National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center 

Salmonid Monitoring Protocol for the San Francisco 

Area Network 

Standard Operating Procedures - Version 4.0 

Natural Resource Report NPS/SFAN/NRR—2010/203
 

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

Standard Operating Procedures - Version 4.0 

Natural Resource Report NPS/SFAN/NRR—2010/203 

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, California 94956 

2

Golden Gate National Recreation Area 

Fort Mason, Building 201 

San Francisco, California 94123-0022 

3

Point Reyes National Seashore Association 

Point Reyes Station, California 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 

address natural resource topics of interest and applicability to a broad audience in the National 

Park Service and others in natural resource management, including scientists, conservation and 

environmental constituencies, and the public. 

The Natural Resource Report Series is used to disseminate high-priority, current natural resource 

management information with managerial application. The series targets a general, diverse 

audience, and may contain NPS policy considerations or address sensitive issues of management 

applicability. 

All manuscripts in the series receive the appropriate level of peer review to ensure that the 

information is scientifically credible, technically accurate, appropriately written for the intended 

audience, and designed and published in a professional manner. This report received formal, 

high-level peer review based on the importance of its content, or its potentially controversial or 

precedent-setting nature. Peer review was conducted by highly qualified individuals with subject 

area technical expertise and was overseen by a peer review manager. 

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

the author(s) and do not necessarily reflect views and policies of the National Park Service, U.S. 

Department of the Interior. Mention of trade names or commercial products does not constitute 

endorsement or recommendation for use by the National Park Service. 

This report is available from the San Francisco 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 Area Network: standard operating procedures - 

version Natural Resource Report NPS/SFAN/NRR—2010/203. National Park Service, Fort 

Collins, Colorado. 

NPS 963/102571, May 2010 
 iii 

Contents 

Page 

SOP 1. Basinwide GSS Juvenile Coho and Habitat Survey ................................................ SOP 1.1

Tables ........................................................................................................................... SOP 1.2

SOP 2. Index Reach Surveys ............................................................................................... SOP 2.1

Figures and Tables ....................................................................................................... SOP 2.2

SOP 3. Specialized Field Methods....................................................................................... SOP 3.1

Tables ........................................................................................................................... SOP 3.2

SOP 4. Spring Smolt Trapping ............................................................................................ SOP 4.1

Tables ........................................................................................................................... SOP 4.2

SOP 5. Spawner Survey ....................................................................................................... SOP 5.1

Figures and Tables ....................................................................................................... SOP 5.2

SOP 6. Permit Requirements ............................................................................................... SOP 6.1

Figures and Tables ....................................................................................................... SOP 6.2

SOP 7. Protocol Revision .................................................................................................... SOP 7.1

Tables ........................................................................................................................... SOP 7.2

Appendixes .................................................................................................................. SOP 7.2

SOP 8. Data Management .................................................................................................... SOP 8.1

Figures .......................................................................................................................... SOP 8.2

SOP 9. Sampling Site Descriptions ..................................................................................... SOP 9.1

Figures .......................................................................................................................... SOP 9.2

Tables ........................................................................................................................... SOP 9.3

SOP 10. Data Summaries and Analysis ............................................................................. SOP 10.1

Figures ........................................................................................................................ SOP 10.2

Tables ......................................................................................................................... SOP 10.4
 iv 

SOP 11. Personnel Training and Safety ............................................................................. SOP 11.1

Tables ......................................................................................................................... SOP 11.2

Appendixes ................................................................................................................ SOP 11.2
v 

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 

FGDC Federal Geographic Data Committee 

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 

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 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
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.1 

SOP 1. Basinwide GSS Juvenile Coho and Habitat Survey 

Version 3.6 

Revision History Log 

Prev. 

Version 

# 

Revision 

Date 

Author Changes Made Reason for 

Change 

New 

Version 

# 

 Jan. 2007 Marcus 

Koenen 

Added revision log, 

removed sampling site 

description, focused on 

field methods. 

Clarification and 

remove 

redundancy 

3.1 

 3.2 Feb. 2007 Michael 

Reichmuth 

Revised changes and 

updated to reflect 

current monitoring 

Clarification and 

updating 

techniques used 

3.2MR 

3.2MR May 2008 Erin Brown Changed SOP 1 to 

basinwide 

 3.3 

3.3 May 2008 Sarah 

Carlisle 

Continued changes 

suggested by MR 

 3.4 

3.4 June 2008 Sarah 

Carlisle 

Linked data collection 

with objectives 

 3.41 

4.41 July 2008 Michael 

Reichmuth 

Reviewed and revised 

protocol 

Clarification and 

revising field 

techniques 

3.5 

3.5 August 

2008 

Marcus 

Koenen, 

Brannon 

Ketcham 

Editorial Review/minor 

revisions 

Clarification and 

consistency with 

Protocol 

Narrative 

3.51 

3.51 November 

2008 

Michael 

Reichmuth 

Address Darren Fong 

comments 

Clarification and 

minor edits 

3.52 

3.52 November 

2008 

Dawn 

Adams 

Formatting For peer review 3.53 

3.53 December 

2008 

Michael 

Reichmuth 

Minor Edits For peer review 3.54 

3.54 November 

2009 

Michael 

Reichmuth 

Added Lit Cited Peer review 

response 

3.55 

3.55 February 

2010 

Michael 

Reichmuth 

Final edits and 

formatting 

Editor and 

internal review 

comments 

3.6 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.2 

Tables 

Page 

Table SOP 1.1. Basinwide survey reach descriptions.......................................................... SOP 1.3

Table SOP 1.2. Habitat measurements equipment list. ........................................................ SOP 1.4

Table SOP 1.3. Snorkel surveys equipment list. .................................................................. SOP 1.4

Table SOP 1.4. Basinwide survey timing. ........................................................................... SOP 1.7
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.3 

Overview 

This standard operating procedure (SOP) details the Basinwide General Systematic Survey 

(GSS) field methods used to collect habitat data, and abundance estimates of juvenile coho 

salmon using electrofishing and snorkeling during summer and fall base flow conditions. The 

information collected during these surveys is used to determine long-term trends in distribution, 

abundance, and condition of juvenile coho salmon, monitoring objective 3. Collected 

information will also be used to identify gross habitat changes, monitoring objective 5. Surveys 

are conducted annually between July and October. Surveys are performed continuously once 

creeks have reached summer base flow conditions. The sampling design includes habitat 

inventory with a systematic approach for selecting pool units to be snorkeled with a subset of 

those pools calibrated using multiple pass electrofishing. Although the surveys are focused on 

coho salmon, information on other fish species is also gathered while electrofishing (see 

potential list of species encountered in Appendix A). 

Study Area 

Basinwide GSS surveys are conducted in select high priority streams and associated tributaries 

within the San Francisco Bay Area Network (SFAN) in Marin County and which currently 

contain populations of both coho salmon and steelhead including Redwood Creek, Pine Gulch 

Creek, and Olema Creek (table SOP 1.1). The start and end points for each survey may be 

adjusted depending on the water year, observed distribution during spawner surveys, and 

changes in water quality. 

Table SOP 1.1. Basinwide survey reach descriptions. 

Watershed Stream 

Survey 

Length 

(km) 

Fish and Habitat Sampling 

Survey between 

Tags Location Start Location Stop 

Olema Mainstem 11.8 Tag 36–150 Vedanta Retreat 

bridge 

Randall Gulch 

confluence 

Pine Gulch Mainstem 10.3 Tag 00–95 MCOSD Bridge Upstream of Teixeira 

Ranch 

Redwood Mainstem 8.5 Tag 00–74 Big Lagoon 

(brackish water) 

Upstream of Muir 

Woods (Tag 74) 

Sample Design 

The sample design is described in the protocol narrative. Basinwide GSS survey reaches are 

described in SOP 9 (Sampling Site Descriptions). 

Field Methods 

Basinwide GSS surveys will utilize techniques described in Dollof et al. (1993). Background 

information is also provided by Duffy (2005). Surveys consist of two-phase sampling in which 

snorkel counts are utilized during the first stage sampling and electrofishing is used to calibrate 

the snorkel count during the second stage. A ratio estimator is then used to determine a 

basinwide juvenile coho population estimate for each watershed. Sampling effort is focused on 

pool habitats to decrease sampling time. Data from legacy index reaches on Redwood, Pine 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.4 

Gulch, and Olema Creeks since 1997 indicates that over 90% of the coho captured during 

summer juvenile surveys were occupying pool habitat units. 

Field Preparations 

Beginning in late May, equipment should be inventoried, organized, and repaired or replaced as 

necessary. Sampling equipment is listed in tables SOP 1.2–3. Personnel should review the 

protocols and additional supporting documents. If new personnel are being trained, several days 

should be scheduled each for electrofishing and snorkeling training and practice. We also 

recommend visiting each site prior to sampling to familiarize new personnel, determine access 

issues, and assess the amount of change since the previous year. 

Table SOP 1.2. Habitat measurements equipment list. 

Number 

Needed Item 

1 30-meter or 50-meter tape measure 

2 Chaining pins 

1 Metric stadia rod 

1 Aluminum clipboard with waterproof datasheets and pencils 

Table SOP 1.3. Snorkel surveys equipment list. 

Number 

Needed Item 

1 Wetsuit/drysuit, hood, mask, snorkel for each diver 

1 Stop watch 

1 Wading boots for each diver 

1 Dive light w/ spare batteries 

1 Wrist cuff w/ pencil 

1 Aluminum clipboard with waterproof datasheets and pencils 

Field Work Overview 

Summer basinwide surveys are conducted on continuous reaches of each creek mainstem. 

Starting with the lowest surveyed reach, the habitat survey field crews make their way upstream, 

classifying habitat units based on characteristics such as length, depth, and complexity. Pools are 

marked for later survey by a snorkeling field crew. Pools are surveyed using Hankin/Reeves 

methods (Dollof et. al. 1993) that includes a two-phase sampling design. Every fifth pool is 

snorkeled (generally 20% of the pools), and a randomly selected sub-sample on 20% of the 

snorkeled pools are electrofished for calibration. Data sheets are presented in the Appendixes. 

Pool Delineation 

Starting with the lowest surveyed pool in a stream, every fifth pool thereafter is flagged for 

sampling via snorkel survey. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.5 

Habitat Typing 

Initial habitat surveys are conducted prior to snorkeling to determine sampling locations. The 

habitat portion of a basinwide survey will generally require a team of two people for safety and 

efficiency, although one person can do it alone if necessary. Beginning at the downstream end of 

a stream or basinwide survey reach and working upstream, the team identifies, classifies, and 

numbers sequentially all habitat units. Habitat units are classified to Level III using the CDFG 

system (Flosi et al. 1998; see Appendix B). The length of each unit should be measured to the 

nearest 0.1 m using a 50-m tape and the average width visually estimated. A hip chain/string box 

may be used to measure length but all string must be collected and removed from the stream. The 

average width of each habitat unit is estimated visually in order to increase sampling efficiency. 

Measured widths to the nearest tenth of a meter are taken for 20% or every fifth unit to calibrate 

visually estimated widths. The data collected will be used to determine coho densities and to 

analyze habitat constraints on salmonid populations. 

To maintain consistency, unit classification and width estimation should be done by the same 

person for the duration of the survey. The maximum depth and crest depth of all pool and 

flatwater units should be measured to the nearest 0.01 m using a metric stadia rod. The difference 

between the maximum and crest depths is used to determine residual pool depth, which is an 

important geomorphic component for salmonid habitat. In general for the SFAN streams, units 

with a maximum depth greater than 0.3 m are considered pools and those less than 0.3 m in 

depth are considered flatwater units. For a 20% subsample, the team should flag every fifth pool 

unit for snorkeling and measure several widths to the nearest 0.1 m with the metric stadia rod 

after recording the visually estimated width. If a selected pool is unsuitable for snorkeling, the 

team may skip it and flag and measure the next pool. In addition to pool measurements, 10% or 

every 10th riffle and flatwater unit will be measured to calibrate estimated widths. All 

measurements and information should be recorded on the Basinwide Habitat Survey Datasheet

(Appendix C) along with notes on 100-m tags, tributaries, and other landmarks. Habitat units in 

side channels are noted but not used in the population estimate or mainstem habitat composition 

summaries. 

Both the number of transects and the distance at which transects are measured will be determined 

by the measured length of the habitat unit to the nearest whole meter. Two transects will be 

measured on all habitat units 8 m or less. Three transects will be measured on all habitat units 9 

m to 15 m in length. Four transects will be measured on all habitat units 16 m to 25 m in length. 

Five transects will be measured on all units 26 m to 35 m in length. Six transects will be 

measured on all units greater than 35 m in length. The locations of transect measurements are 

calculated in the field by dividing the measured length to the nearest whole meter by the number 

of transects to be measured plus one (unit length / (t+1)). All calculated transect locations will be 

rounded to the nearest whole meter. 

Snorkel Surveys 

Because of the skill necessary to accurately identify and count fish underwater, only experienced 

divers (diver with at least one season of diving experience), or those trained and cleared by the 

primary investigators, should conduct snorkel counts. For each unit sampled, the lead diver or 

field supervisor should assess the conditions and determine how many divers and/or passes 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.6 

should be used to sample the unit. Snorkelers use dive lights to search around woody debris and 

undercut banks. 

Snorkel surveys should be conducted on pools identified through the habitat survey, using dive 

lights to search under vegetation, woody debris, and undercut banks. Juvenile coho are counted, 

and the presence of non-target fish and other aquatic species are noted, as well as cover, habitat 

complexity, and general survey conditions, and recorded on the Snorkel Survey datasheet 

(Appendix D). When low densities of fish are present, divers may tally observed fish mentally or 

on a PVC wrist cuff. When many fish are present, it may be easier to call out observations to a 

data recorder standing on the bank. Underwater visibility will be estimated by the diver with 

greater than 1 m considered to be good visibility and less than 0.5 m considered too turbid to 

snorkel. Staff will calibrate for underwater distance using a stadia rod prior to performing 

surveys on each watershed. 

At this time, basinwide snorkel survey estimates should target coho salmon in the mainstem of 

Pine Gulch, Olema Creek and Redwood Creek. Snorkel data will be used to answer questions 

relating to population trends within the surveyed watersheds, as well as for comparisons with 

other regional watersheds. 

Calibration for the snorkel surveys will use multiple pass electrofishing results on a 20% random 

subsample of snorkeled pool units. All calibration pools must contain safe access points for crew 

members and volunteers that will be performing the electrofishing surveys. If randomly selected 

calibration pools are deemed inaccessible, then the next accessible pool will be utilized as a 

calibration pool. Accessibility will be determined by the snorkel survey data recorder to ensure 

that electrofishing calibration pools are snorkeled without the snorkeler knowing that any given 

unit will be used as a calibration unit. 

In Pine Gulch Creek, where the creek access is most limited, the method of bounded counts 

(Murphy and Willis 1996) will be evaluated as a calibration technique instead of multiple pass 

electrofishing. The modification in calibration technique used on Pine Gulch Creek is due to 

access issues within the sampling area of this watershed. In particular, over 50% of the survey 

area requires access through private property and remote stream reaches that are inaccessible to 

electrofishing crews. By utilizing the bounded count method for calibration purposes, a much 

smaller field crew using National Park Service (NPS) staff only can be used to calibrate the 

initial snorkel counts. Due to the decrease in the amount of equipment used for snorkel surveys, 

snorkel crews are able to access remote areas that would be otherwise deemed inaccessible. 

Electrofishing 

Electrofishing should be conducted as soon as possible after the snorkel counts, preferably the 

next day. For electrofishing and water quality monitoring protocols, please refer to SOP 3. 

Collecting Scale and Tissue Samples 

Scales and/or tissue samples will be collected from all juvenile salmonid mortalities in 

concurrence with the current Section 10 Endangered Species Act permit 1046 modification #2 

requirements. Refer to SOP 6 for permitting and tissue collection details. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.7 

Data Management 

Record and verify data values, both observed and measured. Field datasheets should be 

completed, and the collected data entered into electronic databases described in SOP 8. Crew 

members should schedule and perform regular data transfer and backup, as well as conduct 

regular data verification and correction. Finally, crew members should ensure that field forms, 

field notebooks, and other hardcopy records are secure, readily available for viewing and 

reproduction upon request or at the end of the field season. For analysis and reporting of results, 

please refer to SOPs 8 and 10. 

Logistics 

Annual Workload and Field Schedule 

The summer stream aquatic resource monitoring program is the most intensive, comprehensive, 

and time consuming portion of the overall monitoring program. The implementation of sampling 

surveys will begin in late June or early July, continuing through September or October of each 

monitoring season. The level of intensity is intended to provide equivalent surveys to all SFAN 

parks with high priority streams. Essentially, weeks are broken out to include two habitat typing 

days (split crew), two snorkeling days (split crew) and two electrofishing days (full crew). 

Staffing Requirements 

The basinwide GSS sampling is field intensive. In general required field staff includes two field 

staff for habitat typing, two field staff for snorkeling, and five field staff for electrofishing. The 

timing for each survey type (habitat, snorkel, and e-fishing) is staggered during the summer so 

that each survey may be completed with two to four field staff and additional volunteer help on 

electrofishing survey days. For electrofishing, field staff is normally assisted by 1 to 3 volunteers 

per day. Volunteers are not allowed to perform sensitive tasks such as snorkeling, habitat typing, 

operating the electrofisher, or weighing and measuring fish, but they are valuable in assisting 

with transport of equipment and fish, recording information, and increasing field safety during 

electrofishing surveys. 

Sampling Frequency and Timing 

In general, sampling for each stream should be conducted at about the same time of year on an 

annual basis. Sampling will begin on Pine Gulch in early July and end on Olema Creek in midOctober. Table SOP 1.4 provides the recommended seasonal timing for sampling each stream. 

Table SOP 1.4. Basinwide survey timing. 

Watershed Stream Dates 

Fish and Habitat Sampling: Time Needed 

Habitat Typing 

Snorkel 

Surveys 

Calibration 

Pools 

Olema Mainstem September–October 7 days 14 days 8 days 

Pine Gulch Mainstem July–August 5 days 12 days 5 days 

Redwood Mainstem AugustSeptember 5 days 12 days 8 days 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 1.8 

Literature Cited 

Duffy, W. G. 2005. Protocols for monitoring the response of anadromous salmon and steelhead 

to watershed restoration in California. California Department of Fish and Game, California 

Cooperative Fish Research Unit, Humboldt State University, Arcata, California. 

Flosi, G., S. Downie, J. Hopelain, M. Bird, R. Coey, and B. Collins. 1998. California salmonid 

stream habitat restoration manual. Third edition. California Department of Fish and Game, 

Sacramento, California. 

Murphy, B. R., and D.W. Willis. 1996. Fisheries Techniques. Second Edition. American 

Fisheries Society, Bethesda, Maryland. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.1 

SOP 2. Index Reach Surveys 

Version 1.5 

Revision History Log 

Prev. 

Version 

# 

Revision 

Date 

Author Changes Made Reason for 

Change 

New 

Version 

# 

 Jan. 2007 Marcus 

Koenen 

Added revision log, 

removed sampling 

site description, 

focused on field 

methods. 

Clarification 

and remove 

redundancy 

3.1 

 3.2 Feb. 2007 Michael 

Reichmuth 

Revised changes and 

updated to reflect 

current monitoring 

Clarification 

and updating 

techniques used 

3.2MR 

1 May 2008 Sarah 

Carlisle 

Removed Basinwide 

and GSS survey 

references to focus on 

Index Reach Surveys 

only 

 1.0 

1.0 May 2008 Sarah 

Carlisle 

Updated datasheets 

and field protocols 

 1.1 

1.1 May 2008 Sarah 

Carlisle 

Linked data 

collection with 

project questions 

 1.11 

1.11 July 2008 Michael 

Reichmuth 

Reviewed and revised 

protocol 

Clarification 1.2 

1.2MK August 

2008 

Michael 

Reichmuth 

Minor Changes Clarification 1.3 

1.3 August 

2008 

Brannon 

Ketcham 

Moderate changes 1.4 

1.4 October 

2008 

Dawn Adams Formatting; moved 

datasheets to SOP 3 

For peer review 1.41 

1.41 December 

2008 

Michael 

Reichmuth 

Minor Edits For peer review 1.42 

1.42 November 

2009 

Michael 

Reichmuth 

Added Lit. Cited Peer review 

response 

1.43 

1.43 February 

2010 

Michael 

Reichmuth 

Final edits for final 

submittal 

Response to 

editors and 

internal review 

comments 

1.5 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.2 

Figures and Tables 

Page 

Table SOP 2.1. Number of index reaches per watershed. ................................................... SOP 2.3

Table SOP 2.2. Habitat assessment equipment list. ............................................................. SOP 2.5

Figure SOP 2.1. Representation of groundcover, understory, and overstory for 

field habitat characterization. ............................................................................................... SOP 2.6

Table SOP 2.3. Index reach timing. ..................................................................................... SOP 2.8
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.3 

Overview 

This standard operating procedure (SOP) details the field methods used to collect abundance 

estimates for juvenile coho salmon and steelhead trout in index reaches established in parks of 

the San Francisco Bay Area Network (SFAN) during fall base flow conditions. The information 

collected during these surveys is used to determine long term trends in density, size, and age 

composition of coho salmon at preexisting legacy index reach locations, monitoring objective 4. 

The information collected during these surveys is not intended to represent the entire watershed 

condition but it will be used to determine fish condition and population trends specific to these 

legacy index reaches. Survey will be conducted after basinwide GSS surveys are completed in 

late September or early October and will last until late October. Although the surveys are 

focused on juvenile coho salmon, information on other species captured will be gathered. 

Study Area 

Index reach surveys are conducted in select streams and associated tributaries in Marin County 

which currently contain populations of both coho and steelhead including Olema Creek, Pine 

Gulch Creek, and Redwood Creek. Because the value of legacy indexes reaches is the length of 

each data set for each index reach, priority index reaches are delineated in table SOP 2.1 to guide 

field staff during years when field time is limited. 

Table SOP 2.1. Number of index reaches per watershed. 

Watershed 

Total Number of Legacy 

Index Reaches 

Priority Index Reaches to be 

Maintained Annually 

Number of Priority 

Index Reaches 

Olema 8 Reaches: 2, 3, 5, 6, 7 5 

Pine Gulch 7 Reaches: 1c, 2, 3, 5, 6 5 

Redwood 5 Reaches: 2, 3, 4, 5, 6, 5 

Sample Design 

All juvenile salmonids will be sampled at designated index reaches. The overall sampling design 

is described in the protocol and site locations are described in SOP 9. 

Sampling Frequency and Timing 

In general, each stream should be sampled at about the same time of year on an annual basis. 

Sampling should be conducted once basinwide GSS surveys are completed in early fall when 

water levels are at their lowest levels. By sampling at fall base flow, ultimate fish abundance and 

condition can be accurately measured within each index reach. 

Field Methods 

During summer and fall sampling, sampling occurs along index reaches that were established in 

1997. Each habitat unit within the index reach is isolated with block nets and sampled separately 

using standard multiple pass depletion electrofishing methods (Bohlin et al. 1989). Where 

appropriate, seine hauls may be used in conjunction with electrofishing to reduce indirect injury 

or mortality from electrofishing. Data are recorded for size (length and weight), genus, species, 

and age class. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.4 

After the fish sampling is completed, measurements and assessments of each habitat unit are 

made. Measurements include length, average width and depth, substrate composition, and 

instream shelter complexity are quantified at each sample site. Transects are set up across each 

sample site. Depth and substrate type are recorded at points along each transect. Additional 

habitat parameters are determined for the index reach as a whole. The habitat portion of index 

reach monitoring must be completed the same day as fish sampling or very soon thereafter. 

Field Season Preparations 

Beginning in late May, equipment should be inventoried, organized, and repaired or replaced as 

necessary. Personnel should review the protocols and additional supporting documents. If new 

personnel are being trained, several days should be scheduled each for electrofishing and 

practice. Visiting each site prior to sampling is useful to familiarize new personnel, determine 

access issues, and assess the amount of change since the previous year. 

Fish Sampling Method 

The fish sampling portion generally takes a full work day for each reach, including the habitat 

survey. Within the index reach, separate habitat units are identified for electrofishing and habitat 

surveys. The crew will first complete their electrofishing passes on the habitat unit and process 

captured fish (after each pass). The crew will continue working upstream, electrofishing each 

habitat unit and leapfrogging the nets, until the top of the index site is reached. Once the 

electrofishing and fish sampling is completed, habitat surveys are conducted.

