664.175 

67 RB Alder 4208061.048 519723.993 

68 RB Alder just up of canyon 4208001.357 519653.037 

69 RB Alder 4207980.082 519716.184 

70 RB Alder, across from Large Woody Debris jam 4207963.606 519794.387 

71 RB Alder just above landslide 4207857.098 519807.830 

72 RB Alder, tag on root of tree 4207801.899 519871.531 

73 RB Alder just upstream of RB trib 4207752.694 519952.171 

74 LB Alder tree across from eroded wall 4207679.610 520003.675 

75 LB 

Alder across from eroded bank w/ fence at top, 

tag 20m from crk 4207664.878 520063.984 

76 RB Alder at bottom of index #5, Shook's house 4207573.824 520068.445 

77 RB Alder adjacent to Shook's hosue 4207484.707 520134.589 

78 LB Alder 4207460.994 520173.261 

79 LB Maple 4207325.892 520176.420 

80 RB Alder, new tag 4207309.372 520235.323 

81 LB Alder 4207334.608 520331.324 

82 LB Alder 4207238.825 520348.986 

83 LB Alder 4207159.761 520387.798 

84 RB Alder 4207088.410 520417.172 

85 LB Alder across from start of pasture on RB 4207000.446 520467.310 

86 RB Alder 4206924.344 520500.465 

87 RB Alder 4206825.017 520528.970 

88 LB Alder, just above horse crossing bath 4206752.617 520613.920 

89 LB 

Alder across from horse ranch, new tag at old tag 

loc 4206692.017 520657.870 

90 LB Alder, new tag at old tag location 4206616.512 520691.498 

91 LB 

Alder, across from trail to Stewart ranch barn, 

new tag 4206563.081 520745.321 

92 LB Bay 40 m above horse crossing, new tag 4206461.334 520757.824 
 

89 

Table L-1. Location information for monument tags on Olema Creek mainstem (continued). 

tag # 

25–150 

Bank 

side Location information Y Coordinate X Coordinate 

93 RB Alder 10m above start of index #6, new tag 4206401.330 520801.775 

94 RB alder 5m upstream of utility pole, new tag 4206308.602 520850.049 

95 RB Bay new tag old location 4206227.195 520903.004 

96 LB Buckeye, new tag 4206145.173 520947.956 

97 RB Alder 4206074.496 521007.009 

98 RB Alder, 15m bellow horse camp bridge 4206005.630 521075.949 

99 RB Alder 4205962.938 521138.699 

100 RB Alder 4205870.156 521165.314 

101 LB Bay, boulder in front of tree 4205854.933 521262.376 

102 RB Bay 4205821.858 521360.428 

103 LB Alder 4205769.025 521413.788 

104 LB Dead Alder, 20m bellow Hwy 1 bridge 4205719.208 521482.212 

105 RB Alder adjacent to white house 4205703.988 521579.277 

106 RB Alder 4205632.377 521508.346 

107 LB Alder, 5m upstream of 2nd

 HWY 1 bridge 4205525.272 521519.932 

108 RB Alder, 10 m bellow Giacomini crk 4205438.151 521435.379 

109 RB Alder 10m bellow John West Fork 4205373.239 521421.890 

110 RB Alder 4205347.398 521327.284 

111 RB Willow 4205356.739 521257.550 

112 RB Dead Tree 4205364.346 521207.131 

113 RB Alder, right at horse crossing also LB trib 4205315.914 521122.003 

114 RB Bay, hangs over crk 4205239.709 521114.193 

115 RB Alder 4205169.580 521154.411 

116 LB Bay across creek 4205130.335 521169.115 

117 RB Alder across bank, tag at base of down tree 4205091.208 521229.508 

118 LB Buckeye, - fallen 4205053.354 521320.986 

119 RB Alder 4204980.758 521328.241 

120 LB Alder 4204905.298 521377.897 

121 RB Alder 4204870.346 521440.637 

122 LB Alder 4204836.437 521447.321 

123 RB Bay up on bank 4204822.952 521525.078 

124 LB Alder 4204837.694 521472.754 

125 RB Alder up high on bank 4204826.166 521615.510 

126 RB Bay 4204814.512 521709.750 

127 RB Bay 4204798.698 521805.886 

128 LB On down log 4204788.844 521904.832 

129 LB Alder 4204722.337 521962.478 
 

90 

Table L-1. Location information for monument tags on Olema Creek mainstem (continued). 