Establish Reaches 

The top and bottom of each index reach are marked with flagging and aluminum tags labeled 

with the stream name, index #, and “top” or “bottom”. Each year of sampling, the habitat units 

within the established index reach are surveyed. The dynamic stream conditions may result in the 

end of habitat units being outside of the established reach. In these cases, the entire habitat unit 

should be surveyed. 

Sample Water Quality 

Collect water quality samples as described in SOP 3. 

Set Up Block Nets 

To begin sampling, locate the bottom (downstream) tag or flag of the index reach. Starting at the 

bottom of the pool or flatwater habitat unit nearest this tag and working upstream, identify, 

number, and isolate each habitat unit with block nets. Sections of dry streambed and other habitat 

units within the index reach that are not sampled should still be numbered and classified. Install 

nets perpendicular to the thalweg and seal the bottom and ends with rocks and gravel to ensure 

no fish can get through. Riffles with a length less than one stream width are not considered 

separate habitat units and should be included with the downstream unit. 

Electrofishing 

See SOP 3 for electrofishing methods. Note that with this SOP, pool and flatwater habitat units 

will be sampled using standard multiple pass depletion electrofishing methods, allowing 

sufficient time (approximately 5–10 minutes) between passes to allow uncaptured fish to recover 

and suspended sediments to settle. A minimum of two passes will be conducted in these units, 

with additional passes as necessary to achieve a good depletion. In general, if the catch of any 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.5 

species/age class is more than 50% of the previous pass, then another pass should be conducted. 

Riffles can be sampled with a single pass. A pass consists of a sweep from the bottom 

(downstream end) of a unit to the top, then back to the bottom. After each pass check the 

downstream net and remove any fish that have drifted in. Do not remove the net until all passes 

have been completed. Record information for each electrofishing pass on the Index Reach 

Electrofishing Log (SOP 3, Appendix E), including pass time, number of fish captured, and 

electrofisher settings. 

Seining 

Seining is described in SOP 3. A minimum of two passes will be conducted in these units, with 

additional passes as necessary to achieve a good depletion. In general, if the catch of any 

species/age class is more than 50% of the previous pass, then another pass should be conducted. 

Note that after processing, seine captures should not be released until after all electrofishing 

passes have been completed on a unit. Record the total seine capture on the Index Reach 

Electrofishing Log (SOP 3) datasheet, making sure to differentiate it from the electrofishing 

passes.

Processing Fish 

Methods are described in SOP 3. Fish species and measurement data is entered on the 

Electrofishing Datasheet (SOP 3, Appendix E). Start a new datasheet for each habitat unit; if 

more than one sheet is used for a unit, record sheet # and total # of sheets on each sheet. 

Collecting Scale and Tissue Samples 

Scales and/or tissue samples will be collected from all juvenile salmonid mortalities in 

concurrence with current permit requirements. Refer to SOP 6 for details on tissue collection and 

permitting. 

Habitat Assessment 

After electrofishing the entire index reach unit by unit, the next step is to collect habitat 

information including habitat unit dimensions, substrate, instream shelter, woody debris, and 

bank erosion and vegetation. The purpose of the habitat assessment is to record site descriptions, 

in the event of a drastic change in stream conditions between surveys. All habitat units should be 

identified to level III using the CDFG classification system (Flosi et al. 1998; Appendix B). 

Sections of dry stream bed or habitat units that are not sampled for fish should still be numbered, 

classified, and the length measured. If the habitat assessment occurs on a different day than fish 

sampling, a copy of the completed Index Reach Electrofishing Log (SOP 3) should be used to 

ensure the habitat units are identified and classified consistently. Table SOP 2.2 presents the list 

for equipment needed to collect habitat data. 

Table SOP 2.2. Habitat assessment equipment list. 

Number Needed Item 

1 30-meter or 50-meter tape measure 

1 Chaining pins 

1 Metric stadia rod 

1 Aluminum clipboard with waterproof datasheets and pencils 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.6 

Habitat Components 

The following habitat components (figure SOP 2.1) are counted or estimated for the index reach 

as a whole and recorded on the Index Reach Habitat Datasheet (Appendix E). 

Figure SOP 2.1. Representation of groundcover, understory, and overstory for field habitat 

characterization. 

Bank Vegetative Cover: Visually estimate percent cover for the three layers of riparian 

vegetation along the entire index reach (figure 11). Tall trees such as mature alders, bays, 

oaks, firs, and redwoods form the Overstory (OS). Lower growing deciduous shrubs and 

young trees such as elderberry, salmonberry, alders, and hazelnut form the Understory (US). 

Ground cover (GC) is composed of grasses, ferns, blackberries, nettles, rushes, and other low 

growing plants. 

Bank Erosion: Identify the length of the stream banks along the index reach and visually 

estimate the percentage of the channel with active bank erosion. Rate the left and right banks 

(facing downstream) individually. Also identify potential source of this erosion (channel 

scour, animal trail, etc.). 

Dry Channel/Isolated Pools: Indicate whether there are any pools which are disconnected 

from adjacent habitat units (i.e., with no surface flow in or out). If there is discontinuous flow 

along the channel thalweg, visually estimate the percentage of dry channel present in the 

index reach. 

Woody Debris: Count and record all large woody debris (LWD), alive and dead, within the 

bankfull channel along the index section. Research on hardwood riparian forests have shown 

that live trees within the bankfull channel, primarily alder and bay in these watersheds, are 

prominent channel forming features (Opperman 2003). To qualify as LWD, individual logs 

must meet specific size requirements. Logs must be at least 2 m (6 ft) in length and are tallied 

in the following diameter classes: 10-20 cm (4-8 in), 20-50 cm (8-20 in), and greater than 50 

cm (>20 in). Diameter is measured at the mid-point of the log. Stumps, with the root 

structure intact, that are less than 2 m long and at least 20 cm in diameter are tallied 

separately. These “rootwads” are very stable structures and can provide excellent juvenile 

Overstory 

Understory 

Ground Cover 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.7 

fish habitat. Accumulations of more than 10 individual pieces of LWD constitute a large 

woody debris jam. Each jam is tallied separately. There is no need to tally every individual 

log in the jam, just record the jam as a whole. Pieces of wood that are between 5 and 10 cm 

in diameter are considered small woody debris (SWD). We will not be counting individual 

pieces of SWD. Tally only accumulations of ten or more pieces of SWD as SWD jams.

Transect Measurements 

For each habitat unit measure the length to the nearest tenth of a meter and establish up to six 

transects across the width of the unit, perpendicular to the thalweg, using a metric tape measure 

with the zero end at right edge of water (REW) when looking downstream. Both the number of 

transects and the distance at which transects are measured will be determined by the measured 

length of the habitat unit to the nearest whole meter. Two transects will be measured on all 

habitat units 8 m or less. Three transects will be measured on all habitat units 9 m to 15 m in 

length. Four transects will be measured on all habitat units 16 m to 25 m in length. Five transects 

will be measured on all units 26 m to 35 m in length. Six transects will be measured on all units 

greater than 35 m in length. The locations of transect measurements are calculated in the field by 

dividing the measured length to the nearest whole meter by the number of transects (t) to be 

measured plus one (unit length / (t+1)). All calculated transect locations will be rounded to the 

nearest whole meter. Along each transect, wetted stream width is measured to the nearest 0.1 m. 

For pool and flatwater units, the maximum and crest depths should also be measured. Record 

habitat unit length, width, and depth information on the Index Reach Habitat Unit Transect 

Datasheet (Appendix E). 

Instream Shelter 

For each habitat unit, visually estimate the percentage of the water surface area covered by the 

following instream shelter types (Flosi et al. 1998) and record the appropriate instream shelter 

class provided on the Index Reach Habitat Unit Transect Datasheet (Appendix E). 

Undercut Bank and Bedrock Ledge are rated according to the percentage of the unit’s 

perimeter affected. 

Small Woody Debris (SWD) and Large Woody Debris (LWD) are dead branches or logs in 

the water, at least 2 m (6 ft) in length, and < or > 10 cm (4 in) in diameter respectively. 

Accumulations of pieces < 2 m long can also be counted if they form significant cover. 

Root Mass includes woody root structures in the water or extending out from bank. Root 

structures even with the bank should be counted as undercut bank. Logs with roots should be 

divided between root mass and one of the woody debris categories. 

Terrestrial Vegetation consists of live branches, leaves, or herbaceous plants hanging in or 

very near the water. 

Aquatic Vegetation includes watercress, reeds, and other plants rooted in the water. 

Accumulations of floating vegetation (e.g., duckweed) can also be counted if they form 

significant cover. Algae mats should not be counted. 

Bubble Curtain includes white water, cascades, and plunge pools. 

Boulder is >25 cm (10 in) in diameter. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 2.8 

Data Management 

Record and verify data values, both observed and measured. Field datasheets should be 

completed, and the collected data entered into electronic databases described in SOP 8. Crew 

members should schedule and perform regular data transfer and backup, as well as conduct 

regular data verification and correction. Finally, crew members should ensure that field forms, 

field notebooks, and other hardcopy records are secure, readily available for viewing and 

reproduction upon request or at the end of the field season. For analysis and reporting of results, 

please refer to SOPs 8 and 10. 

Logistics 

Annual Workload and Field Schedule 

The summer stream aquatic resource monitoring program is the most intensive, comprehensive, 

and time consuming portion of the overall monitoring program. The implementation of sampling 

surveys will begin in Pine Gulch and end in Olema in late September and early October of each 

monitoring season (table SOP 2.3). 

Table SOP 2.3. Index reach timing. 

Watershed # of Index Reaches 

Index Reach Sampling 

Sampling Dates 

Index Reach Monitoring Time 

Needed 

Olema 6-8 Late September/Early 

October 

6-8 days 

Pine Gulch 5-8 Mid October 5-8 days 

Redwood 5-7 Late October 5-7 days 

Staffing Requirements 

Index reach sampling requires at least 5 individuals per day for each index reach. At least two 

field staff are required to operate the electrofisher and weigh and measure fish while 2 to 3 

volunteers may be used to net fish, transport fish, transcribe data, and carry equipment. 

Volunteers are not allowed to perform sensitive tasks such as operating the electrofisher or 

weighing and measuring fish. 

Literature Cited 

Bohlin, T., S. Hamrin, T. G. Heggberget, G. Rasmussen, and S. J. Saltveit. 1989. Electrofishing: 

Theory and practice with special emphasis on salmonids. Hydrobiologia 173:9–43. 

Flosi, G., S. Downie, J. Hopelain, M. Bird, R. Coey, and B. Collins. 1998. California salmonid 

stream habitat restoration manual. Third edition. California Department of Fish and Game. 

Sacramento, California. 

Opperman J. 2003. Large Woody Debris and Anadromous Fish Habitat in California’s 

Mediterranean-climate Watersheds. Master’s Thesis. University of California, Berkeley; 

Department of Environmental Science, Policy and Management April 7, 2003.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.1 

SOP 3. Specialized Field Methods 

Version 1.5 

Revision History Log 

Prev. Version 

# 

Revision Date Author Changes 

Made 

Reason for 

Change 

New 

Version #

 July 2008 Marcus 

Koenen 

Created SOP 

to synthesize 

common 

methods 

To remove 

redundancy 

from other SOP 

1.0 

1.0 August 2008 Michael 

Reichmuth 

Minor edits 

and comments 

Clarification 1.1 

1.1 August 2008 Brannon 

Ketcham 

Minor edits Clarification 1.2 

1.2 September 

2008 

Michael 

Reichmuth 

Minor edits Clarification 1.3 

1.3 September 

2003 

Michael 

Reichmuth 

Removed 

Presence 

Non-detect 

Info 

Changed to 

reflect current 

funding 

1.4 

1.4 September 

2008 

Dawn 

Adams 

Formatting Peer review 1.41 

1.41 December 

2008 

Michael 

Reichmuth 

Minor Edits Peer Review 1.42 

1.42 November 

2009 

Michael 

Reichmuth 

Added Lit 

Cited 

Peer review 

response 

1.43 

1.43 February 

2010 

Michael 

Reichmuth 

Final edits for 

final submittal

Response to 

editors and 

internal review 

comments 

1.5 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.2 

Tables 

Page 

Table SOP 3.1. Electrofishing equipment list. ..................................................................... SOP 3.4
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.3 

Overview 

This standard operating procedure (SOP) details the specialized field methods used for fish 

sampling. This SOP includes electrofishing, seining, water quality sampling, and fish handling 

techniques. These techniques may be used in conjunction with SOPs 1 and 2. Sampling design, 

and frequency are described in the narrative and specific technique SOPs. Site descriptions are in 

SOP 9. 

Field Methods 

Water Quality 

Water quality parameters, including conductivity, should be measured each day prior to sampling 

activities. Using an YSI 30 or 85 meter, measure and record the water temperature, conductivity 

and specific conductance, and salinity at the tailout of each of the pools or index reaches 

immediately before sampling. If using the YSI 85, measure and record dissolved oxygen as well. 

If sampling in slow moving water, it may be necessary to move the probe slowly and steadily in 

the water to attain an accurate dissolved oxygen reading. Measurements should be taken before 

walking in or disturbing the water. Record water quality measurements, habitat unit information, 

and general reach information on the Index Reach Habitat Log (Appendix E) or Basinwide 

Electrofishing Log (Appendix G). 

For complete calibration and operation techniques for these YSI Probes, refer to the San 

Francisco Bay Area Network (SFAN) Water Quality Monitoring Protocol SOP 3 (Specialized 

Field Methods). 

Electrofishing 

Electrofishing will be conducted for calibration in basinwide GSS surveys (SOP 1) and legacy 

index reaches (SOP 2). Most sampling will be conducted using a battery powered backpack 

electrofisher with an 11-inch aluminum anode ring and rat-tail cathode. See table SOP 3.1 

for all other equipment needed for electrofishing. There are currently two electrofishing units 

available to SFAN Parks, a Smith-Root model 12-B at Golden Gate National Recreation Area 

(GOGA) and a Smith-Root model LR-24 at Point Reyes National Seashore (PORE). Only 

personnel trained and cleared by the primary investigators will operate the electrofishers. 

Operators of the electrofishers will be trained using the fundamental techniques and safety 

precautions presented in the Principles and Techniques of Electrofishing handbook (Kolz et al. 

1998). For safety reasons, no individuals who are pregnant or have a pacemaker may 

participate in electrofishing activities.

To begin, locate the bottom (downstream) end of the selected pool. Install nets perpendicular to 

the thalweg and seal the bottom and ends with rocks and gravel to ensure no fish can get through. 

Once both upper and lower ends have been blocked, begin electrofishing using standard 

methods. 

A pass consists of a sweep from the bottom (downstream end) of a unit to the top, then back to 

the bottom. For index reach sampling: multiple passes will be used as described in SOP 2. For 

basinwide GSS calibration sampling: multiple passes will be used as described in SOP 1. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.4 

Table SOP 3.1. Electrofishing equipment list. 

Number 

Needed Item 

1 Backpack electrofisher with rat-tail cathode and anode probe w/ 11” anode ring 

3 Charged electrofisher batteries 

1 Spare anode ring with 7/16” wrench (can be left in vehicle) 

2 Long handled capture nets (wood or fiberglass handles; not aluminum) 

>3 4’ x 10’ seines, carried in holey plastic tub (which doubles as live car) 

1 YSI 30, YSI 85, or other instrument to measure water temp and conductivity 

6 Clean 5-gallon buckets 

5 Battery powered clip-on aerators with tubes, airstones, and spare D batteries 

>3 Aquarium dip-nets, various sizes 

1 Measuring board with mm scale 

1 Electronic scale with weighing hook in padded plastic case, w/ spare batteries 

1 Nylon mesh weighing bag 

1 Plywood weighing stand 

1 Plastic tool box containing: 

20 Alka seltzer tablets in ziploc bag 

20 Coin envelopes and blotter paper (for scale/tissue samples) in ziploc bags 

1 Surgical scissors 

1 ea. Pesola scales (100g x 1g and 1000g x 10g) 

20 Ziploc bags, spare batteries, pens, pencils, airstones, aerator tubes, etc. 

1 Aluminum clipboard with waterproof datasheets and pencils 

N Waders for crew 

After each pass check the downstream net and remove any fish that have drifted in. Record 

information for each electrofishing pass on datasheets (i.e., Basinwide Electrofishing Log, 

Appendix G; Index Reach Log, Appendix H), including pass time, number of fish captured, and 

electrofisher settings. 

For most of the stream conditions and fish species/age classes encountered, a direct-current 

setting (P16 on the model 12-B) at 150-200 volts (100 volts for riffles and other shallow areas) 

has been found to be most effective with minimal negative effects to juvenile salmonids and 

other fish, and is consistent with National Marine Fisheries Service (NMFS) guidelines (NMFS 

2000). For specifics on the settings and operation of each electrofisher unit, refer to the 

appropriate model’s instruction manual. 

Electrofishing should be conducted with a minimum of three people, one to operate the 

electrofisher and two netters to capture stunned fish. Additional people can help transfer captured 

fish into holding buckets. To keep a consistent effort per unit, staff and volunteers should retain 

the same job function for the entire sampling time in each sampling unit and all passes. All 

captured fish should be immediately placed into clean 5-gallon holding buckets containing fresh 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.5 

stream water, with larger sculpin kept in separate buckets to avoid predation on young of the 

year (YOY) salmonids and other smaller fish. Buckets should be approximately half full to 

ensure sufficient water and oxygen for the fish. Avoid filling buckets too full as this may allow 

fish to jump out. Also avoid overcrowding; redistribute fish among buckets if necessary. Buckets 

should be kept in the shade as much as possible, and aerators should be placed in buckets if fish 

will be held for more than 5-10 minutes. 

If the number of personnel is limited, the fish from each electrofishing pass should be processed 

before continuing with the next pass. With enough people, one group can process fish while the 

other group continues electrofishing. Fish from different passes should be held in separate 

buckets and processed in the order they were captured. Once all electrofishing passes on a habitat 

unit have been completed and all captured fish have been processed and allowed to recover, the 

bottom net can be moved upstream to net off any remaining units and the fish released back into 

the unit from which they were captured. 

Seining 

When possible, one or more passes with a seine will be conducted prior to electrofishing to 

reduce the potential risk of injuries to fish or red-legged frogs. Open units with minimal amounts 

of woody debris or other obstructions that may snag a net are good candidates for seining. Seines 

should be knotless woven nylon, 1/8 inch or similar sized mesh. Fish captured by seine should be 

placed in holding buckets and processed in the same way as electrofishing captures. Fish from 

different seine passes in the same unit may be combined and processed as a single pass event. 

After processing, seine captures should not be released until after all seine passes have been 

completed on a unit. Record the total seine capture on the appropriate datasheet, making sure to 

differentiate it from the electrofishing passes. 

Handling Captured Fish 

All captured fish will be processed after each electrofishing or seine pass. All handling and 

processing of salmonids will be performed by personnel trained and cleared by the project lead. 

Fish identification is important; see Appendix A for a list of species that may be encountered in 

the study area. To minimize handling of fish, a randomly selected subsample of ten coho, ten 

steelhead YOY, and ten steelhead 1+ will be measured to the nearest millimeter and weighed to 

the nearest hundredth of a gram within each unit and pass. For the rest, individuals should be 

tallied. To ensure that all fish are selected for measuring at random, field staff will select each 

fish by making a blind grab, with a dipnet, from the holding bucket. 

Also identify, measure, and weigh non-salmonid fish; if more than ten of any species then weigh 

and measure ten and tally the rest. Based on analysis of past weight/length data, a subsample of 

ten randomly selected fish of each species, per pass, per unit will result in a sample size that is 

adequate for developing a weight-length relationship for salmonids in each mainstem (Carlisle et 

al. 2008) 

Sampled salmonids should be sedated using carbon dioxide (Alka-Seltzer®) to facilitate 

handling and minimize stress to the fish. Other fish may also be sedated prior to handling if 

needed. Fill a clean, 5-gallon bucket (white works best) with a couple inches of fresh stream 

water and add half of an Alka-Seltzer® tablet (use only plain, unmedicated Alka-Seltzer®). 

Place a few fish at a time into the treated water and wait a couple minutes until they are 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.6 

adequately sedated. Fish should be processed once they are sluggish enough for easy handling 

but before they begin to turn over. If fish do turn over they should be processed and/or returned 

to an aerated holding bucket immediately. Adjust the number of fish sedated at a time as 

necessary: if fish are turning over, add fewer at a time; if waiting for fish to become adequately 

sedated is holding up the processing, more can be added at a time. More Alka-Seltzer® may be 

added if necessary, but be conservative (no more than a quarter tablet at a time) and monitor fish 

closely if the dosage is increased. It may be necessary to change the water periodically, 

particularly on hot days and when processing large numbers of fish. 

Processing will ideally involve two people: one to measure fish and one to record the 

information on datasheets. Fish species and measurement data is entered on the datasheet (i.e., 

Basinwide Electrofish Log; Appendix F) Start a new datasheet for each habitat unit; if more than 

one sheet is used for a unit, record sheet # and total # of sheets on each sheet. On the computer 

all units are entered into the same file. Data collected during these surveys will be used to answer 

questions relating to population trends and salmonid distribution in coastal watersheds. 

All salmonids are identified to species and age class (YOY or 1+) and counted. An appropriate 

(see above) sub-sample should be measured (fork length) to the nearest mm, and weighed to the 

nearest 0.01 g (until 2004 fish were measured to the 0.1 g) using an electronic scale. The 1+ 

category includes all fish older than one year (i.e., we do not attempt to differentiate 1+, 2+, 

etc.). In general, steelhead >100 mm fork length are considered 1+ and those steelhead <100 mm 

are considered YOY. This size break may be adjusted up or down if there is an obvious gap in 

the distribution of observed lengths. 

After processing each fish, place it in an aerated recovery bucket, again keeping larger sculpin in 

separate buckets to avoid predation on smaller fish. The recovery bucket should be a different 

color (preferably blue or other dark color) or located away from the holding buckets to avoid 

confusing fish that have and have not been processed. Monitor the recovery bucket to insure 

sedated fish recover fully before being released. 

With enough people, one group can process fish while the other group continues electrofishing in 

the next sample pool. Once the electrofishing pass on a habitat unit have been completed and all 

captured fish have been processed and allowed to recover, the nets can be removed and the fish 

released back into the unit from which they were captured. 

Collecting Scale and Tissue Samples 

For any juvenile salmonid mortality, scales and/or tissue samples will be collected in accordance 

with current permit requirements. Refer to SOP 6 for sample collection, handling, and permitting 

details. 

Literature Cited 

Carlisle, S., M. Reichmuth, E. Brown, and S. C. Del Real. 2009. Long-term coho salmon and 

steelhead trout monitoring in coastal Marin County 2007: annual monitoring progress 

report. Natural Resource Technical Report NPS/SFAN/NRTR—2009/269. National Park 

Service, Fort Collins, Colorado. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 3.7 

Kolz, A. L., J. Reynolds, A. Temple, J. Boardman, and D. Lam. 1998. Principles and techniques 

of electrofishing. Course manual. U. S. Fish and Wildlife Service National Conservation 

Training Center, Branch of Aquatic Resources Training, Shepherdstown, West Virginia. 

National Marine Fisheries Service. 2000. Guidelines for electrofishing waters containing 

salmonids listed under the endangered species act. Protected Resources Division, Santa 

Rosa, California. 

Opperman, J. 2003. Large woody debris and anadromous fish habitat in California’s 

mediterranean-climate watersheds. Thesis. University of California, Berkeley; Department 

of Environmental Science, Policy and Management, Berkeley, California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.1 

SOP 4. Spring Smolt Trapping 

Version 3.6 

Revision History Log 

Prev. 

Version # 

Revision Date Author Changes Made Reason for 

Change 

New 

Version #

 Jan. 2007 Marcus 

Koenen 

Added revision 

log, removed 

sampling site 

description, 

focused on 

field methods. 

Clarification 

and remove 

redundancy 

3.1 

 3.1 Feb. 2007 Michael 

Reichmuth 

Added 

revisions to 

reflect current 

monitoring 

Changes in 

sampling 

3.2MR 

3.2MR May 2008 Sarah 

Carlisle 

Updated 

datasheets and 

field protocols, 

continued 

changes as 

recommended 

by MR 

 3.3 

3.3 May 2008 Sarah 

Carlisle 

Linked data 

collection with 

project 

questions 

 3.31 

3.31 July 2008 Michael 

Reichmuth 

Review and 

make edits 

clarification 3.4 

3.4 August 2008 Brannon 

Ketcham 

Review and 

edit 

Clarification 3.5 

3.5 October 2008 Dawn 

Adams 

Formatting For peer review 3.51 

3.51 December 2008 Michael 

Reichmuth 

Minor Edits For Peer 

Review 

3.52 

3.52 November 2009 Michael 

Reichmuth 

Added Lit 

Cited 

Peer Review 

Response 

3.53 

3.53 February 

2010 

Michael 

Reichmuth 

Final edits for 

final submittal 

Response to 

editors and 

internal review 

comments 

3.6 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.2 

Tables 

Page 

Table SOP 4.1. Fyke/pipe trap set-up supply list in Hagmaier barn storage. ...................... SOP 4.3

Table SOP 4.2. Fyke/pipe trap set-up supply list in RM garage or basement 

(PORE). ................................................................................................................................ SOP 4.4

Table SOP 4.3. Pipe trap monitoring supplies. .................................................................... SOP 4.6
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.3 

Overview 

This SOP details the field methods used to determine long-term trends in abundance and 

condition of juvenile coho salmon, monitoring objective 2. Downstream migrant traps are 

typically constructed in late March and removed in late May. The trapping period is consistent 

with the seasonal outmigration of coho smolt. Once constructed, downstream migrant traps are 

checked and maintained daily. All juvenile coho are counted and a subset are measured and 

weighed to obtain a measure of fish condition. 

Study Area 

Trap sites located at the mouths of Olema, Redwood, and Pine Gulch Creeks. Refer to SOP 9 for 

specific locations of sampling sites. 

Sample Design 

The sample design is described in the protocol narrative. 

Field Methods 

Field Preparations 

Once the winter spawning season is over, staff should begin preparations for the smolt trap 

operations. The field crew should ensure that all equipment is restocked and operable in the two 

weeks prior to trap installation. The fish program has smolt trap monitoring equipment stored in 

the water resources garage at Point Reyes National Seashore (PORE). The trap hardware, 

including pipes, screen and live boxes are stored in a barn at the Pacific Coast Learning Center. 

Sand bags to hold stream gravel, erosion cloth to assist in impounding water, t-posts, and a postpounder will also be necessary for the installation. A list of supplies by storage location is given 

in tables SOP 4.1–2. 

Table SOP 4.1. Fyke/pipe trap set-up supply list in Hagmaier barn storage. 

Number Needed Item 

2 per site trap box (make sure each has a rectangular divider screen, thick plywood piece 

with 6” round hole, and a plywood piece over opening at each end (1 solid and 1 

with 6” round hole and rubber gasket) 

1-3 20’ sections per 

site 

white 6” PVC pipes (also take some of the shorter sections) 

30 per site t-posts of various length and gage (it doesn’t matter if the flat piece has fallen off 

the end, but they should be straight) 

40’ per site wire mesh hardware cloth (round 40’ per site, maybe more for Olema Creek; can 

take used pieces if they are in good shape & not too cut up, otherwise take one of 

the new rolls to each site) 

50 per site white sand bags 

40-50’ per site black erosion cloth 

Equipment Set Up 

As sites are known, equipment should be transported and staged in mid-March. Traps should be 

set up by mid- to late March. Trap installation is weather dependent. Installation takes 

approximately one or two days per site. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.4 

Table SOP 4.2. Fyke/pipe trap set-up supply list in RM garage or basement (PORE). 

Number Item 

Many various sizes of plastic zip ties 

Pair per worker gloves 

shovels, Pulaskis, McLeods 

tin snips for cutting hardware cloth 

1 per site post pounders 

baling wire and small wire cutters (yellow tool box) 

3-5 

traffic cone or small bucket 

plug pipe during setup and processing 

1 4’ x 5’ x 20’ fyke net 

Fyke/Pipe Trap Construction 

The fyke/pipe trap on the mainstem of Olema, Pine Gulch, and Redwood Creeks are based on a 

design used by CDFG on the Noyo River (Gallagher 2000; Barrineau and Gallagher 2001). A 4’ 

× 5’ × 20’ fyke net is supported by t-posts with a fence line extending from each t-post to direct 

fish into the mouth of the fyke net. The trap fence is constructed of 4-ft-wide, 1⁄2-in mesh 

hardware cloth, fence posts, rocks, and sand bags that span the width of the stream in a 

downstream pointing V. T-posts are installed to secure the fyke net fitting at the apex of the V, 

along the fence line at 2-ft intervals. Near the edge of the stream where water is shallower, the tpost spacing may be wider. The hardware cloth should be placed against the upstream side of the 

t-posts, with the bottom 8-12 in buried upstream as a footer into the substrate to prevent water 

from scouring under the weir. Line the downstream side of the weir with sandbags to prevent 

scour. Erosion cloth should be spread over the screen and extending upstream to prevent piping 

of flow under the screen. The erosion cloth and wire-mesh screen should be anchored with a few 

sandbags filled with stream gravel. Stream gravel should also be spread over the erosion cloth 

and screen area to make it appear as a natural stream bottom. The water should pool at the fyke 

net mouth, concentrating flow through the pipe. A small gap is left between the fence line and 

the stream bank on one side to allow steelhead migrating upstream to pass. 

The throat of the fyke net is attached to a series of pipes, which is attached to a plywood trap 

box. The pipe consists of 6-in-diameter PVC in 20-ft sections. Schedule 80 pipe is light enough 

for two people to carry a section. Once the structure is in place, adjust the live box up or down to 

moderate the flow into the box. Flow should be sufficient to carry fish into the box, but not so 

much that fish are entrained by excessive current within the trap box. A screen should be placed 

near the rear of the live box to allow an area of refugia for smaller fish from larger salmonids and 

sculpin. The trap box should remain closed when not attended, and secured with a padlock if in 

an area with any public access. A traffic cone or small bucket is used to plug the upstream end of 

the pipe at the weir and reduce flow into the box when it is being checked. 

Debris screens are placed upstream of the fyke net mouth to prevent clogging of the fyke net, 

pipe, and live box by excessive debris accumulation. Debris screens are constructed using two t-
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.5 

posts with hardware cloth secured on the upstream side. The hardware cloth should only extend a 

few inches below the water surface so only debris floating on top of the water is captured. 

Lowering the debris screens too far could alter the direction of flow going into the trap. 

In addition to setting up the trap, a hobo temperature logger is set up to measure stream 

temperature. The temperature logger is set to collect data at 15-minute intervals and remains in 

the box through the trapping season. 

Upstream Migration Bypass 

A small section of the fencing across the channel is left open to allow for continued upstream 

access to adult Pacific lamprey and salmonids, including adult steelhead. The goal of this bypass 

is to have good flow leading up to the gap from the downstream perspective. Upstream it is 

important to place a sandbag that minimizes flow and essentially masks the area from fish 

moving from upstream to downstream. The bypass should be located far enough away from the 

fyke net mouth that it does not draw too many fish out this open way. 

Sampling Schedule 

Outmigration of coho smolts in central California typically begins in mid-March and peaks in 

mid-May (Shapovalov and Taft 1954). In Lagunitas Creek (Marin County), results from smolt 

trapping from 1983 to 1985 indicated that coho emigration begins in early April and ends in late 

June (Bratovich and Kelley 1988). Steelhead emigration generally begins in early March and 

ends by June (Bratovich and Kelley 1988). In SFAN trapping experience, outmigration has been 

observed primarily in April and May, with the peak occurring in late April to early May. Traps 

should be installed in mid-March when stream conditions allow for trap construction and no 

major storm events are forecast. Trap operations generally end in late May to early June after 

peak outmigration has occurred and coho smolt captures have diminished to only a few smolts 

per week. 

Sampling Frequency 

Traps are checked daily during the smolt trapping season. Traps are checked more frequently if 

adult steelhead are observed in or near the trap, or when storm events are predicted. Spring 

rainfall conditions are highly variable. Because of the downstream location of the traps, 

significant fluctuations in flow can effect the operation and efficiency of the trap. Olema Creek, 

Pine Gulch Creek and Redwood Creek are highly responsive, with peak runoff typically 

occurring 2-4 hours after peak rainfall. To avoid potential or excess mortality, in anticipation of 

storm events, traps are opened to allow flow through, rather than subjecting the trapped fish to 

unknown flow conditions within the box. 

During storm events when stream flow increases, the trap should be checked more frequently 

than once per day and, if necessary, the fyke net should be unzipped and the live box should be 

opened to relieve pressure and prevent the trap from blowing out. Opening the trap during storm 

events will reduce the overall trap efficiency but helps ensure the operation may be restarted 

quickly following the elevated storm flow. In general the trap should only be opened when either 

fish mortalities are likely to occur due to increased water velocities within the trap or if loss of 

equipment may occur due to high flows and debris accumulation. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.6 

Operation of Fyke/Pipe-Style Traps 

Daily trap operation will involve one or two people. Table SOP 4.3 lists supplies needed for 

checking the traps. Upon arriving at the trap, the field crew should check trap condition and 

ensure that all parts are working appropriately, particularly flow into the trap box. Fill out a data 

sheet (Appendix I) with site information, date, time, and water temperature. Check inside the trap 

box to determine approximate number of fish, and clean debris from inside of screen if 

necessary. Remove fish from trap box using appropriate nets and place them in holding buckets 

containing fresh stream water for processing. In general, sculpin should be placed in a separate 

bucket from age 1+ salmonids and salmonid fry. 

Table SOP 4.3. Pipe trap monitoring supplies. 

Number 

Needed Item 

1 short handled large square green net 

1 silver handled landing net 

2-3 small green aquarium dip nets 2 or 3 sizes 

1 data sheets, clipboard, and pencils 

5 5-gallon buckets (one or two dark in color) 

4-5 aerators with tubes, air stones, and extra batteries 

Many alka seltzer in Ziploc bag 

1 NovAqua water conditioner and fish protectant 

Many coin envelopes and filter paper in Ziploc bag 

1 gray toolbox with small scissors etc. 

1 yellow tool box for trap repairs 

1 plywood scale box w/ digital scale in black plastic box, with extra AA batteries 

1 fish rulers 

1 temp logger (to be stationed in trap) 

1 Photonic tag injector in Pelican case 

1 Photonic marking solution in small cooler 

Processing Fish 

The processing is most efficient when there is one person to weigh and measure fish and another 

to record the information on data sheets. 

Each fish that is to be weighed, measured, and/or marked should be sedated using carbon dioxide 

to facilitate handling and minimize stress to the fish. Fill a clean 5-gallon bucket (white color 

works best) with a couple inches of fresh stream water and add a half of an Alka-Seltzer® tablet 

(use only plain, unmedicated). The Alka-Seltzer® adds carbon dioxide to the water, effectively 

slowing the fish down and sedating them. Place no more than two fish at a time into the treated 

water and wait until they are adequately sedated. This is typically when the fish are sluggish 

enough for easy handling but before they begin to turn over. If fish do turn over they should be 

processed and/or returned to an aerated holding bucket immediately. More Alka-Seltzer® can be 

added if necessary, but be conservative (no more than a quarter tablet at a time) and monitor fish 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.7 

closely if the dosage is increased. It may be necessary to change the water periodically, 

particularly on hot days and when processing large numbers of fish. 

Salmonids are identified to species and life stage (fry, parr, presmolt, smolt, resident, or adult), 

measured (fork length is measured nose to fork of caudal fin) to the nearest mm, and weighed to 

the nearest 0.01 g using an electronic scale. Non-salmonid fish and other aquatic species should 

also be identified, aged if possible, measured, and weighed. Age 1+ steelhead and coho are 

separated into the following morphological categories: smolt (faint or absent parr marks, silver 

body, deciduous scales, black fin margins), parr (smaller size, parr marks present), and pre-smolt 

(intermediate characteristics; Bratovich and Kelley 1988; Nelson 1994). Occasional runback 

steelhead spawners are trapped on their way back out to sea; they are generally >40-cm long and are 

classified as adults. Steelhead which are smolt-sized or larger with no smolt characteristics, and 

which exhibit rainbow trout characteristics are classified as residents. Any mortality or injury is 

recorded, as well as the probable cause of death. In general, coho measuring more than 70 mm in 

the spring are assumed to be one year old and potential smolts. Smolts undergo physical change 

in their body, becoming silvery, and developing black tips on their caudal fin (this is true of both 

coho and steelhead). Smolts also have looser scales, and are losing their parr marks and spots. 

While descriptions can be made, the judgment between smolt and presmolt is truly based on 

appearance of the fish and determination in the field. At the downstream monitoring locations, it 

is much easier identify smolt because the fish have fully transitioned. Life stage classification by 

length may be delineated in the future by using length frequency histograms. The corresponding 

age classes will be verified by scale samples and used to determine age-length relationships. 

Mark/Recapture Techniques 

Mark/recapture methods will be used to estimate trap efficiency and smolt population size, and 

determine biotic information on outmigrating smolts. Daily, no more than 30 smolts (or 50% of 

the catch that day) of each species (coho and steelhead) will be anesthetized with carbon dioxide, 

weighed, measured and marked with small but identifiable fin clips or dye on fins using a 

needleless injector. Marked smolts will be released immediately in an open trap box at a 

predetermined site no more than 200 m above the trap site. Mark combinations will be alternated 

weekly. All adults, parr, fry, and recaptured smolts will be released immediately after 

measurement in low velocity areas below the trap. 

Studies using similar methods have demonstrated little marking mortality and no fish will be 

held for retention or survival tests (Thedinga et al. 1994). A study using the same methodology 

on five northwestern California streams revealed that trap mortality was less than 1% for smolts 

and less than 3% for fry (Manning 2001). The highest mortality rates were associated with high 

flow. Trap operations will be suspended if either smolt or fry mortality exceeds 5% during a oneweek period. 

Processing 1+-Aged Fish 

A random sub-sample of steelhead parr, coho and steelhead presmolts, coho and steelhead 

smolts, and steelhead residents are measured and weighed each day for development of biotic 

condition information. This sub-sample is normally 10 of each species; however, all smolts 

anesthetized for mark/recapture purposes, should also be weighed and measured. Sub-samples 

are obtained by taking blind scoops out of the holding bucket with a small aquarium dip net. All 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.8 

steelhead parr, coho and steelhead presmolts, coho and steelhead smolts, and steelhead residents 

are identified and counted. 

Any adult steelhead encountered in the trap should be released downstream immediately. 

Estimate the size of the adult, but do not attempt to weigh or measure it. Use a landing net if it is 

available to transfer the adult steelhead from the live box to the stream. 

Processing Young of Year Salmonids 

After the 1+ salmonids and other larger fish have been processed and released, carefully net out 

all salmonid fry from the trap box. Use caution with the larger nets to avoid crushing fry with the 

rim of the net. All fry are identified to species and counted. Daily, random sub-samples of 10 

coho fry and 10 steelhead fry are measured (fork length to the nearest mm). Sub-samples are 

obtained by taking blind scoops out of the holding bucket with a small aquarium dip net. 

Although identification of salmonid fry can be difficult, it is important that the species (coho and 

steelhead) are differentiated. As long as both species are present, it is rather simple to see the 

distinct differences. Problems may arise when only one or the other is present. The best reference 

for field identification between species is the “Field Identification of Coastal Juvenile 

Salmonids” (Pollard et al 1997). This reference includes color photographs and descriptions of 

each species at the 40 to 50 mm size. In general, the coho at all sizes have a pinker hue, while 

steelhead have an orange or yellow hue. In addition, the dorsal and anal fins of coho are longer, 

sickle-shaped, and more pointed than those of steelhead. For the few individuals that can’t be 

identified by overall appearance or shape of fins, counting the anal fin rays can differentiate 

between coho and steelhead fry. 

Processing Other Species 

Although not a focal effort of this monitoring program, all other species encountered during this 

trapping effort are documented. Daily, random sub-samples of 10 individuals of each species are 

measured and fish over 40 mm are weighed. Sub-samples are obtained by taking blind scoops 

out of the holding bucket with a small aquarium dip net. All others should be counted and 

released downstream. 

Fish Recovery and Release 

After processing each fish, it is placed in an aerated recovery bucket, keeping larger sculpin in 

separate buckets to avoid predation on smaller fish. The recovery bucket should be a different 

color (preferably blue or other dark color) or located away from the holding buckets to avoid 

mixing releasable fish with those that have not been processed. The dark-colored bucket allows 

the fish to darken their color, which is beneficial when they are released back to the pools. Fish 

in the recovery bucket should be monitored to insure sedated fish recover fully before being 

released. 

Fish Mortality 

In case of fish mortality during trapping or processing, scales and/or tissue samples will be 

collected in concurrence with current permit requirements (refer to SOP 6). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.9 

End-of-Season Procedures 

Trap operations close in early June, which corresponds with reduced stream flow and very low 

numbers of fish passing through the trap. The fyke net, live box, pipe, and fencing should be 

completely removed and returned to storage. The sandbags full of gravel should be removed 

from the stream channel and emptied. The sandbags may last a second season, but do decay with 

each use. 

Data Management 

The following data management procedures should be followed. Record and verify data values, 

both observed and measured. Field datasheets should be completed, and the collected data 

entered into electronic databases. Crew members should schedule and perform regular data 

transfer and backup, as well as conduct regular data verification and correction. Finally, crew 

members should ensure that field forms, field notebooks, and other hardcopy records are secure, 

readily available for viewing and reproduction upon request or at the end of the field season. For 

detailed data management procedures refer to SOP 8. For data analysis and reporting 

requirements refer to SOP 10. 

Logistics 

Annual Workload and Field Schedule 

The spring outmigrant smolt traps need to be checked on a daily basis (including weekends) over 

a two- to three-month period between March and June. Checking traps at the three existing sites 

takes six hours. Field staff should also allocate five hours per week for data management. 

Staffing Requirements 

It is expected that this monitoring can be accomplished with two field staff to check all 

downstream traps on a daily basis. Initial trap construction and removing traps at the end of the 

season will require at least three field staff. Field staff should consist of one fisheries ecologist 

and one additional field crew member. Recruiting volunteers to assist with the trapping and 

processing has been done in the past and may continue into the future. 

Literature Cited 

Barrineau, C. E. and S. P. Gallagher. 2001. Noyo River fyke/pipe trap checking protocol. Report 

FB-07. California Department of Fish and Game, Steelhead Research and Monitoring 

Program, Fort Bragg, California. 

Bratovich, P. M. and D. W. Kelley. 1988. Investigations of salmon and steelhead in Lagunitas 

Creek, Marin County, California. Volume I. Migration, spawning, embryo incubation and 

emergence, juvenile rearing, emigration. Marin Municipal Water District. Marin County, Corte 

Madera, California. 

Gallagher, S. P. 2000. Results of the 2000 Steelhead (Oncorhynchus mykiss) fyke trapping and 

stream resident population estimations and predictions for the Noyo River, California with 

comparison to some historic information. Report FB-03, September 2000. California 

Department of Fish and Game, Steelhead Research and Monitoring Program, Fort Bragg, 

California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 4.10 

Manning, D. J. 2001. Carrying capacity and limiting habitat analysis for coho salmon 

(Oncorhynchus kisutch) in streams of northwestern California. Master’s Thesis. Humboldt 

State University, Arcata, California. 

Nelson, J. 1994. Coho salmon and steelhead habitat and population surveys of Scott Creek, Santa 

Cruz County, 1993. California Department of Fish and Game, Region 3, Inland Fisheries, 

Sacramento, California. 

Pollard, W.R., G.F. Hartman, C. Groot, P. Edgell. 1997 Field Identification of coastal juvenile 

salmonids. Department of Fisheries and Oceans and Weyerhaeuser. Harbor publishing, 

Madeira Park, BC Canada. 

Shapovalov, L., and A. C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo 

gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with specific reference to 

Waddell Creek, California, and recommendations regarding their management. California 

Department of Fish and Game Fish Bulletin 98. 

Thedinga, J. F., M. L. Murphy, S. W. Johnson, J. M. Lorenz, and K. V. Koski. 1994. 

Determination of salmonid smolt yield with rotary-screw traps in the Situk River, Alaska, to 

predict effects of glacial flooding. North American Journal of Fisheries Management 

14:837–851. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.1 

SOP 5. Spawner Survey 

Version 3.5 

Revision History Log 

Prev. Version 

# 

Revision Date Author Changes Made Reason for 

Change 

New 

Version #

 Jan. 2007 Marcus 

Koenen 

Created this SOP 

to focus on 

Spawner Survey. 

Reduce 

redundancy 

among 

protocols and 

SOP 

3.2 

 3.2 Mar. 2007 Michael 

Reichmuth 

Review SOP Update protocol 

to current 

survey methods 

3.2MR 

3.2MR May 2008 Sarah 

Carlisle 

Updated 

datasheets and 

field protocols 

 3.3 

3.3 May 2008 Erin Brown Mike’s suggested 

changes 

Sections: 

Overview, 

carcasses, data 

management, 

maps 

3.3 

3.3 August 2008 Michael 

Reichmuth, 

Marcus 

Koenen 

Reviewed and 

revised 

Clarification 3.4 

3.4 September 

2008 

Dawn 

Adams 

Formatting Peer review 3.41 

3.41 December 

2008 

Michael 

Reichmuth 

Minor Edits For peer review 3.42 

3.42 November 

2009 

Michael 

Reichmuth 

Added Lit Cited Peer review 

response 

3.43 

3.43 February 

2010 

Michael 

Reichmuth 

Final edits for 

final submittal 

Response to 

editors and 

internal review 

comments 

3.5 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.2 

Figures and Tables 

Page 

Table SOP 5.1. Location of 14 spawner survey reaches in San Francisco Bay Area 

Network parks. ..................................................................................................................... SOP 5.3

Table SOP 5.2. Equipment list for spawner surveys. .......................................................... SOP 5.4

Figure SOP 5.1. Illustration of a male adult coho salmon showing fork length and 

the location of the operculum .............................................................................................. SOP 5.7

Figure SOP 5.2. Cross section of a redd .............................................................................. SOP 5.7
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.3 

Overview 

This standard operating procedure (SOP) details the methods used to determine long-term trends 

in distribution and abundance, size (length and weight) of spawning coho salmon, monitoring 

objective 1. Typically, surveys are conducted between late November and early February. 

Timing of surveys, however, is highly dependent upon the precipitation accumulations during the 

season. Surveys are conducted approximately every week, although storms and high stream 

flows often dictate less frequent surveys. All salmonid redds, live fish, and carcasses are counted. 

Although the surveys are focused on coho spawning, some information on steelhead spawning is 

also gathered due to the overlap in spawning periods for both species. 

Study Area 

Spawner surveys are conducted in select High Priority streams and associated tributaries in 

Marin County which currently contain populations of both coho salmon and steelhead including 

Olema, Pine Gulch, and Redwood Creek (table SOP 5.1; for detailed directions and maps, see 

SOP 9. Sampling Site Descriptions). One reach is also sampled on Cheda Creek. Reaches are 

typically 2–4 km sections of streams. 

Table SOP 5.1. Location of 14 spawner survey reaches in San Francisco Bay Area Network parks. 

Creek 

Number of 

Spawner 

Reaches 

Start/Stop Points 

(for details see SOP 9) 

Olema Creek 7 1 km above the confluence with Lagunitas Creek to the 

Highway 1 culvert at milepost 19.94 

Pine Gulch Creek 3 Olema-Bolinas Road Bridge to 2 km above the Texeira Ranch 

Redwood Creek 3 Pacific Way Bridge to a small waterfall within Mt Tamalpais 

state park just upstream of monument tag #74 

Cheda Creek 1 A total of about 1.2 km is typically surveyed, including a 0.8 km 

reach below the fish passage improvement and 0.4 km above. 

Sample Design 

The sample design is described in the protocol narrative. Sample sites are described in SOP 9. 