tag # 

25–150 

Bank 

side Location information Y Coordinate X Coordinate 

130 LB Alder in index 8 4204656.427 522021.066 

131 RB Bay 4204620.306 522089.938 

132 RB Buckeye, at lime kiln put in 4204560.403 522168.296 

133 RB Alder, new tag at old tag location 4204503.433 522230.630 

134 LB Alder 4204441.092 522287.328 

135 LB Bay trunk 4204413.980 522384.913 

136 LB Alder 4204367.097 522435.446 

137 LB Alder new tag 4204295.267 522503.949 

138 RB Buckeye 4204207.259 522533.399 

139 LB Alder 4204124.028 522568.488 

140 LB Bay 4204064.158 522657.218 

141 RB Bay 

142 RB Alder 

143 LB Alder 

144 LB Alder, new tag at old tag location 

145 LB Alder, new tag at old tag location 

146 LB Alder 

147 RB Alder at Randalls slide 

148 RB Alder 

149 RB Maple Tree 
 

91 

Table L-2. Location information for monument tags on Pine Gulch mainstem. 

Table L-2. Location information for monument tags on Pine Gulch mainstem (continued). 

tag # 

01- 95 

Bank 

side Location information Y coordinate X coordinate 

1 old LB Alder, 50 m upstream of bridge 

1 new RB Alder, 15m up from old tag 4197115.375 527237.999 

2 RB Alder 4197015.516 527211.856 

3 RB Alder, 10 m upstream of T post fence across crk 4196962.946 527123.077 

4 RB 

right before alders lean across crk, hard see walking 

upstream, behind a bush 4196942.591 527043.614 

5 RB Alder, just downstream of concrete bridge 4196867.253 526999.423 

6 LB Eucalyptus 4196789.117 526935.099 

7 RB Eucalyptus, damll and low down on trunk, hard to see 

8 RB Alder 4196717.369 526810.508 

9 RB Alder just downstream of little bridge 

10 RB Eucalyptus across from green building 4196686.399 526633.263 

11 LB Bay 4196754.944 526572.365 

12 LB Alder 4196752.623 526468.331 

13 LB Alder, 40 m upstream of low metal bridge 4196773.945 526394.507 

14 RB Alder fallen across crk 4196859.605 526352.630 

15 RB Alder across from big pulled up root mass 4196963.556 526310.763 

16 RB Alder 4196997.698 526283.607 

17 RB Alder 

18 LB Alder 4197110.257 526218.444 

19 RB 

Alder, fallen tree across crk, right at our smolt stie from 

2000 4197195.185 526162.902 

20 LB Alder, smaller 4197267.218 526098.361 

21 LB Alder 4197356.608 526096.038 

22 LB 

Alder hard to see low down up bank 5m, dwns of wood 

foot bridge to sunny house 4197469.632 526090.324 

23 LB Alder 4197540.372 526067.474 

24 LB Branch of fallen Bay 4197583.926 525974.199 

25 LB Alder 4197663.053 525936.551 

26 RB Alder 4197730.626 525882.681 

27 LB Alder 4197798.354 525808.281 

28 LB Alder 4m up bank 4197879.277 525820.676 

29 RB Bay 4197944.499 525735.417 

30 LB Alder near big gravel LB 4197994.087 525686.895 

31 RB Alder, near house with dogs 4198029.327 525749.323 

32 RB Alder 4198129.210 525725.185 

33 4198195.000 525661.500 

34 4198258.507 525615.830 

35 4198184.180 525528.124 

36 
 

92 

Table L-2. Location information for monument tags on Pine Gulch mainstem (continued). 

tag # 

01- 95 

Bank 

side Location information Y coordinate X coordinate 

37 4198293.698 525421.716 

38 4198377.482 525356.726 

39 4198411.531 525272.847 

40 4198456.282 525202.427 

41 4198532.737 525163.039 

42 4198567.442 525073.438 

43 4198658.314 525034.343 

44 4198742.092 524987.572 

45 

46 4198865.825 525105.046 

47 4198938.265 525173.394 

48 4199000.109 525137.804 

49 RB Alder 

50 LB Alder pasture is up on LB 4199177.588 525202.130 

51 LB Alder, near where road goes up hill 4199281.644 525214.345 

52 RB Alder, broad gravel RB 4199302.187 525131.137 

53 RB Alder? 4199388.123 525118.847 

54 LB Alder 4199492.083 525084.739 

55 RB Alder just upstream of log jam 4199579.412 525027.808 

56 LB Bya, down 4199621.388 524966.263 

57 RB Alder there are redwoods in area 

58 LB Alder 

59 LB Redwood 

60 RB Alder 

61 RB Alder

62 RB Alder pink flagging not blue 

63 RB Alder pink flagging not blue 

64 RB Bay pink 

65 LB Alder, just upstream of concrete slab, pink 

66 MC Fallen log in middle of stream, pink 4200402.647 525132.832 

67 RB pink 

68 MC Bay, pink 

69 LB Alder, downstream of wooden bridge, no flagging 4200605.823 525000.228 

70 LB Alder, Pink 

71 LB Alder, blue flag 

72 

73 LB Alder 

74 LB Alder blue 

75 LB Alder blue 

76? RB Alder, upstream of log jam, blue 4200934.926 524574.181 
 

93 

Table L-2. Location information for monument tags on Pine Gulch mainstem (continued). 