Field Methods 

Field Season Preparations and Equipment Set Up 

Prior to the rainy season, staff should check all access points for spawner survey reaches, and 

walk reaches to insure that aluminum monument markers are present. Where necessary, markers 

should be replaced, and the monument log should be updated to reflect locations of each tag. The 

tags, stamps to mark the tags, and aluminum nails are contained within the fisheries program 

garage at Point Reyes National Seashore (PORE). All monument tags are spatially located with 

UTM coordinates. Replacement or relocation of any tag (e.g., a fallen tree) should include an 

update of the tag UTM coordinates. Tags are lost through a variety of means including fallen 

trees, animal gnawing, and even tree growth (we have observed alders with the last bit of the tag 

sticking out of the bark). Surveys to replace tags should be conducted annually prior to the 

spawner surveys, with UTM coordinated collected at the time of replacement. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.4 

Field staff should check waders, repairing the leaky ones, and make sure there is an adequate 

supply (at least 15) of wading rods marked to the nearest centimeter. These rods are used for 

measuring fish and visibility, as well as probing undercut banks and helping the surveyor balance 

on the uneven substrate. 

Most importantly, spawner survey kits should be checked to insure that all supplies are included 

for the survey. These kits should also be refilled following each field survey event. Each kit 

should include equipment in table SOP 5.2. 

Table SOP 5.2. Equipment list for spawner surveys. 

Number Needed Item 

1 Clipboard and waterproof copies of the datasheet 

1 Species identification cards 

3 Pencils 

1 List of monument tags 

1 Polarized sun glasses* 

1 Hole punch 

1 Tweezers 

1 Knife 

1 Coin envelopes 

1 Filter paper 

20 Plastic bags 

1 Biodegradable survey flagging 

3 Sharpie permanent markers 

*Recommended, although not included in most kits. 

Timing of Field Surveys 

As the rains begin, staff should ready themselves for the winter survey season. Normally the 

salmonid watersheds need 5–7 inches of rain within a 30 day period to initiate flows necessary 

for fish to swim upstream. Often spawner response is concentrated in one or two storm related 

flow or freshet events. In particular, Redwood Creek is cut off from ocean access by a sand bar. 

Fish cannot enter the system until flows are great enough to breach the bar. Typically the flows 

required to breach the sand bar on Redwood Creek, or allow fish to migrate up Olema or Pine 

Gulch Creeks, are described as the first flush (a water quality term indicating that the hydrologic 

network within the watershed is connected and flowing). Surveys should be initiated with the 

onset of rains to determine exactly which flow and when fish are able to access these smaller 

coastal watersheds. Based on female redd residency times watersheds should be surveyed weekly 

to accurately capture the timing of spawning (Burton et al. 2002; van den Berghe and Gross 

1986). Because the surveys are confounded by environmental factors (stream discharge and 

turbidity) the surveys are often less frequent. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.5 

Conducting Field Spawner Surveys 

Once program biologists determine survey dates, the staff will coordinate with local volunteers 

to assist surveys. For safety, teams of at least two people should be assigned to each survey 

reach. Each team is provided with a spawn survey kit, datasheets, clipboard, map, and list of 

monument tags within each reach. 

Each team begins the survey from the downstream end of a predetermined reach and walk 

upstream. Water clarity should be measured at the start of each survey using the 2-m survey rod. 

Water clarity should be measured by lowering the survey rod into the nearest pool until the end 

of the survey rod is barely visible. For the purpose of this project water clarity is defined as the 

distance in centimeters from the water surface to the end of the survey rod and gives us an 

estimate of our survey efficiency when visibility is limited. 

To conduct survey, team members walk in the channel and on the banks, avoiding pool tailouts 

and redds. Inspect the stream for live fish and carcasses by probing banks, woody debris, and 

pools with a 2-m survey rod (see section on equipment). It is important to remain observant and 

use your senses while conducting the survey. Look upstream ahead of you, fish may seek cover 

when observers are as much as 30 m downstream. Females splash when constructing redds and 

fish can be heard migrating through riffles. Carcasses often emit a pungent odor and may have 

been carried onto the stream bank by a scavenger. The techniques for collecting live fish, 

carcass, and redd data are described below. All information should be entered into the Spawner 

Survey and Redd Survey Datasheets (Appendixes J and K). 

Recording Location 

To monitor the distribution of spawning within a watershed, the location of all live fish, 

carcasses, and redds must be recorded. These locations are recorded in reference to the 100 m 

stream section markers that are located along the mainstem of Olema, Pine Gulch, Redwood, and 

Cheda Creeks (see SOP 9). 

When recording spawner survey information use the last two or three digits of the code (the 

hundreds of meters upstream). Record location of an observation as these last two or three digits, 

on the closest downstream monument tag (see SOP 9), plus the estimated distance upstream. For 

example, if a redd is found 40 m above tag OL 01 48 you would note the location as 48 + 40. 

Each row on the datasheet should contain the location of a single observation (either a live fish, 

carcass, or redd). If there are multiple observations of live fish or carcasses at a single location, 

repeat the location information on each new row. All redd observations should receive a unique 

location in order to eliminate the possibility of duplicate site locations. 

If you cannot locate a tag within 100 m, please note your approximate location in the comments 

section of the datasheet. If large portions of a survey reach have missing tags, clearly note the 

missing tag numbers and reference the live fish, carcass, and redd observations to permanent 

landmarks such as bridges and buildings. Spawner kits for each survey reach should contain a 

map and a list of tag numbers and locations for that reach. 

Species and Sex Identification 

Identifying the species and sex of all observations is necessary to accurately determine the total 

number of returning coho and steelhead adults as well as the sex ratio of returning salmonid 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.6 

adults. Place a check mark in one of the three categories in the species column of the datasheet. 

All observers will be trained in species identification. However, it is often difficult to identify 

spawning fish in the field. Use the ? option if you are unable to identify the species. A 

comprehensive spawning fish identification key is provided in each spawner survey kit. This 

summary of coho and steelhead ID characteristics should be carried in the field by all survey 

teams. 

Most coho salmon are three years old at spawning. However, a variable proportion of precocious 

two year old males also return to spawn. These smaller males are commonly referred to as 

“jacks”. Age can not be accurately determined without carefully analyzing annual growth rings 

on scales. However, most jacks are less than 50 cm (20 in) long and are much smaller than the 

three-year olds. 

Live Fish 

Note the sex and approximate length to the nearest 5 cm of all live fish. If you cannot positively 

identify a fish’s sex, use the ? option. Surveyors should make every effort not to disturb 

spawning fish. Actively spawning fish can be observed safely from a vantage point on the bank. 

Carcasses 

For all intact carcasses, note the sex and measure the fork length (figure SOP 5.1) (tip of the jaw 

to fork of the tail) in centimeters using a graduated survey rod. To confirm the gender of the 

carcass, slice open the body cavity beginning at the anus and inspect the gonads. Note the 

approximate number of eggs retained by the females. In the comments section of the datasheet, 

note the general condition of the carcass (e.g., fresh intact or skeleton). For partial carcasses or 

carcass fragments do your best to ID species and sex based on whatever features are present 

(e.g., tail, anal fin, color of gums). Record estimated lengths of partial carcasses in the 

comments. 

In addition to counting and noting the location of carcasses, we are also interested in collecting 

tissue samples and scales for genetic and age analysis. The removal of tissue will also serve as a 

mark to prevent double counting of carcasses in subsequent surveys. The genetic analyses will be 

performed by researchers at the National Marine Fisheries Service Genetics Laboratory. Inspect 

the carcass for holes punched in the operculum (figure SOP 5.1) or any hatchery marks such as 

adipose and maxillary clips. If the fish is already marked, note the number of punches from one 

side of the fish in the datasheet column labeled Recap Code. If the fish has any hatchery marks, 

cut off the upper portion of the head from the tip of the snout to behind the eye and store it in a 

zip lock bag for future analysis. 

Redd Identification 

Program staff will train observers in redd identification. After storms, areas of excavated gravel 

are often difficult to distinguish from the surrounding riffle and females may construct numerous 

“false” redds before choosing a suitable spawning site. Use the ? option in the datasheet column 

labeled Def (definite) / ? if you are not certain that a feature is actually a redd. All definite redds 

should have a distinct pit and tailspill feature . If possible identify the species that constructed the 

redd. This is not always possible since coho and steelhead spawning periods overlap and redd 

construction may look similar. Use the survey rod to measure the total length (top of pit to end of 

tail spill) and average width in meters (figure SOP 5.2). Measure new redds only if redd 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.7 

excavation by spawning adults is completed. Re-measure new redds observed on the previous 

spawning survey to ensure an accurate post redd excavation measurement was recorded. Do not 

step on redds. The eggs are typically buried beneath the tail spill. Each redd should be marked 

with plastic or biodegradable survey flagging to prevent double counting and trampling in 

subsequent surveys. Write the date, location, and species on a piece of flagging and tie it to 

vegetation (a few feet above the water) near the redd. If there are numerous redds at a particular 

location, assign a location and flag for each redd observed. If a fish is observed holding on a redd 

location, record the species and number of fish holding on the redd. A print out of the number of 

redds and redd locations from the previous week will be carried on each survey to decrease 

double counting of redds and to determine the number of new redds in areas of superimposition. 

If there is flagging at the location from a previous survey conducted this season, hang a new flag 

only if there has been recent excavation. Please make notes in the comment section if numerous 

redds are observed at the same location. 

Figure SOP 5.1. Illustration of a male adult coho salmon showing fork length and the location of the 

operculum (adapted from Lusch 1985). 

Figure SOP 5.2. Cross section of a redd (from Sandercock 1991). 

Post-Collection Procedures 

Field sheets should be collected by program staff at the end of each survey. Because these sheets 

are often wet, staff should insure that the information on the sheet is legible. Surveyors are 

requested to put contact information on the sheet, so any questions can be followed up quickly. 

Direction of Flow 

Undisturbed Substrate 

Tailspill 

Egg Deposition Site 

Pool 

Riffle 

Pit 

Operculum 

Location of Marking

Fork Length 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.8 

End of Season Procedures 

Following each survey, and at the end of the season, field staff should keep a table showing 

results of each watershed survey. Typical reporting should summarize the peak number of fish 

counted during surveys. Because the same fish may be counted in multiple surveys, results are 

generally not additive and addition of totals between surveys should not be included as part of 

this preliminary reporting process. If possible, staff should designate a species for all redds in 

which the species field was not defined. This can be determined using both the redd size 

information and the date in which the redd was first observed. In general steelhead redds are 

smaller than coho redds and most of the steelhead spawning occurs during the end of the coho 

spawning period. 

Field kits should be cleaned and stored. An inventory of survey supplies should be completed for 

future reorder needs. 

Data Management 

The following data management procedures should be followed. Record and verify data values, 

both observed and measured. Field datasheets should be completed, and the collected data 

entered into electronic databases. Crew members should schedule and perform regular data 

transfer and backup, as well as conduct regular data verification and correction. Finally, crew 

members should ensure that field forms, field notebooks, and other hardcopy records are secure, 

readily available for viewing and reproduction upon request or at the end of the field season. See 

also SOP 8 (Data Management). Refer to SOP 10 for analysis and reporting of results. 

Logistics 

Annual Workload and Field Schedule 

Spawner survey times are variable throughout the winter months with surveys performed 

between winter storm events. In general surveys are performed on a weekly basis starting with 

the first major rain event in late November or early December and ending in early February. At 

least one survey should be performed on each high priority watershed between storm events 

which often requires performing surveys on weekends and holidays. Surveys typically require 

two to four hours to complete and field staff should allocate four hours per week for data 

management. 

 

Staffing Requirements 

It is expected that this monitoring can be accomplished with four to eight field staff depending 

on the length of stream to be surveyed. Field crews must consist of at least one fisheries 

biologist, two additional field crew members, and at least three volunteers. Recruiting volunteers 

to assist with spawner surveys is essential to ensure proper coverage and safety. Volunteers 

should be scheduled for field surveys at least one to two days prior to conducting each survey. 

Literature Cited 

Burton, K., L. Lowe, and H. Berge. 2002. Cedar River Chinook salmon (Oncorhynchus 

tshawytscha) redd survey report, 2001: Spatial and temporal distribution of redds, carcass 

age, sex and size frequency distribution, redd residency duration and the incidence of redd 

superimposition on incubating Chinook redd mounds. Seattle Public Utilities, Seattle, WA. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 5.9 

Lusch, E. 1985. Comprehensive guide to western game fish. Windsor Press. Online. 

(http://www.krisweb.com/krisweb_kt/trtour/coho.htm) accessed September 2004. 

Pollard, W. R., C. Groot, and G. F. Hartman. 1997. Field identification of coastal juvenile 

salmonids. Harbour Publishing Company, Madeira Park, British Columbia. 

Sandercock, F. K. 1991. Life history of coho salmon (Oncorhynchus kisutch). Pages 395–446 in

C. Groot and L. Margolis, editors. Pacific salmon life histories. UBC Press, Vancouver, 

British Columbia. 

Van den Berghe, E. F., and M. R. Gross. 1986. Length of breeding life of coho salmon 

(Oncorhynchus kisutch ). Canadian Journal of Zoology 64:1482–1486. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.1 

SOP 6. Permit Requirements 

Version 2.1 

Revision History Log 

Prev. 

Version # 

Revision 

Date 

Author Changes Made Reason for Change New 

Version #

1.0 Mar. 2007 Michael 

Reichmuth 

Review SOP Make sure the 

protocol reflects 

current 

methodology 

1.1 

1.1 May 2008 Erin Brown Table of content, 

overview, permitting 

requirements and 

reporting, added scale 

and tissue stuff, and 

references 

Work list changes 1.2 

1.2 August 

2008 

Brannon 

Ketcham 

Edit and review Updates and 

clarification 

2.0 

2.0 Sept 2008 Dawn 

Adams 

Formatting Peer review 2.01 

2.01 December 

2008 

Michael 

Reichmuth 

Minor edits For peer review 2.02 

2.02 November 

2009 

Micheal 

Reichmuth 

Added Lit Cited Peer review 

response 

2.03 

2.03 February 

2010 

Michael 

Reichmuth 

Final edits for final 

submittal 

Response to 

editors and internal 

review comments 

2.1 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.2 

Figures and Tables 

Page 

Table SOP 6.1. Permit requirements.................................................................................... SOP 6.4

Figure SOP 6.1. Location of scale and tissue samples and size of fin clip required 

for a 90 mm fish ................................................................................................................... SOP 6.6

Figure SOP 6.2. Illustration of male coho salmon showing body locations for 

scale and tissue sample collection........................................................................................ SOP 6.7

Figure SOP 6.3. Example of a tissue sample envelope and field descriptions. ................... SOP 6.7
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.3 

Overview 

This SOP describes the permitting process that is required in order for the NPS to conduct coho 

salmon and steelhead trout monitoring within the SFAN network. 

The National Park Service (NPS) is authorized by the National Marine Fisheries Service 

(NMFS) under Section 10 of the Endangered Species Act (ESA; permit #1046 modification #2) 

to take adult and juvenile federally endangered coho salmon (Oncorhynchus kisutch), threatened 

steelhead (O. mykiss), 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/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 

utilization, 6) adult salmonid spawner escapement monitoring, and 7) juvenile salmonid rescue 

and relocation. 

All principal investigators are required to obtain a California Department of Fish and Game 

(CDFG) scientific collecting permit (SCP) 2081(b), prior to sampling for coho salmon, 

steelhead, California red-legged frog (Rana aurora draytonii), California freshwater shrimp 

(Syncaris pacifica), and tidewater goby (Eucyclogobius newberryi). Although California redlegged frogs, California freshwater shrimp, and tidewater gobies are not the focus of the I&M 

program monitoring efforts, this permit is necessary for the incidental catch of these organisms 

during coho and steelhead monitoring. The CDFG permit would apply 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. 

In addition, the NPS is authorized under U.S. Fish and Wildlife Service (USFWS) permit # PRT702631 (subpermit #GGNRA-2) to take federally listed California red-legged frogs, California 

freshwater shrimp, and tidewater gobies in conjunction with salmonid presence/absence surveys 

and population studies for the purpose of enhancing the salmonid survival. All principal 

investigators must be approved by USFWS prior to conducting salmonid surveys. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.4 

Permit Types 

Endangered Species Act Section 10 Permit 

NMFS has authorized the NPS to take federally endangered coho salmon, threatened steelhead, 

and Chinook salmon associated with fish population and habitat studies. The current permit is 

valid from November 30, 2006 through February 29, 2012. It is suggested that researchers apply 

for the Section 10 permit one year in advance of proposed activities (table SOP 6.1). 

The NPS is only authorized to take a certain number of coho, steelhead and Chinook salmon, at 

each life stage, for each of its monitoring programs. For the authorized amounts of annual take of 

ESA-listed salmonids please refer the Section 10 permit. A copy of the permit will be located in 

the glove box of the fisheries field vehicle at all times, as well as in the file cabinet in fisheries 

division of the Natural Resources office in Point Reyes National Seashore (PORE). All new 

principal investigators must submit a written request to NMFS prior to conducting monitoring 

activities. 

CDFG Scientific Collecting Permit 

The SCP authorized by the CDFG is required for all primary investigators. A SCP application 

must be obtained by each principal investigator prior to conducting monitoring activities. The 

permit is valid for two years of study and must be renewed on a biannual basis (table SOP 6.1). 

Applications for the permit should be submitted to the CDFG at least eight months prior to the 

expiration of the most current permit as processing can take up to this amount of time. The most 

current permit is valid through the end of 2012. Copies of the permits will be located in the 

fisheries field vehicle at all times as well as in the fisheries office. 

U.S. Fish and Wildlife Service Section 10 Permit 

Due to the potential for incidental catch of California red-legged frogs, California freshwater 

shrimp, and tidewater gobies, which can occur during regular monitoring efforts, the NPS is 

required to possess a valid Section 10 permit issued by the USFWS under the ESA to handle 

these organisms. Individuals on the project team must meet training requirements to be added to 

the permit. A resume including all pertinent training and work experience must be submitted to 

the USFWS for each principal investigator prior to conducting monitoring activities. The 

USFWS Section 10 permit is managed by the GOGA Aquatic Ecologist. The current permit 

expires in May of 2012. 

Table SOP 6.1. Permit requirements. 

Permit 

Who the 

Permit Covers Application Time Frame Reporting Cycle 

NMFS Section 10 

Permit 1046 

Principal 

Investigator 

12 months in advance, valid 

until February 24, 2012 

Annually by May 1 

CDFG scientific collection 

permit 2081(b) 

Individuals 8 months in advance, 

permits issued for 2 years 

Bi-annually, at the end of 

permitting cycle 

USFWS Section 10 

Permit 

Principal 

Investigator 

90 days in advance, permit is 

valid until May 12, 2012 

Annually by January 31 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.5 

Permit Reporting Requirements 

NMFS Section 10 

The NMFS requires annual ESA permit reports and a final report, which is to be submitted at the 

end of each Section 10 permitting period. All reports are conducted online and due to the NMFS 

on May 1. 

CDFG Scientific Collection 

The CDFG requires that a Report of Specimens Collected or Salvaged (RSCS) be submitted 

within 30 days of the expiration of the SCP permit. Permits are valid for two years; therefore, 

reports will be submitted on a bi-annual basis. Each individual to whom a SCP is issued must 

provide their own RSCS. Even if the applicant is not renewing a permit, he is required to submit 

a final report within 30 days of the expiration of the permit. 

For detailed directions on how to complete an RSCS refer to the CDFG website: 

www.dfg.ca.gov/licensing/pdffiles/SC_REPT.xls. The CDFG also requires records of field 

observations of threatened, endangered, or special concern species to be submitted to the Natural 

Diversity Data Base. The California Native Species Survey Form and instructions for completing 

it are posted on the CDFG website at www.dfg.ca.gov/whdab/html/animals.html. 

USFWS Section 10 

An annual report of activities shall be submitted to the Recovery Permit Coordinator at the 

Sacramento USFWS Office by January 31 of each year. The report should include (1) an 

introduction addressing the reasons and objectives for taking the species; (2) methodologies used 

for data collection and analysis; (3) a results section that summarizes the data collected on any 

federally listed species while conducting monitoring efforts under the permit; and (4) a 

conclusion that provides recommendations for the recovery of the species. 

Collecting Scale and Tissue Samples 

Scales and/or tissue samples will be collected from all juvenile salmonid mortalities and adult 

carcasses found during monitoring activities. Tissue collection will be conducted in a manner 

consistent with the guidelines of the NMFS Pacific Southwest Research Center, Genetics 

Laboratory. 

Scale Samples 

When sampled for scales, salmonids should be sedated using carbon dioxide (Alka-Seltzer) to 

facilitate handling and minimize stress to the fish. Using the open blade of a pair of surgical 

scissors, gently scrape “against the grain” to collect scales from the side of the fish, above the 

lateral line and slightly behind the dorsal fin (figure SOP 6.1). Collect three to six scales from 

each fish since some scales may be difficult to age due to false annuli, regeneration, and other 

anomalies (Collins 2003). Wipe scales off blade of scissors onto a piece of blotter and place in 

sample envelope. Avoid scraping off too much of the protective slime coating, and be careful not 

to take too many scales from one spot on the fish. 

Fish should be allowed to recover in a recovery bucket containing a fish conditioner to ward off 

potential of infection associated with the scale sampling. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.6 

Figure SOP 6.1. Location of scale and tissue samples and size of fin clip required for a 90 mm fish; 

clipped material should be at least as big as illustrated above. A larger fish would have a smaller 

proportion of caudal fin clipped.

Juvenile Tissue Samples (from Draft NMFS Tissue Collection Protocol) 

Fin clips are used for genetic analysis of fish. This work is conducted primarily through the 

NOAA-Fisheries Laboratory in Santa Cruz, California. Tissues have been used to develop the 

population genetics structure of salmonids in California. In particular, collection of tissue 

samples from coho salmon occurring in previously undocumented watersheds (Pine Gulch 

Creek) has been used to determine the expansion of source populations to new watersheds. 

Tissue samples should be collected from the upper caudal fin of the fish. Scissors should be used 

to clip a small portion (approximately 1 cm2) of the upper caudal fin (figure SOP 6.1). Under 

most circumstances, tissue samples should not be collected from fish less than 90 mm fork 

length. Special circumstances, including juveniles documented in a new watershed, may 

necessitate sampling of smaller fry. 

Place fin clip on blotter paper and place in envelope. Samples need to dry; sun drying in the field 

works best and can be done quickly. Fungus and bacteria become a problem if tissue samples are 

not adequately dried within 8 hours from time of collection. 

Adult Tissue Samples 

Tissue is removed from both opercula (gill covers) with a hole punch. The number of punches 

(1–4) corresponds to the survey number. The Project Leader will determine the number of 

punches prior to beginning field work. Record the number of punches in the “Mark Code” 

column of the data sheet. Use the tweezers to remove the punches and place all collected tissue 

in a folded piece of filter paper. Scale samples should be collected from all fresh fish (fish with 

both eyes clear) that have not been mauled by predators. Use the tweezers to remove 5 to 10 

scales from the side of the fish between the lateral line and dorsal fin (figure SOP 6.2). Rinse the 

hole punch and tweezers in the stream before and after sampling each carcass to prevent cross 

contamination between samples. Because fungal growth degrades the quality of the samples, the 

samples should be thoroughly air-dried after the survey, preferably in the sun, and stored in a 

dessicator. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.7 

Figure SOP 6.2. Illustration of male coho salmon showing body locations for scale and tissue sample 

collection (adapted from Lusch 1985).

 

Sample Storage and Processing 

For scale and tissue samples, rinse scissors thoroughly before and after each sample to prevent 

cross-contamination. Place each sample on a piece of blotter paper approximately 2 cm x 4 cm, 

folded over, so the sample is sandwiched between the two halves, and insert into a sample 

envelope. Scale and tissue samples from the same fish should be placed on separate pieces of 

blotter paper, but may be put into the same envelope. Figure SOP 6.3 is an example of the data 

form on the sample envelope and field descriptions. 

Figure SOP 6.3. Example of a tissue sample envelope and field descriptions. 

Upon returning from the field, all scale and tissue samples should be thoroughly air dried, 

preferably in the sun. After drying, samples can be stored in an airtight container containing 

desiccant. Samples should be left in their original field collection envelopes until further 

processing. If envelope replacement is necessary, make sure to copy all information onto the new 

envelope and double-check for transcription errors. Information from each envelope should be 

ID Spec 

Stream Leng 

Reach Wght 

Date Sex 

Coll Note 

ID: Location number for Spawner Surveys. 

 Predetermined ID for all other surveys. 

Stream: Stream name or code 

Reach: Reach name/number, location description, or 

monument tag #

Date: Date (mm/dd/yy)

Coll: Collector’s initials

Spec: Species/age code 

Leng: Fork length in mm 

Wght: Net weight to the nearest 0.1g 

Sex: M/F for adult carcass samples (leave blank for 

juvenile salmonids) 

Note: indicate type of sample (scales, tissue, or both) and 

note information about fish 

Operculum 

Area for Tissue 

Sample Collection 

Area for Scale 

Collection

Fork Length 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

 SOP 6.8 

entered into the fish database using the Scale/Tissue Form. Record a unique sample ID # on each 

sample envelope. An example of the sample ID format is OL-03-017: the first part is a two-digit 

letter code for the stream, the second part is a two-digit number code for the year, and the last 

part is a three-digit sequential number for that stream and year. The example is for the 17th 

sample from the Olema Creek watershed in 2003. 

Tissue Sample Submittal to the NMFS Genetics Lab 

Tissue samples will be divided in half. Half of the genetic materials will be sent to the NMFS 

Genetics Laboratory in Santa Cruz, California, and half retained and archived by the SFAN 

Fisheries program. Sample collection follows NMFS protocol and is performed as part of the 

Section 10 permit 1046. 

Literature Cited 

Collins, B. W., editor. 2003. Interim restoration effectiveness and validation monitoring 

protocols, California Coastal Salmonid Restoration Monitoring and Evaluation Program. 

California Department of Fish and Game, Fortuna, California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.1 

SOP 7. Protocol Revision 

Version 1.3 

Revision History Log 

Prev. 

Version # 

Revision 

Date 

Author Changes Made Reason for 

Change 

New 

Version #

 4 June 2008 Sarah Carlisle Created SOP 7 1.0 

1.0 July 2008 Sarah Carlisle, 

Marcus 

Koenen 

Completed 

addressing 

reviewer 

comments 

 1.1 

1.1 August 

2008 

Dawn Adams Formatting Peer review 1.11 

1.11 December 

2008 

Michael 

Reichmuth 

Minor Edits For peer 

review 

1.12 

1.12 November 

2009 

Michael 

Reichmuth 

Added and 

addressed reviewer 

comments 

Peer Review 

Comments 

1.2 

1.2 February 

2010 

Michael 

Reichmuth 

Final edits for final 

submittal 

Response to 

editors and 

internal review 

comments 

1.3 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.2 

Tables 

Page 

Table SOP 7.1. Current SFAN Salmonid Monitoring Protocol documents. ....................... SOP 7.4

Appendixes 

Page 

Appendix SOP 7A: PWR Protocol Review Checklist ......................................................... SOP 7.5 

Appendix SOP 7B: Peer Review Comments to 2005/2006 Draft and Responses from 

Protocol Authors ........................................................................................................... SOP 7.9 

Appendix SOP 7C: Peer Review Comments to 2009 Draft and Responses from Protocol 

Authors ........................................................................................................................ SOP 7.26 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.3 

Overview 

This standard operating procedure (SOP) explains how to make changes to the Salmonid 

Monitoring Protocol and accompanying SOPs, and explains procedures for tracking these 

changes. San Francisco Bay Area Network (SFAN) or park staff members that edit the protocol 

narrative or any SOP need to follow this procedure to eliminate confusion in data collection and 

analysis methods. All SFAN aquatic resources staff should be familiar with this SOP in order to 

identify and use the most current methodologies. 

This SOP also contains a table listing the most current version of the protocol narrative and each 

of the SOPs. This table will provide a single reference for ensuring that the most current 

documents are being used. Also included is a section containing comments from protocol review, 

responses to those comments and approvals. 

Protocol Revision Procedures 

1. The authors of the Salmonid Monitoring Protocol Narrative and accompanying SOPs 

have made every effort to incorporate the most scientifically sound methodologies for 

collecting and analyzing fisheries data. However, all protocols require editing as new and 

different sample collection, analysis, and data management information becomes 

available. Required edits should be made as soon as they are deemed necessary and 

appropriate reviews conducted. 

2. All edits will be reviewed for grammatical and technical accuracy and overall clarity. 

Minor changes or additions to existing methods will be reviewed “in-house” by the 

SFAN aquatic professionals and other appropriate network staff. However, if a complete 

change in methods is anticipated, then an outside review is required. Subject matter 

experts familiar with fish monitoring and data analysis will be utilized as reviewers. 

3. Edits and protocol revisions will be documented in the Revision History Log that 

accompanies the Protocol Narrative and each SOP. Only changes in the Protocol 

Narrative or specific SOP that is edited will be logged. “Version numbers 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 ...). Record the previous version number, date of revision, author of the revision, 

identify paragraphs and pages where changes are made, and the reason for making the 

changes along with the new version number” (Peitz et al. 2002). 

4. Notify the SFAN Lead Data Manager of any changes to the Protocol Narrative or SOP so 

that the new version number can be incorporated in the Metadata of the database. The 

Data Manager will then edit the database per any changes to the Protocol Narrative and 

SOPs. 

5. Post new versions on the internet and notify all individuals known to have a previous 

version of the Protocol Narrative or SOP. A list of current protocol and SOP version 

numbers is maintained in table SOP 7.1. 

6. When any significant changes in the sampling protocol occur such as changes in 

techniques or equipment, or changes in staff, there should be an “overlap” of methods 

and personnel (Oakley et al. 2003). This requires using both the old and new techniques 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.4 

on a given measurement or activity and having both the outgoing and new staff members 

perform the measurements concurrently. 

Table SOP 7.1. Current SFAN Salmonid Monitoring Protocol documents. 

Document Name 

Current 

Version Version Date 

San Francisco Bay Area Network Salmonid Monitoring, Protocol 

Narrative 

4.0 Feb. 2010 

SOP 1. Summer/Fall Basinwide Juvenile Coho and Habitat Surveys 3.6 Feb. 2010 

SOP 2. Summer/Fall Index Reach Surveys 1.5 Feb. 2010 

SOP 3. Specialized Field Techniques 1.5 Feb. 2010 

SOP 4. Spring Smolt Trapping 3.6 Feb. 2010 

SOP 5. Spawner Survey 3.5 Feb. 2010 

SOP 6. Permit Requirements 2.1 Feb. 2010 

SOP 7. Protocol Revision 1.3 Feb. 2010 

SOP 8. Data Management 1.3 Feb. 2010 

SOP 9. Sampling Site Descriptions 1.2 Feb. 2010 

SOP 10. Data Summaries and Analyses 3.9 Feb. 2010 

SOP 11. Personnel Training and Safety 1.5 Feb. 2010 

Protocol Review 

Reviewer Comments 

Appendix SOP 7A contains the PWR Protocol Review Checklist used by peer reviewers. 

Appendix SOP 7B summarizes comments and responses from the writing team. 

Review Approval and Distribution 

Key personnel involved with the development, implementation, and review of this monitoring 

protocol will be on the electronic mailing list for receipt of this document and subsequent major 

revisions. These include: 

• Jennie Skancke, Water Quality Specialist San Francisco Bay Area Network 

• Brannon Ketcham, Hydrologist Point Reyes National Seashore 

• Tamara Williams, Hydrologist Golden Gate National Recreation Area 

• Darren Fong, Aquatic Ecologist Golden Gate National Recreation Area 

• Marcus Koenen, I&M Coordinator San Francisco Bay Area Network 

• Paul Johnson, Wildlife Biologist Pinnacles National Monument 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.5 

Appendix SOP 7A: PWR Protocol Review Checklist 

Appendix SOP 7A. PWR Protocol Review Checklist (continued) 

Section 1 Overall Organization and Presentation of Protocol Narrative 

 1. Is the overall monitoring protocol well-organized with sections clearly delineated? 

2. Does the protocol have a title page with authors’ names, protocol version number and 

date? (Protocol version numbers should be constructed to allow for both major and minor 

changes.) Is there a Table of Contents, abstract, and the three basic sections: 1-Narrative, 2-

Standard Operating Procedures (SOPs), and 3-Supplementary Materials or Appendixes 

recommended in the NPS standards published by Oakley et al. 2003 

(http://science.nature.nps.gov/im/monitor/protocols/ProtocolGuidelines.pdf). 

3. Is there a complete and accurate table of contents with page numbers? (Chapters should 

be paginated consecutively, i.e. Chap. 1 (pp. 1-20), Chap. 2 (pp. 21-28), Chap. 3 (pp. 29-

44), etc. to allow for modular updates.) 

4. Are the tables and figures clearly labeled and understandable? 

5. Is the protocol bound so that it lies flat, preferably in a 3-ring binder? 

Section 2 A. Background and Objectives (Chapter 1) 

1. Does the protocol narrative provide a rationale or justification for why a particular 

resource or resource issue was selected for monitoring? Is the history and background for 

this resource issue well-referenced with supporting literature cited? 

2. Does the protocol narrative discuss the linkages between this and other monitoring 

projects? 

3. Does the protocol narrative describe how monitoring results will inform management 

decisions? 

4. Does the protocol narrative contain careful documentation of the monitoring objectives or 

monitoring questions being asked? 

5. Does the protocol narrative identify specific measurable objectives such as thresholds or 

trigger points for management actions? 

Section 3 B. Sampling Design (Chapter 2) 

1. Is there a clear and logical rationale for selecting the sampling design over others? 

2a. Were the criteria for site selection clearly discussed including stratification, spatial 

design, and whether this monitoring will be co-located and/or integrated with other VS 

monitoring protocols? (See Checklist, Section 1A2.) 

2b. Has the target population or “sampling frame”, and the sampling units, been identified? 

In other words, is the desired level of inference clear? 

3. Is the sampling frequency and replication identified? 

4. Is the timing of sampling defined? 

5. Are the location of sampling sites clearly identified? 

6. Is the level of change that can be detected for the amount or type of sampling being 

instituted identified? (See Checklist, Section 1A5.) 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.6 

Appendix SOP 7A. PWR Protocol Review Checklist (continued) 

Section 4 C. Field Methods (Chapter 3) 

 1. Are preparations for the field season and equipment setup included? Are requirements for 

permitting and compliance discussed? 

2. Does the protocol include clear and detailed information on taking measurements with 

example survey forms included? (Protocol variables and measurements may be discussed 

in detail in a SOP. A complete set of forms should be included in either the supplementary 

materials or a SOP.) 

3. Is the method of access for sampling sites provided? 

 4. Is there an overview of procedures for establishing, monumenting, and maintenance of 

plots discussed in one or more SOPs? 

 5. Does the protocol include details for the post-collection processing of samples or 

vouchers? 

6. Does the protocol include procedures to be followed at the end of the field season? 

Section 5 D. Data Handling, Analysis and Reporting (Chapter 4) 

1. Does the protocol provide an overview of the process for entering, editing, and storing 

data, identification of database software, and whether the database is consistent with the 

recommended I&M database template structure? (For water quality protocols, see specific 

water quality guidance in Part B or WRD’s General Comments 15, and checklist items in 

Section 2, items 8-10, below.) 

2. Are quality assurance (QA) and quality control (QC) procedures presented for the various 

levels of data collection and analysis? (See water quality Part B guidance or General 

Comments 15 as appropriate.) 

3. Is the data structure clearly presented and sufficient to capture the required information to 

meet the stated goal? Is there an overview of the database design? 

4. Are there recommendations for routine data summaries and statistical analysis to detect 

change? 

5. Is there a recommended reporting schedule? 

6. Is there a recommended report format with examples of summary tables and figures? 

7. Is there a recommendation for long-term trend analysis (e.g. every 5 or 10 years)? 

8. Does the protocol narrative include an adequate description of metadata and data archival 

procedures? 

9. Does the protocol narrative describe the frequency of testing and review of protocol 

effectiveness? 

Section 6 E. Personnel Requirements and Training (Chapter 5) 

 1. Does the narrative include a listing of the personnel and describe their roles and 

responsibilities, and qualifications? 

2. Does the protocol include a discussion of training procedures for personnel? 

Section 7 F. Operational Requirements (Chapter 6) 

 1. Are facility, vehicle and equipment needs identified? 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.7 

Appendix SOP 7A. PWR Protocol Review Checklist (continued) 

 2. Is there a summary of key partnerships with agencies, organizations and individuals that 

are part of the monitoring program and a description of their contribution? Is there a list of 

relevant cooperative agreements and other partnership agreements, if applicable? 

 3. Is a schedule for the annual fieldwork and administrative needs required to implement 

this protocol included? 

4. Is there an overall budget that summarizes the annual and periodic costs of 

implementation of the protocol? Does it seem reasonable? 

 5. Does the staffing plan and budget demonstrate that adequate resources have been 

allocated to data management, analysis, and reporting activities (ca. 30% are 

recommended)? 

Section 8 G. Literature Cited (Chapter 7) 

1. Are the literature citations relevant, sufficient and consistently formatted? 

Section 9 Standard Operating Procedures (Selected essential SOPs in addition to those 

mentioned in the narrative outline are identified in the checklist below. For Water 

Quality protocols, Part B Guidance or WRD’s General Comments 15 should be 

consulted when developing SOPs.) 

 1. Is there a table of contents for the SOPs? 

 2. Are changes to each SOP clearly identified with a title, version number or revision date, 

and page numbers? Changes to protocol modules (Chapters or SOPs) should be reflected in 

the overall protocol version number and protocol revision history log either through a minor 

or major revision; however, you may also wish to develop a numbering scheme for SOPs, 

e.g. SOP 1.00, 1.01... 

 3. Is there a SOP with instructions for revising the protocol and a revision history log? 

 4. Is there a SOP with instructions for preparation before the field season? Is there a SOP 

with instructions for procedures and equipment storage during and after the field season? 

(Also see numbers 10 and 11 below.) 

5. Is there a SOP for training field personnel? 

6. Is there a SOP that clearly defines protocol variables and how to measure them? (See 

Checklist, Section 1C2.) 

 7. Are there clear and detailed driving and other navigational instructions to sampling sites?

8. Are the details of Data Management identified in one or more SOPs? Topics to be 

included are at minimum identified in Section 1D and may include customized data 

management routines. Specifically for water quality monitoring data, does the SOP specify 

how data will be reported to WRD for entry into the Environmental Protection Agency’s 

STORET database? 

 9. For water quality monitoring and other monitoring as appropriate, is there a quality 

control SOP associated with each protocol that adequately documents QC objectives for 

measurement sensitivity (detection limits), measurement precision, measurement systematic 

error (bias as percent recovery), data completeness (including adequacy of planned sample 

sizes and statistical power – this topic may be in the SOP on Sampling Design), and (if 

applicable for lab measurements only) blank control? Are instrument calibration details 

included either in the QC SOP or in a separate calibration SOP? 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.8 

Appendix SOP 7A. PWR Protocol Review Checklist (continued) 

 10. For water quality protocols, is there a SOP that includes an explanation of how data 

comparability (a quality assurance basic) was considered in choosing which protocols and 

chemical labs to utilize? Do protocol SOPs contain enough field and lab method details to 

allow others to determine if data produced is comparable enough to other regional data sets 

to be considered credible by regulatory agencies interested in the data? 

 11. Do aquatic protocol SOPs adequately describe the details of all Sampling Protocols 

(Field and Laboratory), as well as equipment needs and operation, sampling techniques, 

sample preservation and handling and logistics? 

12. Are all major procedures required for the protocol sufficiently explained? Are any 

SOPs missing? 

13. Are the literature citations with the SOP relevant, sufficient and consistently formatted?

Section 10 Supplementary Materials or Appendixes 

 1. Is there a table of contents with Section 3 – Supplementary Materials that clearly 

identifies the materials provided in this section of the protocol? 

 2. Are the supplementary materials relevant, sufficient and consistently presented? 

Consistent formatting is desirable, but not always possible. 

 3. Are data collection forms provided either in this section or in an SOP? 

 4. Is there a section for the Administrative Record that provides the history of protocol 

development and refinement? (The published protocol may be presented either in Section 2 

or Section 3 depending upon its contribution to the current protocol.) 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.9 

Appendix SOP 7B: Peer Review Comments to 2005/2006 Draft and Responses 

from Protocol Authors 

This appendix is the product of a query run on a MS Access protocol review database developed 

to track 118 reviewer’s comments on the 2005/2006 draft protocol and responses made by the 

writing team. 

SOP Number Reviewer Comment Response

Narrative

Insufficient information on analytical Revised sampling design and data 

techniques, power analysis, database analysis sections.

design, metadata, data summaries, and 

trend analysis were provided in this 

document.

Provide a single map showing all proposed Narrative Fig,2 shows all Parks where 

study areas. monitoring will be performed.

If not on a map, provide a table indicating Both a map is provided in Narrative along

which streams are in which park. with tables in SOP 8

How will NPS standardize techniques with We currently use standard techniques 

other institutions and are comparison and and calibration methods as stated in 

calibration studies proposed? narrative. Comparisons will be made in 

trend and synthesis reporting as stated in

 data analysis SOP.

Reports on vertebrate and invertebrate Monitoring questions and objectives were 

assemblages are proposed but no revised.

measurable objective is provided.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.10 

SopNum Reviewer Comment Response

Why are spring assemblage surveys Index reaches are already established in 

proposed for PINN and JOMU. How will other parks and we can look at species 

these be combined with permanent assemblage changes in all parks 

systems in other parks. described. PINN is not part of the 

protocol.

Why are adult counts not proposed for Adult counts are performed in MUWO 

MUWO. and it is now clearly documented in the 

SOP.

How will NPS calibrate survey results from Stated in Basinwide survey sampling 

 snorkeling? design in protocol narrative.

40-50 random sites are needed to assess Sampling design revised.

an entire drainage.

Are there standards to reduce data entry Addressed in SOP 7

errors and analytical errors?

How will data generated through applying Data analysis section expanded and 

the SOPs be synthesized into overall enhanced.

population and assemblage assessments?

To much detail on SOPs in this document. Redundancy reduced throughout protocol

 Reduce the size of this document so it is and SOP.

not redundant in SOPs

The sampling design was not clearly Sampling design was revised.

presented.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.11 

 

SopNum Reviewer Comment Response

 

 Reviewer encourages coordination with Coordination with Redwood National Park 

Olympic, Redwood, and Northern may be helpful but would be more useful 

Cascades National Parks? Are they using to compare with watersheds in closer 

the same monitoring? Method comparability proximity.

It may be appropriate to look at entire Created annual reports instead of 

drainages in order to use one as a control watershed reports explained in Data 

for doing restoration on another. Analysis SOP. Also, monitoring focus is 

Especially if trends between drainages are now on population trends. Not on 

similar. evaluating effectiveness of 

management efforts.

What is the sampling design chosen? Sampling designs were revised based on 

Make clear. power analyses. Clarified in both the 

protocol and SOPs.

However, the mixture approach to basin- Index reaches can not be applied to the 

wide abundance estimates conflicts with entire stream so Basinwide surveys 

standard methods. Explain why this provide this information. Index reaches 

approach would provide more info than are also no longer used as calibration 

standard methods. points as described in a previous draft of

 the protocol.

The monitoring questions provided a Objectives were revised.

mixture of those that could be addressed 

directly with data gathered using the 

protocols presented and those that would 

require more specific research efforts. 

Make these clear.

Implications of summer surveys on Level of detection based on power 

detecting change due to management analysis is presented.

actions. What level of detection do we 

expect to gain from SOP1 and will this 

protocol be able to detect changes caused 

by management actions?

What habitat constraints exist in the parks Habitat and environmental constraints 

that currently impede or limit salmon briefly discussed.

recovery efforts?

 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.12 

SopNum Reviewer Comment Response 

 

 Clarify the use of terms community, and Reviewed terms and usage seems to be 

assemblage. Also make sure use of the fine.

word "data" is plural.

Make clear how the protocols will answer The protocol is designed to monitor 

some of the complex monitoring questions trends. Determining cause and effect is 

 that address the attempts to understand not the goal. Monitoring questions were 

the mechanisms causing any changes refined to clarify.

through time.

Describe management activities that Described in the rational for selecting this

impaired or currently impair fish. resource section.

Reviewer suggests modeling the entire This is what our multiple life stage 

salmonid life cycle to determine if factors sampling will accomplish, see data 

not described by dry-season monitoring analysis fig 4.11 for an example of how 

would increase knowledge on population limiting factors will be determined.

dynamics. This would help explain annual 

variation.

For PINN and JOMU a limited index site Index reaches are already used in JOMU.

approach is suggested PINN is not part of the protocol.

Bohlin, Brown, Moyle 1991, Ketcham et al References updated.

2004a, and Solazzi et al are not cited. 

Pearcy needs editor and publisher. 

References should include city.

Section 2.4 should be headed genetic Genetic analysis removed as part of 

monitoring and should have similar protocol.

construction to other sections in the 

document.

No reference found for Stillwater Sciences Freshwater Shrimp are no longer in the 

2004, Serpa 1994, 1996, 1997, 1998. document. All references checked.

How will data from vertebrate assemblages Monitoring objectives revised. Focus is 

be converted into quantitative indicators? on population trends of coho salmon and 

Will IBIs, O/E models, or both be steelhead trout.

employed.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.13 

Narrative, SOP1

SopNum Reviewer Comment Response

Use mark recapture instead of multiple This is not appropriate for sampling 

pass electrofishing. endangered species and is not permitted 

by NOAA fisheries.

How does NPS define stable population Monitoring objectives were revised.

and what characteristics is this based on? 

 How will contradictions among the 

indicators be resolved?

How will the effects of nonnatives be Nonnatives were removed from the main

assessed? objectives and questions.

Non-random index sites cannot be used Sampling design was refined.

for inferring to other sites or reaches. This

 requires random or probabilistic sampling 

design.

Narrative, SOP1-2

Each monitoring question should be linked Both questions and objectives were 

to a measurable objective, a test refined.

hypothesis, a study design, and 

quantitative indicator.

Narrative, SOP1-3

There is no set of testable hypothesis and Detection capability is included.

objectives do not include detection 

capability.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.14 

SopNum Reviewer Comment Response

Provide Greg Brown's title and affiliation. Affiliation updated.

The database design is not clear. Data management SOP updated and 

revised.

Narrative,SOP1

Past and proposed rehabilitation actions Focus of protocol shifted away from 

should be described and followed by evaluation of specific management 

explicit study designs, indicators, efforts to population monitoring.

calculations, and detection limits.

Narrative,SOP1-3

Statistical analysis to detect change were Sampling design and data analysis were 

not extensively described enhanced.

The use of volunteers and other staff on Added to Chapter 5 in protocol narrative.

crews adds considerable crew error and 

safety concerns.

No rationale or criteria were provided for Sampling design was revised

site selection, replication, sampling 

frequency, site number, or detection 

limits.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.15 

SopNum Reviewer Comment Response

Statistical analysis to evaluate the effects Removed restoration monitoring 

 of restoration were not described objectives from the protocol.

Narrative,SOP2

Have prey refuges in traps been addressed in trap setup in SOP 2

considered? Explain fish screen and 

current techniques.

Narrative,SOP3

Are carcasses marked to avoid recounting Addressed in SOP 3 in field methods.

and to evaluate carcass loss?

Narrative/SOP1

We should acknowledge that index reaches Addressed in sampling design overview 

 are systematically selected rather than in the narrative.

sequential independent sampling and 

describe the pros and cons.

Explain increase in snorkeling and bounded Explained in narrative in sampling design 

 counts methods. How will we use under basinwide survey.

bounded counts to strengthen our 

estimates.

Describe how sites were selected and Sampling design revised.

consult a statistician on site locations and 

design before embarking the monitoring 

plan.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.16 

SopNum Reviewer Comment Response

Narrative/SOP2

Reviewer encourages continued trapping We always try our best but it is often not

during some storm events but possible, storm events can lead to 

acknowledges that this may not be mortalities if left in place and large storm

possible. events can lead to loss of equipment. 

Smolt traps must be monitored closely 

during storm events.

SOP

Specify how often the crew reports to the Details on reporting including schedule 

coordinator. revised.

SOP1

Has it been determined that steelhead and Yes, see NOAA fisheries biological 

coho are distinct populations? opinion and critical habitat delineation for 

both species.

What is the sampling reach length for fish In narrative: 100 meters in Index Reach 

assemblage sampling? Section.