tag # 

01- 95 

Bank 

side Location information Y coordinate X coordinate 

77 RB Bay, fallen 4201027.904 524531.199 

78 MC Dead wood, blue 

79 LB Alder, blue flag 

80 RB Alder, blue flag 4201207.164 524349.347 

81 MC logs fallen across crk 4201288.893 524289.929 

82 RB Alder 

83 LB Redwood 4201422.592 524145.794 

84 RB Alder 

85 MC Alder, on MC gravel bar 4201445.939 524025.576 

86 RB Alder, young 

87 MC Maple, fallen tree across creek, (where old 88 was) 

88 RB Maple 4201599.602 523895.331 

89 LB Alder, site of old tag 94 4201665.673 523818.992 

90 RB Alder 4201752.343 523771.234 

91 RB Alder 4201786.191 523746.271 

92 LB Alder 4201833.672 523686.914 

93 LB Alder 4201913.831 523641.588 

94 RB Bay 4201936.650 523575.461 

95 LB Alder 4202031.945 523500.144 
 

94 

Table L-3. Location Information for Monument Tags on Redwood Creek Mainstem. 

Table L-3. Location Information for Monument Tags on Redwood Creek Mainstem (continued). 

tag # 

00- 74 

Bank 

side Location information Y coordinates X coordinates 

0 RB bridge near pelican in 4190845.620 537306.030 

1 RB Alder, just dwnstream of RB shingle house 4190921.140 537239.550 

2 LB Alder, 5m from stream, hard to see 4190975.950 537163.560 

3 RB Buckeye 4191046.980 537090.520 

4 LB Alder, downstream of cement bridge 4191093.680 537007.160 

5 LB Alder 4191156.420 536970.390 

6 LB Alder 4191233.200 536959.780 

7 LB Alder 4191316.810 536924.210 

8 RB Alder 4191377.330 536859.000 

9 RB Alder 4191434.650 536795.390 

10 LB Alder 4191528.480 536745.680 

11 LB Alder 4191594.150 536686.600 

12 LB Alder 4191683.430 536694.820 

13 RB Alder, broken tree 4191773.200 536679.160 

14 LB Alder 4191811.340 536622.170 

15 LB Alder 4191887.430 536653.710 

16 RB Alder 4191947.550 536632.330 

17 RB Alder 4192006.620 536680.550 

18 LB Alder 4192072.780 536751.220 

19 LB Alder 4192148.190 536749.560 

20 LB Alder, 5.4m off creek 4192228.610 536800.190 

21 RB Alder 4192272.130 536841.380 

22 LB Alder, 10 m upstream of foot bridge 4192289.120 536917.130 

23 RB Alder 4192347.180 536991.710 

24 RB Alder, upstream of big WDJ 4192379.690 537058.190 

25 LB Alder 4192471.950 537099.020 

26 RB Alder 4192523.810 537133.670 

27 RB Alder 4192604.830 537184.940 

28 RB Alder 4192661.040 537205.720 

29 RB Alder 4192688.690 537271.220 

30 RB Alder 4192777.510 537349.110 

31 LB Alder 4192834.210 537436.850 

32 RB Alder 4192905.770 537454.820 

33 LB Alder, tree is leaning back, tag a little hard to see 4192932.200 537537.040 

34 RB Alder 4192961.240 537590.080 

35 RB Alder 4193026.800 537669.560 

36 LB Alder 4193077.960 537698.820 

37 LB Alder 4193098.510 537770.520 

38 LB Dead tree 4193143.200 537834.860 
 

95 

Table L-3. Location Information for Monument Tags on Redwood Creek Mainstem (continued). 