What is the assessment unit? Is it a site, Sampling design revised.

reach segment, all stream length in a 

catchment, or all stream length in the set 

of catchments?

Reviewer believes it is useful to include Limited funding will limit monitoring 

amphibians and all fish in stream objectives.

assessment.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.17 

SopNum Reviewer Comment Response

Biomass is often a poor indicator for cold Monitoring will also use total count along 

water streams. with biomass to observe trends.

Terrestrial ecosystems only account for Sources of variation discussed in 

half of stream response, what about other background information but focus of 

sources of variation? monitoring is on detecting trends not on 

identifying cause and effect.

Is NPS satisfied with calibration results for Calibration is done each year on each 

 snorkeling vs. electrofishing coho. Fig. 4.9? watershed. While you would want the 

best, the calibration is done just for that 

one result. The figure that was presented

 was an example.

Why are 10 salmonids and 5 non- 10 of each species are measured, this is 

salmonids weighed and measured? Is this based on past years data, I added 

sufficient? How will this info be used in reasoning for 10 fish in SOP1. 

assessment? Information is used for fitness.

Clove oil works best as a sedative. Not approved by USDA and NOAA 

Fisheries

Seining may produce more injury than e- It is true that seining can produce more 

fishing. Wading rods are efficient at exterior injury if not done properly but 

measuring widths than tapes. this is outweighed by non-external efishing injury. Need to refer to NOAA efishing guidelines. Both wading rods and 

tapes have the same level of accuracy.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.18 

SopNum Reviewer Comment Response

Visual estimates are a lot less precise than Yes but they are needed for sampling 

 measured habitat widths. efficiency.

We have found qualitative estimates QA/QC enhanced in database.

useful for assessing data quality.

Table 4.2 Is there anyway to reduce the Large confidence intervals is still a 

confidence intervals? Only large trends problem. Additional pilot being 

will be detected. considered to refine techniques.

What level of effort is used in seconds Equal effort is used on each pass, but 

per square meter and is the entire habitat effort is affected by habitat complexity 

unit fished? in the unit. Habitat units were clarified in 

the protocol.

No text or data was provided on power Sample design and data management 

analysis, database design, or metadata. sections revised.

I did not see how index reach data for Inference from Index reach is limited. 

salmonids were used to estimate trends This is clarified in the protocol.

for watersheds.

Sculpin is a genus and not a species. Changed species to fish to be more 

general with sculpin. Added genus to 

recording on SOP 1 in case species is 

not determined.

Monitoring questions should be restricted Monitoring question and objectives were 

to the summer index period. Habitat refined.

constraints, species distribution, and 

responses to rehabilitation are likely season

 specific.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.19 

 SopNum Reviewer Comment Response

 Franklin Creek methods are not Reasoning already addressed due to 

comparable because snorkeling is not water quality.

performed.

Some sort of composite report is needed Addressed with addition of annual reports

versus individual basin reports. instead of watershed reports.

A memory stick is better than cds. Storage units will change with technology.

I did not see citations for Chatham & References checked.

Neuman, Ketcham & Brown, Kolz et al. 

Opperman, and Simonson et al. City 

should be provided for all non-journals.

Appendix D. Sculpin and Lamprey should Yes they should but this is unrealistic in 

be ID to species. the field and is not the focus of the 

monitoring effort.

No rationale or criteria were provided for Sampling design was revised.

site index selection, temporal or spatial 

replication, site number, or detection limits.

What is considered sufficient time for Clarified waiting time between passes in 

uncaptured fish to recover before doing SOPs.

another pass?

Include long term trends in steelhead as a Objectives were refined.

measurable objective.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.20 

 SopNum Reviewer Comment Response

 Explain why Chalone and Franklin Creeks PINN no longer included in protocol. 

differ from other creeks. More information provided on Franklin 

creek.

How will ocean conditions be linked to or These protocols are not intended to 

separated from reach conditions in the describe ocean conditions and so there is

park. no need to link or separate from reach 

monitoring.

How will seasonal variation be evaluated? Season variation was removed from 

narrative question/objective. NPS will 

not be evaluating seasonal variations, 

only annual variations.

Sampling design was not clearly Sampling design was revised.

presented.

40 times wetted width or 150 m is needed We do not do 40 wetted widths but 100 

for precise estimates of species and meters is the most we can do with one 

proportionate abundance. crew in a day. We could only increase 

this number if we increase our crew size 

and equipment.

Snorkeling is inadequate for assessing Snorkeling has been documented as 

vertebrate species richness. being accurate to describe a population 

of salmon by Hankin and Reeves and is 

widely used on the west coast.

There is no evidence that electrofishing Refer to NOAA guidelines and snorkeling 

harms fish populations, which is the level is a more efficient way of sampling for a

of interest. population.

Table 3.2 Discrepancy in days allotted per Discrepancy in days fixed with new 

 reach between table 2.1. tables and reorganization.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.21 

SopNum Reviewer Comment Response

By sampling headwater streams first Added GSS section to SOP 1 and 

before the mainstem we could be sampling included stream connectivity close to 

 the same fish twice. minimize possibility of double sampling.

Electrofishers should be serviced in winter, Electrofisher does not require yearly 

 Permits should also be done in the winter. servicing, permits are completed based 

on the required permit reporting schedule,

 added clause in reporting narrative 

reporting schedule.

Do not make basinwide estimates on index Sampling design revised. Index reaches 

 sections unless they are randomly are no longer used to calibrate basinwide 

selected. estimates.

I am not convinced that snorkeling and The calibration is described by Dollof et 

electrofishing produce comparable results. al.

 Can data be supplied to confirm the 

two sampling procedures can be 

calibrated?

Merging rehabilitation sites with index sites Rehabilitation based index sites have 

biases assessments. been removed from the sampling 

protocol.

SOP1-3

No information on measurements, field SOP 1-3 has handling procedures and 

forms, or sample processing were forms with instruction in the appendix.

provided.

Appendix G. Allow time for training of This is allowed.

staff and train them.

 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.22 

SopNum Reviewer Comment Respons 

SOP2

Lamprey and sculpin should be identified No field ID characteristics have been 

to species. established for quick ID of each species.

Need to address periods when trapping is Addressed issue in SOP 2 Trap 

suspended and what effect this has on Operations section

annual production estimates.

What is the watershed of interest and is Watershed of interest is clearly defined 

the trap location appropriate? Does the in the locations SOP.

trap locations allow assessments of the 

same aquatic resources as the fish and 

habitat surveys?

Why would trapping efficiency decline with Reviewer didn't realize that Fig.4.4 was 

 time Fig.4.4 in SOP2 only an example for that one field 

season. Efficiency can decline with late

 spring freshets.

Did not find citation for Gallagher 2000a. All references reviewed.

All non-journal articles should include city, 

state, publisher.

In Fig 1 explain environmental conditions Added analysis for this in SOP 9 to help 

associated with peaks and troughs. explain environmental cues.

No evidence of power analysis Sampling design was revised.

Include an objective criteria to define the Clarified trapping season in Sampling 

end of trapping season. Frequency and Timing in SOP 2

 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.23 

SopNum Reviewer Comment Response

 There is no spatial or temporal replication Sample design section revised. Spatial 

proposed. and temporal pattern is fully described 

to track population trends.

Citation missed for Crone & Bond, Flint, References reviewed.

Koski, Lusch, Sandercock, Solazzi, and 

Taylor & Associates. The Ketcham and 

Brown poster is not citable other than as 

pers comm. Provide city for non-journal 

articles.

Reviewer does not think that traps are We have revised the objectives. We are

appropriate tools for indicating habitat not making inference about distribution, 

constraints. Population distribution, response to rehabilitation, and aquatic 

response to rehabilitation, and aquatic assemblages here. The focus is on 

assemblages. population trend of coho smolt and 

steelhead trout.

The monitoring questions should be Monitoring objectives were refined.

restricted to the spring index period. 

Habitat constraints, species distributions, 

and responses to rehabilitation are likely 

season specific.

Prey cover in the trap box would be useful SOP 2 states that fish screens are used 

to help against predation. Most predation

 is caused by sculpin which are ambush 

predators so cover would only help 

sculpin prey on juvenile salmonids.

SOP3

Should be coho adult SOP SOP was revised entirely for 

clarification.

Are flags removed at the end of the No, we use biodegradable flagging so 

survey? that we do not need to remove the flags.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.24 

How is clarity measured? Section on water clarity is revised.

The field form should include a query and This information gathered by staff gages

space for information on recent freshets on all three watersheds. See freshwater 

or other environmental conditions that dynamics protocol. Water clarity is a 

reduce detection effectiveness. field on the form to indicate observer 

efficiency (See SOP 9).

Use a ski pole insead of a 2m survey rod. Ski poles are more expensive then the 

broom sticks that we make into rods. 

Plus broom sticks are longer.

Reviewer thinks NPS can find people to Yes, deleted out of SOP.

work on holidays

The rationale for the site number, and Sampling design revised.

detection limits are not provided.

Reviewer believes steelhead redds can be Addressed steelhead vs. coho redds on 

distinguished from coho redds. Can adult SOP 3 including how to distinguish 

traps be used to estimate steelhead? between the two post collection. Focus 

of monitoring objectives is on adult coho;

 monitoring adult coho not economically 

possible at this time.

No info on Power Analysis Sampling design revised.

The monitoring questions are not all Monitoring questions and objectives were 

specific for this indicator. They are revised. Main question for SOP3 is 

largely driven by ocean conditions. timing and distribution of spawning which 

is not driven by ocean conditions.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.25 

SopNum Reviewer Comment Response

 The sampling sites are listed but the This was clarified in the narrative. Sites 

rationale, criteria, and procedures for their are based on access and reach length.

selection are not provided.

SOP4

No monitoring questions, measurable Monitoring objectives revised. Additional

objective, testable hypothesis are information and examples provided in 

presented. Also lacking graphic and data analysis SOP.

tabular results.

SOP5

No SOP 5 provided for shrimp monitoring Will not be included in this protocol

SOP9

How will fish assemblage extent, condition, Monitoring objectives revised to focus on

annual variation, and fish assemblage coho and steelhead.

themselves be described?

What data will NPS use to compare status Addressed in SOP 9 Data Analysis in 

and trends with other watersheds? annual reports section.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.26 

Appendix SOP 7C: Peer Review Comments to 2009 Draft and Responses from 

Protocol Authors 

A draft of the SFAN Salmonids Monitoring Protocol was submitted to Dr. James Agee, PWR 

Protocol Review Coordinator, and Dr. Penny Latham, PWR Regional I&M Coordinator in 

January 2009. Dr. Agee forwarded the protocol to two anonymous peer reviewers. In April 2009, 

review comments on the protocol were received. This appendix summarizes the deficiencies and 

suggested corrective actions noted by the reviewers. The text in italics represents the authors’ 

changes to the document based on the reviewers’ comments. Hard copies of reviewer comments 

are on file. 

Italic represents authors change in text in response to reviewer comment. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.27 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.28 

PWR PROTOCOL REVIEW CHECKLIST 

A = administrative guidance, S = an item related to scientific merit, 

C = general reviewer comment, R = response from protocol authors

Overall Organization and Presentation of Protocol Narrative 

A 

1. Is the overall monitoring protocol well-organized with sections clearly delineated? 

Yes, the protocol sections are clearly delineated. However, the protocol seems 

too long (261 p, 44 tables, 66 figures) and has extraneous detail for work in a 

low number of streams. I suggest reducing numbers of tables and figures to 

those that are most relevant.

R 

Excerpted from peer review guidance by Dr. Agee 

A 

2. Does the protocol have a title page with authors’ names, protocol version number 

and date? (Protocol version numbers should be constructed to allow for both major 

and minor changes.) Is there a Table of Contents, abstract, and the three basic 

sections: 1-Narrative, 2-Standard Operating Procedures (SOPs), and 3-

Supplementary Materials or Appendixes recommended in the NPS standards 

published by Oakley et al. 2003 

YES(http://science.nature.nps.gov/im/monitor/protocols/ProtocolGuidelines.pdf). 

A 

3. Is there a complete and accurate table of contents with page numbers? (Chapters 

should be paginated consecutively, i.e. Chap. 1 (pp. 1-20), Chap. 2 (pp. 21-28), 

Chap. 3 (pp. 29-44), etc. to allow for modular updates.) YES

S 4. Are the tables and figures clearly labeled and understandable? Overall, yes. 

A 5. Is the protocol bound so that it lies flat, preferably in a 3-ring binder? YES

Section 

1 

A. Background and Objectives (Chapter 1) 

S 

1. Does the protocol narrative provide a rationale or justification for why a particular 

resource or resource issue was selected for monitoring? YES. Is the history and 

background for this resource issue well-referenced with supporting literature cited? 

A 2. Does the protocol narrative discuss the linkages between this and other monitoring 

projects? YES. Table 1 and page 7. 

A 

3. Does the protocol narrative describe how monitoring results will inform 

management decisions? YES. In particular, guiding restoration efforts. Another 

important management implication may be the detection of non-native fish 

species in the future?

S 

4. Does the protocol narrative contain careful documentation of the monitoring 

objectives or monitoring questions being asked? The monitoring objectives are 

specifically outlined in a stand-alone section. 

S 5. Does the protocol narrative identify specific measurable objectives such as 

thresholds or trigger points for management actions? YES, p.12.

Section 

1 

B. Sampling Design (Chapter 2) 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.29 

S 1. Is there a clear and logical rationale for selecting the sampling design over others? 

YES. 

S 

2a. Were the criteria for site selection clearly discussed including stratification, 

spatial design, and whether this monitoring will be co-located and/or integrated with 

other VS monitoring protocols? (See Checklist, Section 1A2.) YES .

S 2b. Has the target population or “sampling frame”, and the sampling units, been 

identified? In other words, is the desired level of inference clear? YES.

S 3. Is the sampling frequency and replication identified? YES.

S 4. Is the timing of sampling defined? YES, broadly. Could benefit from more 

specifics such as in Table 4.

R Also seeTable 5 

S 5. Are the location of sampling sites clearly identified? YES. 

S 6. Is the level of change that can be detected for the amount or type of sampling 

being instituted identified? (See Checklist, Section 1A5.) YES.

Section 

1 

C. Field Methods (Chapter 3) 

A 1. Are preparations for the field season and equipment setup included? YES. Are 

requirements for permitting and compliance discussed? YES, p. 44

S 

2. Does the protocol include clear and detailed information on taking measurements 

with example survey forms included? YES. (Protocol variables and measurements 

may be discussed in detail in a SOP. A complete set of forms should be included in 

either the supplementary materials or a SOP.) YES.

A 3. Is the method of access for sampling sites provided? YES, via maps and tables.

S 

4. Is there an overview of procedures for establishing, monumenting, and 

maintenance of plots discussed in one or more SOPs?. Plots (transects) are not 

permanent . 

R 

Location information and documentation is clearly documented in SOP 8 and SOP 9. 

The location and sampling areas are not related to plots but to stream segments. The 

Stream segments are related to stream monuments that are used to document spatial 

location. 

S 5. Does the protocol include details for the post-collection processing of samples or 

vouchers? YES.

A 6. Does the protocol include procedures to be followed at the end of the field season? 

YES for data. 

Section 

1 

D. Data Handling, Analysis and Reporting (Chapter 4) 

A 

1. Does the protocol provide an overview of the process for entering, editing, and 

storing data, identification of database software, and whether the database is 

consistent with the recommended I&M database template structure? (For water 

quality protocols, see specific water quality guidance in Part B or WRD’s General 

Comments 15, and checklist items in Section 2, items 8-10, below.) YES, SOP 8.

S 

2. Are quality assurance (QA) and quality control (QC) procedures presented for the 

various levels of data collection and analysis? (See water quality Part B guidance or 

General Comments 15 as appropriate.) YES, p. 128. 

S 3. Is the data structure clearly presented and sufficient to capture the required 

information to meet the stated goal? Is there an overview of the database design? 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.30 

YES.

S 4. Are there recommendations for routine data summaries and statistical analysis to 

detect change? YES.

A 5. Is there a recommended reporting schedule? YES. 

A 6. Is there a recommended report format with examples of summary tables and 

figures? YES. 

S 7. Is there a recommendation for long-term trend analysis (e.g. every 5 or 10 years)? 

YES.

S 8. Does the protocol narrative include an adequate description of metadata and data 

archival procedures? YES.

S 9. Does the protocol narrative describe the frequency of testing and review of 

protocol effectiveness? YES.

Section 

1 

E. Personnel Requirements and Training (Chapter 5) 

A 1. Does the narrative include a listing of the personnel and describe their roles and 

responsibilities, and qualifications? YES. 

S 

2. Does the protocol include a discussion of training procedures for personnel? YES, 

p. 42, but this is brief. It would be good to incorporate safety considerations in 

main protocol. 

 Excerpted from peer review guidance by Dr. Agee

R Based on comments SOP 11 was developed to include training and safety of field 

personnel. 

Section 

1 

F. Operational Requirements (Chapter 6) 

A 1. Are facility, vehicle and equipment needs identified? YES for equipment. Not 

sure about facility or vehicle.

R See revised budget Table 6, facility needs are discussed throughout the document 

narrative amd SOP 1-5 when necessary. 

A 

2. Is there a summary of key partnerships with agencies, organizations and 

individuals that are part of the monitoring program and a description of their 

contribution? Is there a list of relevant cooperative agreements and other partnership 

agreements, if applicable? YES

A 3. Is a schedule for the annual fieldwork and administrative needs required to 

implement this protocol included? YES.

S 

4. Is there an overall budget that summarizes the annual and periodic costs of 

implementation of the protocol? YES. Does it seem reasonable? No. From Table 6, 

the program annually relies on $92,500 from Cal. Dept. of Fish and Game. This 

is 62% of the total budget, and only guaranteed thru FY 10. This is an issue that 

needs to be addressed relative to objectives and proposed monitoring. 

R 

See revised budget Table 6. “The current budget is augmented by grants through 

FY2013. The monitoring program has received funding from the CDFG competitive 

grants program since 2002. Given the past and current level of funding, combined 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.31 

with the current status of the CCC ESU coho populations, CDFG will likely continue 

their support of this monitoring program. 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.” 

A 

5. Does the staffing plan and budget demonstrate that adequate resources have been 

allocated to data management, analysis, and reporting activities (ca. 30% are 

recommended)? The data management is $7,000 of $75,000. This seems excessive 

on an annual basis, particularly after database construction. The crews should 

be able to enter and conduct QA/QC. The project lead creates summaries and 

meets reporting requirements. 

R 

Note the budget Table 6 has been revised. Comments from other reviewer and 

general I&M guidance suggests that this amount is well within reason given the 

extent of data collection. 

Section 

1 

G. Literature Cited (Chapter 7) 

S 1. Are the literature citations relevant, sufficient and consistently formatted? NO. see 

PRC comments following this list. 

R Made new literature citations for each SOP and revised the literature cited for the 

protocol narrative. 

Section 

2 

Standard Operating Procedures (Selected essential SOPs in addition to those 

mentioned in the narrative outline are identified in the checklist below. For 

Water Quality protocols, Part B Guidance or WRD’s General Comments 15 

should be consulted when developing SOPs.) 

A 1. Is there a table of contents for the SOPs? YES. Xiv. But it would be best to have 

single TOC

R Current guidance is to have a general TOC in the narrative with a separate and 

more detailed TOC for each SOP.

A 

2. Are changes to each SOP clearly identified with a title, version number or revision 

date, and page numbers? Changes to protocol modules (Chapters or SOPs) should be 

reflected in the overall protocol version number and protocol revision history log 

either through a minor or major revision; however, you may also wish to develop a 

numbering scheme for SOPs, e.g. SOP 1.00, 1.01...YES. xviii.

A 3. Is there a SOP with instructions for revising the protocol and a revision history 

log? YES. Xviii

A 

4. Is there a SOP with instructions for preparation before the field season? Is there a 

SOP with instructions for procedures and equipment storage during and after the 

field season? (Also see numbers 10 and 11 below.) No, but was addressed in text.

 from Agee Letter 

R SOP 11 Personnel Training and Safety SOP was added to protocols to address this 

issue. 

S 5. Is there a SOP for training field personnel? No.

R SOP 11 Personnel Training and Safety was created and is now part of the salmonid 

monitoring protocols. 

S 6. Is there a SOP that clearly defines protocol variables and how to measure them? 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.32 

(See Checklist, Section 1C2.) No.

R 

PRC: “I would conclude YES but not all in one SOP, which seems fine” 

Protocol Narrative, Table 2, and SOPs 1-5. Variables are defined in monitoring 

questions and how they will be measured in the monitoring objectives. SOPs 1-5 also 

explain how variables will be measured. SOP 10 also includes details on Analysis 

and reporting. 

A 7. Are there clear and detailed driving and other navigational instructions to sampling 

sites? I did not see these but may have missed.

R PRC: “Map details of SOP #9 seem to be sufficient.” SOP 9 includes maps and a 

narrative description of all sampling sites and stream reaches. 

S 

8. Are the details of Data Management identified in one or more SOPs? Topics to be 

included are at minimum identified in Section 1D and may include customized data 

management routines. YES. Specifically for water quality monitoring data, does the 

SOP specify how data will be reported to WRD for entry into the Environmental 

Protection Agency’s STORET database? Water quality collection is limited to data 

to adjust electrofisher.

S 

9. For water quality monitoring and other monitoring as appropriate, is there a 

quality control SOP associated with each protocol that adequately documents QC 

objectives for measurement sensitivity (detection limits), measurement precision, 

measurement systematic error (bias as percent recovery), data completeness 

(including adequacy of planned sample sizes and statistical power; this topic may be 

in the SOP on Sampling Design), and (if applicable for lab measurements only) blank 

control? Are instrument calibration details included either in the QC SOP or in a 

separate calibration SOP? NA

S 

10. For water quality protocols, is there a SOP that includes an explanation of how 

data comparability (a quality assurance basic) was considered in choosing which 

protocols and chemical labs to utilize? Do protocol SOPs contain enough field and 

lab method details to allow others to determine if data produced is comparable 

enough to other regional data sets to be considered credible by regulatory agencies 

interested in the data? NA

S 

11. Do aquatic protocol SOPs adequately describe the details of all Sampling 

Protocols (Field and Laboratory), as well as equipment needs and operation, 

sampling techniques, sample preservation and handling and logistics? YES

S 12. Are all major procedures required for the protocol sufficiently explained? Are 

any SOPs missing? YES

S 13. Are the literature citations with the SOP relevant, sufficient and consistently 

formatted? YES

Section 

3 

Supplementary Materials or Appendixes 

A 

1. Is there a table of contents with Section 3 – Supplementary Materials that clearly 

identifies the materials provided in this section of the protocol? YES. It’s on page 

xvi, might be repeated as page 207.

A 2. Are the supplementary materials relevant, sufficient and consistently presented? 

Consistent formatting is desirable, but not always possible. YES

A 3. Are data collection forms provided either in this section or in an SOP? YES. 

A 4. Is there a section for the Administrative Record that provides the history of 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.33 

protocol development and refinement? A summary event table is highly 

recommended in addition to the supporting materials required in the Protocol Review 

File Checklist, e.g. the initial study plan or protocol development summary, the 

results of protocol development studies, peer review comments and responses during 

the development phase, and/or any published protocol on which a major portion of 

the methodology included in this protocol is based. (The published protocol may be 

presented either in Section 2 or Section 3 depending upon its contribution to the 

current protocol.) YES, p. xviii

Individual Comments and Responses 

Additional comments from Administrative Reviewer: 

C I reviewed the protocol entitled, “Salmonid Monitoring Protocol V.3.67” by Ketcham et al. 

2008. I specifically addressed the scientific and some administrative items in the Protocol 

Review Checklist. The protocol represents a significant body of work, high levels of effort, 

and an important contribution by NPS to coho salmon monitoring efforts along the 

California Coast. I believe that the implementation of this protocol represents an important 

component of monitoring for the SFAN network. The monitoring of multiple life history 

stages of fish provides very useful information with much management relevance. 

 

C Overall, I found the protocol and corresponding SOP’s to be very cumbersome to wade 

through, and believe that the authors overindulge in detail and analysis. The protocol and 

SOP’s would be greatly improved after a more concise and reduced presentation of 

information. The length of the protocol/SOP’s (261 pages) coupled with 44 Tables and 66 

Figures seems excessive for a program directed primarily at counting coho salmon in four 

streams. Many of the tables have redundant information, and could be combined. In its 

current format, I believe that the protocol lacks a “plug and play” practicality that is 

important for new staff. 

R 

Excerpted from peer review guidance by Dr. Agee 

C The protocol is designed to intensively monitor much of the entire lengths of four streams 

(out of SFAN=7 watersheds; 43 streams). There is much merit to the decision/philosophy to 

do a few things well under limited budgets, but the protocol should recognize the “cost” and 

possible lack of representation from this approach. In other words, the sampling design 

limits the application of the data collected. The protocol would benefit from some discussion 

and explanation about inference and ability (or lack thereof) to extrapolate. 

R The following paragraph was added to the Rational for Selecting this Resource to Monitor 

section of the narrative to address the comment stated above. 

“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 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.34 

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 monitoring will be 

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

C The sampling design and methods appear to focus primarily on the monitoring of one 

species, coho salmon. The origin of these coho salmon remains unknown to the reader as to 

whether these fish are wild, natural, or hatchery produced. The protocol may be more aptly 

titled, “A Monitoring Protocol for Coho Salmon in Four SFAN Streams”. It remains unclear 

as to what types of useful information will be attained on the fish assemblages (e.g. other 

species in streams). It seems like there is excellent opportunity to characterize the entire 

assemblage via snorkel, trapping, and electrofishing surveys, but such information is only 

casually mentioned throughout the document. In other words, why not record and analyze 

data for all species encountered during snorkel and trapping surveys. 

R Chapter 1 states “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.” Also “In the mid-1980s, local citizen groups began informally documenting wild 

coho spawning in Lagunitas and Olema Creeks.” Also “The life history of winter run 

steelhead follows the same general life cycle pattern...” The protocol was not changed from 

salmonid monitoring protocol because ancillary data is collected on steelhead. Although we 

realize the focus of the objectives are on coho, ancillary data such as fish size, redds, and 

number of adults are collected on steelhead. Information on non-salmonid species is also 

collected but our sampling techniques would require significant revisions to monitor trends 

for other species. 

C Perhaps the greatest issue that needs to be addressed is the budget. From Table 4, it appears 

that the program relies heavily upon the California Fish and Game and Americorps for 

$92,500 each year. This represents 62% of the entire annual monitoring budget, and those 

funds are only guaranteed through FY 10. That suggests that this program is not viable in the 

future at the proposed and current level of sampling. 

R Revised Table 6 and added to budget. Monitoring priorities and budget shortfall section was 

also clarified along with Table 7. 

C I think that the Salmonid Monitoring Program is critical, but it is doubtful that the proposed 

extent and intensity of sampling can be achieved thru the existing Inventory and Monitoring 

budget. If that high level of sampling is desired by the SFAN network, the Inventory and 

Monitoring program should provide additional annual funds for this protocol. 

R See revised budget Table 6 and 7. While it would be ideal that funding would come from a 

sustainable source such as the I&M program, it has also been the vision that funding for the 

inventory and monitoring program will not be able to cover all costs. It is to the NPS’s 

benefit to capitalize on opportunities such as seeking outside funding to enhance our ability 

to monitor NPS resources. The partnership with CDFG is a great example of sharing costs 

for long-term monitoring. We recognize that there are potential pitfalls in that CDFG could 

reduce their share of the budget. It should also be recognized that since I&M is also 

congressionally funded, our own funding is far from secure. The priorities outlined in table 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.35 

7 give us flexibility to adapt to changing funding circumstances. 

 I highly recommend that the authors construct a line-item budget that defines the actual costs 

of annual spawner surveys, habitat surveys, smolt trapping, snorkel surveys, and calibration 

surveys. This budget should specifically define what CDFG actually contributes (e.g. smolt 

trap or other) to the program. With that information, the authors can then define and 

implement a core monitoring program for the $75,000 provided by the Inventory and 

Monitoring Program. Anything provided by other entities would add to the core NPS 

monitoring program. 

Also, the budget should account for a more realistic estimate of equipment costs (>$2,500), 

particularly based on this equipment intensive protocol. There will be costs associated with 

replacing and maintaining electrofishers, dive suits, traps, water quality instruments, waders, 

nets, etc.. I recognize that the park programs probably contribute equipment, but the costs 

will likely exceed $2,500/year. 

R Revised Budget and Budget in Operational Requirements section of narrative, see Tables 6 

and 7. The equipment cost was changed to represent the true costs. Currently the funds from 

CDFG are integrated into the monitoring program and it is not expected to change in the 

foreseeable future. The revised table 6 now shows the funds that CDFG contributes to the 

program and Table 7 reflects the minimum cost for each survey type. 

C Lastly, I think it is great to use volunteers for monitoring, but redd counting is not conducive 

to volunteer efforts. It is clear that redd counting can result in high observer variability, 

particularly with reliance on volunteers with little experience. I recommend the use of highly 

trained fisheries technicians to accomplish this important work. 

R As noted in the narrative “No inexperienced volunteers are used as survey reach leads. All 

survey leads are trained staff or trained volunteers with “experience” that can 

independently identify both redds and spawners.” At SFAN we have the benefit of working 

with many very experienced volunteers – many who have more experience than some paid 

technicians starting out. The monitoring program will continue to train and use volunteers 

for in order to meet specific monitoring objectives. 

C Thank you for the opportunity to review this important monitoring program. I hope the 

comments prove useful to the authors, and I hope that this protocol is implemented. I wish to 

remain anonymous. 

R Yes, the comments are very helpful. 

 The following line specific comments are meant to improve the clarity, brevity, and 

precision of the manuscript: 

Line Specific: [Page # correspond to January Consolidated Draft – all correlate with 

Narrative Protocol Section] 

C Page 2. It seems as though the “Life History” section should appear later in the document. 

Also, I thought this protocol was monitoring the entire fish assemblage, not solely coho and 

steelhead? 

R Since the title of the protocol is “Salmonid Monitoring Protocol” we feel that it is important 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.36 

to describe the life history near the beginning of the protocol. Based on our review of the 

protocol objectives, information collected through this program will be focused on 

salmonids in order to meet the protocol objectives. 

C Figure 2. Caption for Figure 2 should read “life cycle”. Images in the copy provided to 

reviewer were of low resolution. 

R Fixed life cycle on figure2 in Life History section of narrative. Resolution seems reasonable 

on digital and our printer copy. We apologize if reviewer received a poor copy. 

C Page 3, paragraph 1. Unclear whether authors are referring to summer or winter steelhead. 

I presume winter steelhead. 

R Added to Life History section of narrative “The life history of winter run steelhead follows 

the same general life cycle pattern...” 

In general we only have winter run steelhead in this area so there is not a need to discuss 

various run types in depth. 

C Page 4, top. It is important to note that the effectiveness of monitoring salmon is 

compromised by high variability in Pacific salmon populations and by their migratory 

nature. These pose inherent challenges to detecting significant trends. 

R See Rational for Selecting this Resource. Ocean variability is discussed in this paragraph. 

Also see Power Analysis summary in narrative for discussion on ability to detect trends 

given the high variability. 

C Page 6, Figure 3. Caption for Figure 3 should read “life cycle”. Images in the copy provided 

to reviewer were of low resolution. 

R Fixed life cycle on figure2 in Life History section of narrative. Resolution seems reasonable 

on digital and our printer copy. We apologize if reviewer received a poor copy. 

C Page 7, Table 1. A column at the end that shows “Duration of Monitoring” would be helpful 

(e.g. 1980-1999). 

R I agree this would be nice however we don’t currently have this information for other 

agencies. 

C Page 8. I recommend more specific monitoring questions and objectives. I also recommend 

including only those objectives that will be answered or addressed by this protocol. The 

sentence, “The following questions may be answered in part......” seems unsatisfactory. 

As written, the monitoring objectives do not appear to be true objectives. Instead, what about 

1.) Determine long-term trends in the distribution and abundance of adult coho salmon 

within reference??? sites of four SFAN streams; 2). Determine long term trends....juvenile 

coho...... 

R The monitoring objectives are focused and seem reasonable. The monitoring questions 

stated after the objectives are retained as guidance for future efforts if funding increases or 

additional opportunities for focused research arise. The statement “but additional 

information will need to be gathered through park or partner efforts.” also clarifies that it is 

not the intent of this program to currently answer these questions. 

C Page 10, Figure 4. I found this Figure to be too busy and confusing. 

R Although we acknowledge that this is a busy figure, we feel that this figure should remain in 

the document as it links the monitoring proposed in the protocol directly to management 

issues such as introducing non-native species. This figure has been a useful tool used to 

explain our monitoring program to resource managers. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.37 

C Page 19, last paragraph. Could the habitat surveys be conducted less frequently to reduce 

costs? 

R No, see Dolloff et al 1993, habitats will change annually due to variations in flow. 

C Page 21, paragraph 2. Redd surveys can be effective for steelhead, and should be 

considered. Disagree with the last sentence in the paragraph. These surveys are used widely 

throughout Oregon and Washington to estimate returns of adult steelhead. If you have the 

crews during the spawning period, it would be good to consider surveys for steelhead. 

R In narrative, Sampling Design Overview, Winter Season, the last sentence was removed and 

replaced with the following sentence. “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).” 

The author agrees with the reviewer that steelhead spawner surveys are possible but as 

stated before the program has decided to focus on coho since their habitat is more confined 

within the monitored watersheds. In addition steelhead have a spawning window of over five 

months and the added cost to continue surveys does not justify the loss in personnel time for 

other surveys such as smolt trapping. 

C Page 29, Table 4. This table is useful, but would benefit from more specificity. For instance, 

could you: 1) define months for summer, winter, and spring; 2) add a column on frequency 

of surveys and number of surveys; etc. 

R Revised table 4 as requested. 

C Page 39, first sentence. Does this mean project lead and two technicians for 26 pp? 

R See Ch. 7 Operational Requiremnets revised itemized budget in Table 6. 

PRC Comments 

C The salmonid protocol initially covered more streams than at present. There is no current 

plan to monitor fish at PINN or JOMU (at least nothing outlined in the plan) so references to 

those two parks should be removed. 

R Revised the narrative Study Area section to clarify the issue of various parks. Author feels 

the need to keep reasoning behind excluding JOMU and PINN in the protocol since these 

are two other parks served by the network I&M program. 

C The “double-strike” font (p. ii, p. xiv, and other places) is visually disruptive. Please convert 

these to a regular-looking font. 

R Double strike font ws removed. An SOP on training field personnel and safety was added. 

C A single table of contents would be helpful (for narrative, SOPs and Appendixes) moving 

the TOC for SOPs from page xiv to v 9and also the TOC for Appendixes) 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.38 

R The list of SOPs was augmented to the main TOC. However, the list of Appendixes are 

provided after the list of tables and figures to be consistent with other TOC developed by the 

network. Detailed TOC are now provided for longer SOPs within those SOPs. 

C Figure 5 (priority watersheds) was left off the figure numbering system, so all the figures 

listed on p. x after Figure 4 should be renumbered (current 5 to 6, 6 to 7, etc.). 

R Fixed caption issue with figure 5 which fixed the numbering system throughout the 

document. 

C Although on page 1 several SFAN parks are listed, in reality only four streams in the 

GOGA/PORE/MUWO area are proposed for monitoring. The protocol needs to be clear 

about this. 

R Removed JOMU from Introduction and Purpose on page 1 so that only GOGA,PORE, and 

MUWO are stated. 

C P1. Fong et al. in press is not in literature cited. 

R Corrected on page 53 of Literature Cited 

“Fong, D., D. Press, and M. Koenen. 2009. San Francisco Bay Area Network (SFAN) 

streamflow monitoring protocol v2.87. Natural Resource Report. National Park Service, 

Fort Collins, Colorado.” 

C P8. There are no procedures to monitor fish at JOMU or PINN, so how can “the following 

questions..be answered in part by this monitoring protocol?”, specifically how is fish 

diversity changing within Franklin Creek at JOMU and within Chalone Creek at PINN? 

R This monitoring question has been removed from the document. 

C P15. Study are does not encompass JOMU and PINN. Last paragraph: so is JOMU a 

medium priority, as PINN is specifically excluded but JOMU not? 

R Revised Narrative Ch. 2 Sampling Design, Study Area “Medium priority streams include 

watersheds that lie within GOGA, PORE and JOMU.” 

C P17, par. 1 l.4: ‘its’, not ’it’s’ 

R Corrected 

C P20, par 3, l2. Dolloff et al. (1993) 

R Corrected 

C P20, last par. The references to tables and figures need to be updated. I think the tables and 

figures originally were modular (starting with table and figure 1 in each SOP) and now are 

continuous. Table 1 of SOP 9 is now table 23, and Figures 1-2 would be Figures 34-36. 

R Fixed number issue especially with figures and with Seasonal Sampling Design section of 

Narrative to reflect the continuous numbering currently present in the document. 

C P22. Figure 1 should be Figure 6. References to Figures 5 and 6 in last par. should be 6 and 

7. As the figures are all off by 1 from now on, I won’t further mention that these need to be 

renumbered and carefully referenced in the text. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.39 

R Corrected figure numbers 

C P27, last line: Dolloff et al. (1993). 

R Corrected 

C Literature cited. This needs a major cleanup. Of the 82 citations, only 38 are cited in the text. 

The other should be removed. 

R These other citations were in the SOPs. We have removed them and now made Literature 

Cited for each SOP. 

C The ones I found in the text include Anderson and McGuire, Bjorkstedt, Brown and 

Ketcham, Brown et al. 1994, CDFG (all four) Carlisle et al., Collins, Cooperrider and 

Carson, Dolloff et al., Downie and Petersen, Duffy, Garza and Gilbert-Horwath, Gurka, 

Hankin and Reeves, Irvine et al., Johnston et al., Ketcham et al. (the 2004 ones), Moyle et 

al., ODFW, Palmer, Pearcy, PFMC, Piepho and Oguto, Pollard et al., Press, Reichmuth et al. 

(all three), Rodgers et al., Schwarz, Starcevich, Van Leeuwen et al., and Williams et al. 

R Removed all SOP specific citations, added missing citations, and removed citations that 

were not in the text. 

C Individual citations that need editing: 

Bjorkstedt: change the font on web citation. 

CDFG: order by year: 1978 first, etc. 

Fong et al (from p. 1) missing 

Garza and Gilbert-Horwath. Latter author needs initials

Ketcham et al. (last one) – assume this is 2004c from page 5? 

Reichmuth et al. there are two of these, both listed as 2006. One needs to be “a” and one “b”.

P169. For Bi-annual CDFG permit, it’s “principal investigator” 

P253-256 missing, text goes from 252 to handwritten 257.

R Bjorkstedt: citation.- citation is now within NRTR guidelines

CDFG: order by year: 1978 first, etc.-fixed 

Fong et al (from p. 1) missing- found and fixed “(Fong et al. 2009)”

“Garza and E.Gilbert-Horwath.” Corrected. 

Ketcham et al. (last one) – assume this is 2004c from page 5?- Yes, fixed

Reichmuth et al. there are two of these, both listed as 2006. One needs to be “a” and one “b”. 

– fixed smolt report is “a” and watershed report is “b” 

P169. For Bi-annual CDFG permit, it’s “principal investigator” – (R) corrected

P253-256 missing, text goes from 252 to handwritten 257. – (R) I do not see this mistake on 

my digital copy.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.40 

Reviewer #1 Comments:

Overview: 

This is an impressive document that describes the rational for and elements of a program for 

monitoring salmon and steelhead in San Francisco Bay area National Parks. The 

presentation of information is straightforward and, for the most part, easy to follow. The 

authors should be commended for documenting and seeking peer review of their monitoring 

program. 

 

Background and objectives: 

This section provides adequate background for the monitoring program. I offer the following 

comments for helping the reader understand this section: 

1. The background (chapter 1) describes the SFAN and states that data collected will 

help evaluate changes in fish communities in the SFAN. Monitoring described here 

is, however, restricted to the Point Reyes National Seashore streams. I recognize that 

their may be agency requirements for this description of the area, but it would be 

more accurate to focus on Redwood, Olema and Pine Gulch creeks or PORE. 

2. The conceptual model presented is process oriented and not very helpful in 

understanding linkages among life stages being monitored. I encourage the authors to 

consider simplifying this model and focusing on what the information from each life 

stage is providing. 

3. The objectives are constructed around sampling methods for different life stages, 

leading to redundancy and some confusion. For example: objective 3 includes 

gathering information on condition from snorkel surveys – something that is not 

possible. I encourage the authors to think about response measures (abundance, size, 

condition) and to use these measures in stating objectives. 

R 1. Monitoring is proposed for both PORE and GOGA streams and is focused on 

Redwood, Olema, and Pine Gulch Creeks as stated in the Study Area section of the 

protocol narrative. 

2. Authors feel that it is necessary to provide linkages to management. The conceptual 

model provides a direct link from monitoring to processes that may be managed by 

the parks. This will be an important tool for parks to use when developing a natural 

resources maintenance backlog that can be utilized to prioritize funding allocations. 

3. Objectives were reworded so that they are constructed around desired trend. 

Sampling methods are retained in the objective to be clear about how trend will be 

determined. I understand the ambiguity with using the word “snorkel” in objective 3 

and agree that condition can not be obtained using snorkel surveys alone. The word 

“snorkel” was removed from objective 3 as these surveys include both snorkel and 

electrofishing phases. The revised objective which states GSS implies the use of 

snorkel surveys combined with electrofishing as a calibration measure. 

Sampling design: 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.41 

The sampling designs for adult salmon and smolts are appropriate and defensible. The 

sampling design for juvenile salmon, however, incorporates both randomized snorkel 

observations of pools and electrofishing of index reaches. The continuation of sampling 

index reaches should be reconsidered. 

Discontinuing long-term data sets is always problematic. However, if these long-term data 

sets are providing biased information they compromise their usefulness. The authors 

acknowledge that previous reviewers have cautioned that index reach sampling cannot be 

used to make inferences about basin (population) responses. Furthermore, making inferences 

about the population status is implicit in the objectives stated earlier. 

The basic problem is that habitat conditions change with hydrology. During wet years, coho 

salmon will use areas unavailable during drier years. Conversely, during dry years, the area 

occupied by coho salmon will contract. Imagine an index reach located in an area of 

transitional habitat. During drier years you might find few coho salmon in this reach and 

conclude that abundance declined when in fact the distribution simply shifted downstream. 

I recommend phasing out index reach electrofishing as follows: 1) begin using electrofishing 

to validate snorkel observations such as suggested by Hankin and Moore. 2) if overlap of 

randomly selected sites with index sites is insufficient, include some index reaches, and 

finally 3) set a time for comparing index reach data with randomly selected site data. Test 

for differences and move on. 

R 

Excerpted from peer review guidance from Dr. Agee. We acknowledge that there is bias 

with this method and note this in the text. 

Analytical techniques: 

The analytical techniques described in the report are current and appropriate. My only 

concern is with the smolt trapping methodology. My observations have been that expanded 

estimates of smolt movement can be strongly biased by: 

1. Failure of marked coho salmon smolts to move after capture. That is, a smolt is 

capture and marked, then re-introduced so as to test trap efficiency. If for behavioral 

reasons, that fish does not continue migration the number of marked fish at large is, 

in effect, smaller than assumed in calculations. 

2. A basic assumption of all mark-recapture experiments (smolt trapping) is that the 

proportion of marked individuals does not change during the experiment. However, 

salmon smolts respond to environmental cues and often move in pulses. Assume you 

mark some constant fraction of the smolts entering the trap. If on day one you 

capture 5 smolts and mark all 5 of them (100%), then on day 2 a pulse of 50 smolts 

enters your trap. Instead of having 100% of the population marked you have only 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.42 

10% of the population marked. This day-to-day variation in proportion of marked 

individuals, I think, contributes to inflation of production estimates. 

Neither of these problems is unique to this monitoring program and are not stated as 

criticisms. Rather, I bring them up in hopes that you may find a creative solution to them. 

R We will do our best to find a creative solution for the problems in the future. In the 

meantime, we are using the best available and accepted methods and the current estimator 

for smolts from the peer reviewed literature. 

Reviewer #2 Comments 

The sampling protocol is relatively well thought out, and I support most of the protocol. 

The following comments deal with clarifications or changes that I feel would substantially 

strengthen the monitoring effort. Report locations in bold underline relate to the 

comments preceding the references. 

 

General Overview of Challenges for Sampling 

1. Coho in central (and much of northern) California are substantially locked in a 3 year life cycle of 

production, since most females are 3 years old at maturity. One consequence is that tracking 

abundance should follow the 3 relatively independent cohorts (as recommended in the protocol). A 

second is that the impacts of “bad” years and weak year classes can repeat as a legacy every 3 years. 

In addition, the fixed life cycle and early winter spawning means that central coast coho are subject 

to substantial risk of year class failure or suppression due to winter drought (or even rainfall delay) 

affecting adult access, or to smolt outmigration during drought or to redd destruction by large mid to 

late winter storms. Even in the freshwater, stochastic events can be major potential drivers of year 

class abundance. The more recent impacts of adverse ocean conditions have had further devastating 

impacts upon coho year class strength. 

Therefore: the most substantial implication of the above conditions is that analyzing “power of test” 

to detect a decades-long 10% or 30% or even a 50% change in coho populations may not be 

biologically realistic for populations that have shown 2 orders of magnitude difference in density 

between the 3 different years classes (1994 vs 1995 and 1996) or even between individual years of 

the same year class (1994 to 1997 to 2000). 

(page 13, 1st

 paragraph and throughout the protocol) 

Therefore: even the index sampling reaches are capable of detecting the large differences in year 

class strength that have been observed over the l5+ years. The electro-fishing sampling of index 

sampling reaches should be continued as a low effort juvenile sampling because of their long-term 

record and as a source of age and size data for juvenile coho (see below). 

R We plan to maintain the index reach monitoring as a low effort juvenile monitoring study. 

At very low spawner density the few fish present frequently spawn and “disappear” without being 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.43 

detected by even the intensive spawner surveys. Juvenile fish are often present (often at substantial 

densities in small streams, where a few redds can nearly saturate rearing habitat) when apparently no 

adults were present. 

Therefore: in poor spawner years the monitoring effort may have to be increased to gage abundance 

or even presence of adults. A similar problem exists for fall sampling in poor years, when the few 

juveniles may be very spotty in their distribution within the watershed and within a few pools 

(usually the “best”) even in reaches where they are present. 

(Page 21, spawner reaches, last paragraph) (page 28, Winter Surveys) 

R Sampling for adults is currently performed at its maximum frequency while maintaining a 

safe work environment. It is not possible to complete stream coverage more than once a 

week with our current crew size. Conducting multiple life stage monitoring will also help us 

gage our survey accuracy. 

3. Deviations from the 3 year life cycle are a potentially crucial factor for monitoring. Adult returns 

will include a variable, but significant, fraction of males that spend only 1 summer in the ocean. 

These 1 year ocean male are important for maintaining gene flow between the 3 numerically 

relatively independent year classes. Demographically, the potentially large differences between 

strength of consecutive year classes, means that 2 year old males must be recorded separately from 3 

year old males in the adult spawner counts (which the protocol calls for but does not emphasize the 

importance of accurately distinguishing age). In a very weak year class preceding a strong year class, 

it is possible for a majority (or most) of the adults to be (precocial) males. A large “adult run” may 

have very low potential egg and juvenile production. 

(page 2, life history is correct “in general”, but the deviations are of substantially ecological 

significance) 

Therefore: Scales may have to be taken from many intermediately-sized fish (among carcasses) 

to clearly determine the appropriate rearing age class. 

(page xxii, monitoring object 1 on winter surveys) 

R Scales are currently sampled from all carcasses for the purpose of ageing. Although a scale 

analysis is not part of our current monitoring objectives, we are currently working with 

researchers from U.C. Berkeley to analyze both adult and juvenile scale samples. For live 

fish precocial males are visually estimated based on size and clearly noted when presenting 

results. See SOP 5 Live Fish Section “Most coho salmon are three years old at spawning. 

However, a variable proportion of precocious two year old males also return to spawn. 

These smaller males are commonly referred to as “jacks”. Age can not be accurately 

determined without carefully analyzing annual growth rings on scales. However, most jacks 

are less than 50 cm (20 in) long and are much smaller than the three-year olds. 