tag # 

00- 74 

Bank 

side Location information Y coordinates X coordinates 

39 RB Alder, 50m downstream of Miwok ped. bridge 4193108.900 537899.240 

40 RB Alder 4193166.850 537976.830 

41 RB Alder 4193248.120 538016.930 

42 RB Alder 4193319.420 538042.290 

43 RB Alder 4193367.850 538100.700 

44 RB Alder 4193465.980 538094.400 

45 LB Alder 4193529.590 538045.540 

46 RB Alder, just downstream of concrete bridge 4193634.610 538034.710 

47 LB Alder, 100m upstream of concrete bridge 4193692.650 537973.360 

48 RB Alder 4193773.470 537931.630 

49 RB Maple 4193809.230 537861.870 

50 LB 

Alder, just downstream of board bridge, from 

parking lot 4193872.010 537784.430 

51 LB Alder 4193898.990 537686.180 

52 LB Alder, downstream of cascade 4193946.340 537612.890 

53 LB Alder 4194030.370 537540.090 

54 LB Alder 4194082.060 537451.710 

55 LB dead tree 4194118.000 537413.720 

56 RB Bay 4194185.640 537356.250 

57 RB Bay 4194285.850 537357.340 

58 LB fence post 4194392.970 537317.260 

59 RB Maple 4194476.720 537345.240 

60 LB Bay 4194568.640 537330.200 

61 LB bay, upstream of bridge, upstreamside of tree 4194633.670 537263.340 

62 LB Redwood 4194715.430 537225.400 

63 LB Redwood, 10 m up from bottom of index 6 4194790.410 537150.140 

64 4194863.830 537076.620 

65 4194905.790 536993.420 

66 4194927.220 536909.660 

67 4194954.450 536815.490 

68 4194986.950 536742.250 

69 4195038.870 536676.470 

70 RB Maple, downstream of log across creek 4195076.110 536592.120 

71 LB 

tree root, just downstream Alice Eastwood Trail 

sign 4195127.020 536523.670 

72 LB Redwood 4195160.220 536440.300 

73 LB Redwood, small 4195156.520 536343.490 

74 LB Redwood 4195167.030 536280.090 

 

97 

Appendix M. Landowner Access Agreement 

POINT REYES NATIONAL SEASHORE/PRNSA 

1 BEAR VALLEY ROAD 

POINT REYES STATION, CA 94956 

ACCESS/ENTRY AGREEMENT 

Coastal Marin Long-term Coho Salmon and Steelhead Monitoring Program 

PURPOSE

The following agreement details the requirements of the landowner regarding implementation of 

the Long-Term Coho Salmon and Steelhead Monitoring Program in Coastal Marin County. The 

long-term monitoring project has been conducted in these areas for the past nine years. The 

watershed property is contained within the following historic land grand areas: Tomales Y 

Baulines, Punta de los Reyes, Ranch las Baulines, Saucelito Rancho, Rancho de Nicasio. 

All monitoring locations in Olema and Cheda Creek are located within National Park Service 

lands. Within the Redwood Creek watershed, all monitoring locations are on either National Park 

Service or California State Park land. The NPS and State Parks have a working agreement with 

regard to access, monitoring and restoration. Within private lands on Pine Gulch Creek, the 

National Park Service has working arrangements with landowners access to the stream and 

existing monitoring equipment. 

The project monitoring is conducted through this monitoring program is conducted under Section 

10 Permit 1046 issued through the National Marine Fisheries Service. The National Park Service 

is also working to develop a memorandum of understanding with regard to monitoring effects on 

state listed species. 

Information collected through this monitoring program will be maintained and reported by the 

National Park Service. 

REQUIREMENTS

The National Park Service agrees to: 

Support and maintain the long-term fisheries monitoring program on NPS lands. 

Maintain existing relationships with private landowners for access on their property. This is an 

issue only in Pine Gulch Creek. In this area, the NPS is facilitating development of a water 

operations program hat includes construction of off-stream irrigation ponds. The farmers are 

working with the NPS on this project and have allowed access as necessary for hydrologic and 

fisheries monitoring. 

DURATION OF NOTICE

The term of this agreement shall extend for the duration of the project (up to five years), for 

maintenance, inspection, and monitoring purposes from the last date of execution shown below. 

This is provided that the California Department of Fish and Game shall give landowner 
 

98 

reasonable actual notice prior to each needed access. Reasonable and actual notice may be given 

by mail, in person, or by telephone. 

This agreement can be amended only by prior written agreement of both parties executing this 

permit. 

LIABILITIES

Reasonable precautions will be exercised by the National Park Service to avoid damage to 

persons and property. 

Date ____________________ _______________________________ 

Don L. Neubacher, Superintendent 

Point Reyes National Seashore 
The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and 

other information about those resources; and honors its special responsibilities to American Indians, Alaska Natives, and affiliated 

Island Communities. 

NPS 963/102568, May 2010 
National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center 

1201 Oakridge Drive, Suite 150 

Fort Collins, CO 80525 

www.nature.nps.gov 

EXPERIENCE YOUR AMERICA TM