Live Fish: Note the sex and approximate length to the nearest 5 cm of all live fish. If you 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.44 

cannot positively identify a fish’s sex, use the ? option. Surveyors should make every effort 

not to disturb spawning fish. Actively spawning fish can be observed safely from a vantage 

point on the bank. “ 

Also see carcass section “In addition to counting and noting the location of carcasses, we 

are also interested in collecting tissue samples and scales for genetic and age analysis.” 

Similarly, a portion of juvenile coho spend more than 1 year in freshwater. In Waddell and Scott 

creeks in Santa Cruz County, the small percentage (about 2%) of yearlings cannot readily be 

recognized by size difference (length-frequency), because the fish grow relatively little in their 2 year 

in the stream. These holdovers are not the runts (runts don’t survive the 1st

 winter) but are from the 

larger half of the young-of-year. Yearlings tend to be among the larger half of the juveniles, but 

because of substantial variation in fish size within and between sites, they can only be distinguished 

by checking scales. In a weak year class following a strong year class, the small percentage of 

holdover yearlings can constitute a substantial portion (in some cases in Scott and Waddell, all) of 

the weak “year class”. In Prairie Creek the percentage of yearling coho has been found to be 

substantially larger because of generally very slow coho growth. The situation in Marin streams may 

be similar to Santa Cruz or somewhere between Prairie Creek and Santa Cruz. 

Therefore: scale samples should be taken from coho captured during fall electro-fishing and from 

spring smolt trapping to determine ages in at least the weaker year classes. 

Because of their somewhat larger size, and having survived 1 previous winter, yearling coho may 

have disproportionally high winter survival and be a much higher proportion of smolts. Coho 

juvenile ages are given passing mention in the protocols, but should be emphasized as a crucial 

monitoring metric. Analysis (back-calculation) from smolt scales also provides information on how 

much of the smolt’s size was due to growth in late winter and spring (which probably substantially 

varies among years due to water temperatures and turbidity). 

(page xxii, monitoring objectives 2, 4, smolt and fall sampling objectives) (page 28, Index Reach 

Surveys and Spring Surveys) 

R Although we are interested in taking scales from juvenile and smolt life stages we currently 

can only do such sampling on years when fish abundance is low due to the current staffing 

level and work load. During years of high coho abundance field staff are completely 

absorbed with collecting size information and marking fish. 

4. Smolt numbers and sizes are a better measure of freshwater production than fall juvenile 

numbers because of the importance of over-winter mortality. However, a potentially substantial 

number of smolts may be inefficiently sampled in late winter and spring because of movement 

during storm flows. Even with a large and expensive weir, the Shapolvalov and Taft (1954) study 

at Waddell Creek cautioned that their smolts counts had problems in some years and that they had 

no way of checking on the magnitude of winter movements that were missed. 

(page 12, 1st

 paragraph, smolt surveys) 

Therefore: both fall juvenile sampling (with measurement of fish sizes) and spring smolt sampling 

(with fish sizes and scales, #2) is needed. Stream flow related cautions in using smolt “counts” and 

attempts to determine trapping efficiency in higher flows are needed. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.45 

(page xxii, monitoring objective 2, smolt trapping)

R We agree with this comment and this is one of the reasons why we are using a multiple life 

stage monitoring design in this protocol and why smolt trapping is prioritized above juvenile 

monitoring in case of reduced funding. 

5. Although coho sampling is the subject of this set of protocols, the value of enumerating other fish 

species is mentioned as a way monitor watershed condition. However, sculpins (Cottus asper, C. 

aleuticus and C. gulosus) are difficult to sample with an electro-fisher. Their cryptic nature and 

concentration is cover or in shallow, fast-water habitats also means that observational data have little 

validity. Getting good sculpin numbers requires too much effort and subjects salmonids to additional 

electrofisher effort; the informational value for assessing stream health is minimal compared to the 

substantial effort and reduced salmonid sampling efficiency. This is especially true for the high 

densities of C. gulosus found in upper Redwood Creek. 

Therefore: Noting general abundance and species compositon of sculpins (and threespine 

stickleback) is probably sufficient; population abundance data should not be a goal. 

(page xxii, last sentence of 1st

 paragraph, other species)

R Changed sentence in Executive Summary “and any other species incidentally encountered 

during sampling.” 

6. The coho sampling protocol emphasizes sampling pools, where most of the coho are normally 

found. However, at progressively higher densities coho spread out from the deeper pools to shallower 

or simpler pools and then to shallow glide and run habitats. The protocol calls for systematic 

sampling of pools (including potentially all depths and qualities, but the electro-fisher sampling will 

include some other habitats that may show this shift. 

For steelhead most yearlings are also in pools, but a substantial percentage of young-of-year fish 

are in shallow habitats (runs and riffles). When coho are abundant they also substantially exclude 

young-of-year steelhead from the pools. The coho protocols will not give good proportional 

information on the year to year abundance of steelhead. 

Therefore: Sampling for steelhead will have to be modified and include more sampling of riffle and 

run habitat by electro-fishing. Additionally, where and when coho are abundant, coho abundance will 

be a (the) dominant factor in steelhead abundance, and affect interpretations of steelhead “trends” 

(page xxii, last sentence of 1st

 paragraph, steelhead sampling). 

R For this very reason we have clearly stated throughout the protocol that we are focusing 

monitoring efforts on one species, coho salmon. If more resources become available we will 

expand the monitoring program to increase our knowledge on the status of steelhead within 

the parks. Past observations in these watersheds are consistent with this comment. However, 

we are using the methods described by Dollof et. al. in 1993 which is focused on pools and 

has not been adapted for other unit types. 

Other minor comments: 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 7.46 

Page 7, Table 1 and 1 sentence in paragraph 1. Waddell/Scott creeks are in Santa Cruz County, 

but sampling has also been conducted on Gazos Creek in San Mateo County. 

R See Narrative, Other Regional Monitoring Programs, Table 1 added Gazos Creek, fixed 

county of origin, and added NMFS to agency for Redwood, Gazos, Waddell, and Scott 

Creeks. 

 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.1 

SOP 8. Data Management 

Version 1.3 

Revision History Log: 

Prev. 

Version # 

Revision 

Date 

Author Changes Made Reason for Change New 

Version 

# 

NA July 2008 D. Press First draft of SOP. 1.0 

1.0 August 

2008 

D. Adams Formatting NRTR template 1.1 

1.1 December 

2008 

Michael 

Reichmuth 

Minor edits For peer review 1.2 

1.2 November 

2009 

Michael 

Reichmuth 

Added Lit Cited Peer review 

response 

1.21 

1.21 February 

2010 

Michael 

Reichmuth 

Final edits for final 

submittal 

Response to 

editors and internal 

review comments 

1.3 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.2 

Figures 

Page 

Figure SOP 8.1. Table relationships in the master smolt database, 

Smolt_MasterXP.mdb. ......................................................................................................... SOP 8.5

Figure SOP 8.2. Smolt monitoring data entry form. ............................................................ SOP 8.7

Figure SOP 8.3. Table relationships in the spawner monitoring database, 

Spawner_MasterXP.mdb. .................................................................................................... SOP 8.8

Figure SOP 8.4. Spawner monitoring data entry form. ..................................................... SOP 8.10

Figure SOP 8.5. Redd search form, with default values based on sample record in 

figure SOP 8.4. ................................................................................................................... SOP 8.11

Figure SOP 8.6. Redd measurement update form, with records based on criteria 

set in figure SOP 8.5. ......................................................................................................... SOP 8.11

Figure SOP 8.7. Table relationships in the summer monitoring database, 

Summer_MasterXP.mdb. ................................................................................................... SOP 8.13

Figure SOP 8.8. Habitat typing data entry form. ............................................................... SOP 8.17

Figure SOP 8.9. Electrofishing data entry form. ............................................................... SOP 8.19

Figure SOP 8.10. Transect width and depth data entry subform. ...................................... SOP 8.20

Figure SOP 8.11. Substrate tally data entry subform......................................................... SOP 8.20

Figure SOP 8.12. Snorkeling data entry form.................................................................... SOP 8.22

Figure SOP 8.13. Index habitat data entry form. ............................................................... SOP 8.23

Figure SOP 8.14. The basinwide calculation initiation form............................................. SOP 8.25

Figure SOP 8.15. Degrees of freedom form for fish population calculations. .................. SOP 8.26

Figure SOP 8.16. Basinwide fish population estimate results form. ................................. SOP 8.26

Figure SOP 8.17. Degrees of freedom form for fish population calculations. .................. SOP 8.27

Figure SOP 8.18. Basinwide habitat results form. ............................................................. SOP 8.28
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.3 

Overview 

Two critical long-term goals of the San Francisco Bay Area Network (SFAN) Inventory and 

Monitoring Program (I&M) are to: 

• integrate natural resource inventory and monitoring information into National Park Service 

(NPS) planning, management, and decision making 

• share NPS accomplishments and information with other natural resource organizations and 

form partnerships for attaining common goals and objectives 

For the stream fish monitoring program to meet I&M Program goals, a detailed management 

plan is needed to ensure data quality, interpretability, security, longevity and availability. 

This SOP describes how the monitoring protocol meets these data management objectives 

through data entry specifications, database design, quality assurance and control measures, 

metadata development, data maintenance, data storage, and data archiving. In this SOP, 

particular attention is paid to the use of three Microsoft Access project databases used to store 

and maintain winter spawner, spring smolt, and summer juvenile stream fish monitoring data. 

Procedures for data handling and quality assurance/quality control for all monitoring protocols 

implemented by the SFAN monitoring program are detailed in the program’s Data Management 

Plan (Press 2005) and in the National I&M Program’s Data Management Plan (National Park 

Service 2008). All literature cited references are provided in the protocol narrative. 

Database Designs 

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 

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

event data is 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. 

Table Structure: Table relationships for the stream fish smolt database are presented in SOP 8.1. 

The database meets basic compliance with the Natural Resource Database Template (NRDT), an 

application developed by the NPS I&M Program. Data organization is based on the concept of 

surveys, occurring at a specified date, time, and location, recorded in an event table. The 

EventID field in the event table serves as the database primary key, and links to related tables in 

the database associated with the survey events. The LocationID field in the event table links to 

the locations table, thus providing a geo-spatial reference to the data. EventID and LocationID 

codes provide the unique keys for databases built on the NRDT model. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.4 

Event data is represented in the smolt database by the table tblSmoltSurveys. A new record is 

generated each time a smolt trap is checked. TblSmoltSurveys stores data relating to date, time, 

location, general weather and stream conditions, and additional comments on the status of the 

smolt trap. 

Each record in tblSmoltSurveys is linked to tblLocations by the LocationID field. In general, the 

field staff places smolt traps in the same location on each monitored stream every year. 

However, smolt trap locations have and will continue to vary slightly over the years due to 

access issues and stream conditions. The LocationID value is an information-rich text code that 

identifies the stream, based on the stream code, and years of use for each smolt trap location. For 

example, OL-01-SMOLT-2000-2005 would represent the smolt trap location on the Olema 

Creek Mainstem (stream code OL-01) for the years 2000 to 2005. Fields in tblLocations that 

provide a spatial reference for the smolt trap locations include X_Coord, Y_Coord, 

Coord_System, Datum, and UTM_Zone. A descriptive location and directions to the smolt trap 

can be provided in the memo field Loc_Notes. 

TblSmoltCounts catalogs the counts of each species collected in the smolt trap each time it is 

checked. For some species, such as coho salmon and steelhead trout, it is essential that separate 

count records are entered for each life stage of the species captured. For example, separate fish 

count records should be entered for coho smolts, parr, and fry. The count record for each 

species/life stage is divided into the live count and dead count. In addition, the number of new 

fish, recaptured fish, and fish marked is indicated in the count record. The total number of fish 

caught for each species/life stage can be calculated by summing LiveTotal plus DeadTotal or by 

summing New plus Recaptured. The field Species uses codes to denote the species captured, 

which is linked to the look-up table tluSpecies. TluSpecies indicates scientific name, common 

name, and TSN for each species. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.5 

Figure SOP 8.1. Table relationships in the master smolt database, Smolt_MasterXP.mdb. 

Not all fish that are captured are measured (see SOP 4. Spring Smolt Trapping), but records of 

those fish that are measured are entered into tblSmoltMeasurements. The table stores individual 

fish fork length, fish weight (TotalWeight-BagWeight), fish mark location if applicable, and fish 

mark color if applicable. Check boxes note if the measured fish was injured or dead. Mark 

location code and mark color fields are applicable to both newly marked fish and recaptured fish, 

with the difference noted in the mark location code used. For example, values of NLC and RLC 

in the NewMark/Recap field stand for new and recaptured lower caudal mark locations, 

respectively. The mark location codes are linked to and defined in the look-up table 

tluNewRecap_Codes. For ease of summarizing and reporting, each fish is assigned a numeric 

length category based on fork length. The field LengthCat is linked to tluLengthCategory, in 

which each LengthCat value is defined by a 5 mm length range. For example, a fork length of 

108 mm is assigned a length category of 19, which indicates a length range of 106-110 mm. 

Finally, each fish in the fish measurements table is assigned a numeric FishID value, a simple 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.6 

AutoNumber field. The FishID helps to keep the records listed in the order in which they were 

entered, which is essential for error-checking the data. 

Field staff and volunteers present when checking the smolt traps are listed in tblObservers. 

Codes based on the first two letters of the last name and first name are used to record observers. 

Each observer code is listed in tluObservers, where the corresponding observer’s first name, last 

name, and contact information are maintained. 

The EventID field is used to link the primary table tblSmoltSurveys with related records in the 

secondary tables, tblSmoltCounts, tblSmoltMeasurments, and tblObservers. As recommended in 

guidance for the NRDT Version 3.1 (National Park Service 2006), the EventID is an 

automatically generated globally unique identifier (GUID). In MS Access, a GUID is a type of 

binary autonumber field that is sometimes referred to as a Replication ID. Like integer 

autonumbers, GUIDs are automatically generated but are extremely unlikely to be repeated 

among different MS Access databases. TblSmoltSurveys has an additional SmoltID field, which 

is a simple AutoNumber field. The SmoltID field is primarily used to perform quick searches for 

particular records of interest. 

User Interface and Data Entry: The smolt monitoring database employs one simple data entry 

form, frmSmoltSurveys, within which are embedded three subforms for entering fish count, fish 

measurement, and observer records (figure SOP 8.2). The subforms are respectively titled 

sbfSmoltCounts, sbfSmoltMeasurements, and sbfObservers. The observers subform passes data 

through the query qryObserver_DataEntry, which allows for display of the full name of the 

corresponding OBSCODE in the data entry window. 

The macro titled mcrSmoltForm runs a few actions within the smolt data entry form. First, once 

the stream name is entered, the StreamID, Watershed, and WatershedID fields in 

tblSmoltSurveys are automatically generated by looking up these related values in 

tluStreamNames. Second, the macro opens frmObservers when the “Add New Observer” button 

is clicked. Once the user has entered the new observer name and contact information into the 

form, the macro requeries the OBSCODE drop-down list in the observer subform. 

Visual Basic code embedded in the fish measurements subform performs two operations. First, 

the FishWeight value is calculated by subtracting the BagWeight from the TotalWeight. Second, 

the appropriate LengthCat (length category) code is generated based on the ForkLength value. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.7 

Figure SOP 8.2. Smolt monitoring data entry form. 

Spawner Monitoring Database 

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

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 is related to the observations of spawning coho salmon or 

steelhead trout and the measurements of redds encountered during the survey. See SOP 5 

(Spawner Survey) for additional survey information and methods. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.8 

Table Structure: Table relationships for the stream fish spawner database are presented in Figure 

SOP 8.3. The database meets basic compliance with the NRDT, an application developed by the 

NPS I&M Program. Data organization is based on the concept of surveys, occurring at a 

specified date and time, recorded in an event table. The EventID field in the event table serves as 

the database primary key, and links to related tables in the database associated with the survey 

events. The SectionCode field in the fish and redd measurement tables links to the stream tag 

table, thus providing a geo-spatial reference to the data. The SectionCode field, which represents 

a 100 m stream length, marked in the field at the downstream end with a tree tag, is equivalent to 

the LocationID field in the NRDT. 

Figure SOP 8.3. Table relationships in the spawner monitoring database, Spawner_MasterXP.mdb. 

Event data is represented in the spawner database by the table tblSpawnerSurveys. A new record 

is generated each time a survey is performed on a particular stream or stream reach. 

TblSpawnerSurveys stores data relating to stream name, survey reach, date, time, general weather 

and stream conditions, and additional comments. To assist with grouping and summarizing the 

data by field season, each survey is attributed to a spawner season, such as 2007-2008. This is 

particularly helpful since the runs of spawning salmonids in the SFAN parks generally occur 

between December and February. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.9 

TblSpawnFishMeasurements stores all coho salmon and steelhead trout encountered during the 

survey. The field SpCode uses codes to denote the species observed which is linked to the lookup table tluSpecies. TluSpecies indicates scientific name, common name, and TSN for each 

species. Both live and dead fish are recorded in the table, which is specified in the field 

FishCondition. Fish length measurements are stored in the table, which must be estimated for 

live fish. Fish carcass information additionally includes weight, checkboxes if tissue and scales 

are taken, and an indication of the carcass mark code if one was applied or observed (see SOP 5). 

Redd measurement data is stored in the table tblSpawnReddMeasurements. All redds observed 

are attributed to either coho or steelhead, if known, in the ReddSpecies field. The position of the 

redd is noted as right bank (RB), left bank (LB), or mid-channel (MC) in the Bank field. The 

table calculates redd area from the redd length and redd width fields. In addition, the species and 

number of fish attending the redd when it is observed are recorded in the table. Finally, because 

redds may be encountered on multiple surveys and their dimensions may change over time, the 

ReddUpdate and UpdateDate fields indicate if and when the data relating to a particular redd is 

changed. 

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

downstream 100 m section tag. Each tag, entered into the SectionCode field, represents the 

beginning of a 100 m stream section. The Location field indicates how many meters upstream 

from the nearest tag that the observation was made. For example, SectionCode “RW-01-38” and 

a Location value of 20 indicates that an observation was made 3.8 km plus 20 m upstream on the 

Redwood Creek Mainstem (stream code RW-01). Stream codes for each stream monitored are 

cataloged in the table tluStreamNames. Stream tag locations are stored in tblStreamTags. Fields 

in tblStreamTags that provide a spatial reference for the tag locations include X_Coord, 

Y_Coord, Coord_System, Datum, and UTM_Zone. In addition, the Loc_Notes field indicates the 

tree species and stream bank where the tag is located. 

As with the stream fish smolt database, field staff and volunteers that conduct the spawner 

survey are listed in tblObservers. Each observer code is listed in tluObservers, where the 

corresponding observer’s first name, last name, and contact information are maintained. 

The EventID field is used to link the primary table tblSpawnerSurveys with related records in the 

secondary tables, tblSpawnFishMeasurements, tblSpawnReddMeasurements, and tblObservers. 

As recommended in guidance for the NRDT Version 3.1 (National Park Service 2006), the 

EventID is an automatically generated GUID. TblSpawnerSurveys has an additional SpawnID 

field, which is a simple AutoNumber field. The SpawnID field is primarily used to perform 

quick searches for particular records of interest. 

User Interface and Data Entry 

The spawner database employs one simple data entry form, frmSpawnerSurveys, within which 

are embedded three subforms for entering fish observations, redd observations, and observer 

records (figure SOP 8.4). The subforms are respectively titled sbfSpawnFishMeas, 

sbfSpawnReddMeas, and sbfObservers. The observers subform passes data through the query 

qryObserver_DataEntry, which allows for display of the full name of the corresponding 

OBSCODE in the data entry window. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.10 

The macro titled mcrSpawnerForm runs a few actions within the spawner data entry form. First, 

once the watershed and stream names are entered, the WatershedID, StreamID, and StreamCode 

fields in tblSpawnerSurveys are automatically generated by looking up these related values in 

Figure SOP 8.4. Spawner monitoring data entry form. 

tluWatershed and tluStreamNames. For each fish and redd observation, the macro creates the 

correct SectionCode based on the StreamCode and Section# values. Finally, the macro opens 

frmObservers when the “Add New Observer” button is clicked. Once the user has entered the 

new observer name and contact information into the form, the macro requeries the OBSCODE 

drop-down list in the observer subform. 

Database users should only enter data collected on newly observed redds in the redd 

measurement subform embedded within frmSpawnerSurveys (figure SOP 8.4). For older redds 

for which new measurements have been recorded in the field, the user must first select the 

“Update Redds” button in order to open the redd search form, frmReddSearch (figure SOP 8.5). 

When it opens, the redd search form default values for spawner season, watershed, and stream 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.11 

name are set equal to the current values in frmSpawnerSurveys. The user must enter the section 

code (i.e., OL-01-98) and then select the “FindRedds” button in order to bring up the redd record 

that they wish to edit. The form frmReddUpdate (figure SOP 8.6) will only display redd records 

that match the search criteria set in frmReddSearch. The user then simply finds the redd for 

which they have new measurements or information, edits the record, checks the update 

checkbox, and notes the date that the new information was collected in the re-survey date field. 

Figure SOP 8.5. Redd search form, with default values based on sample record in figure SOP 8.4. 

Figure SOP 8.6. Redd measurement update form, with records based on criteria set in figure SOP 8.5. 

Summer Monitoring Database 

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

fish monitoring activities 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. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.12 

The data in the summer database are organized around field events, where a different event is 

represented for 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. See SOP 1 (Basinwide GSS 

Juvenile Coho and Habitat Survey) and SOP 2 (Index Reach Surveys) for additional summer 

survey information and methods. 

Table Structure: Table relationships for the stream fish summer database are presented in figure 

SOP 8.7. The database meets basic compliance with the NRDT. Data organization is based on 

the concept of surveys, occurring at a specified date and time, recorded in an event table. The 

EventID field in the event table serves as the database primary key, and links to related tables in 

the database associated with the survey events. The SubProject field identifies the event record 

as a snorkel, electrofishing, habitat typing, or index reach habitat assessment record. The 

SectionCode fields in the electrofishing event table, snorkeling event table, and stream habitat 

unit measurement table links to the stream tag table, thus providing a geo-spatial reference to the 

data. The SectionCode field, which represents a 100 m stream length, marked in the field at the 

downstream end with a tree tag, is equivalent to the LocationID field in the NRDT. 

Event data is represented in the summer database by the table tblEvents. A new record is 

generated each time a monitoring activity is performed on a particular stream section or habitat 

unit. Event records are generated for each stream unit electrofished, each stream unit snorkeled, 

each index reach habitat assessment, and each habitat typing survey. TblEvents stores basic data 

common to all of these monitoring activities, such as stream name, field season, date, time, and 

data entry date. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.13 

Figure SOP 8.7. Table relationships in the summer monitoring database, Summer_MasterXP.mdb. 

The summer database relates tblEvents to a series of tables equivalent to the NRDT’s 

tbl_Event_Details by one-to-one relationships, depending on the activity performed and noted in 

the SubProject field. These tables store event or survey data specific only to that activity type. 

For example, the habitat unit type, number of passes, and basinwide unit code for each stream 

unit snorkeled is entered into tblSnokelSurveys. 

For each summer monitoring activity, staff and volunteers who conduct the field work are listed 

in tblObservers. Codes based on the first two letters of the last name and first name are used to 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.14 

record observers. Each observer code is listed in tluObservers, where the corresponding 

observer’s first name, last name, and contact information are maintained. 

The EventID field is used to link the primary table tblEvents with all related tables in the summer 

monitoring database. As recommended in guidance for the NRDT Version 3.1 (National Park 

Service 2006), the EventID is an automatically generated GUID. TblEvents has an additional 

NumberID field, which is a simple AutoNumber field. The NumberID field is primarily used to 

perform quick searches for particular records of interest. 

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, entered into the SectionCode field, represents the beginning of a 100 m 

stream section. The Location field indicates how many meters upstream from the nearest tag that 

the observation was made. For example, SectionCode “RW-01-38” and a Location value of 20 

indicates that data was collected 3.8 km plus 20 m upstream on the Redwood Creek Mainstem 

(stream code RW-01). Stream codes for each stream monitored are cataloged in the table 

tluStreamNames. Stream tag locations are stored in tblStreamTags. Fields in tblStreamTags that 

provide a spatial reference for the tag locations include X_Coord, Y_Coord, Coord_System, 

Datum, and UTM_Zone. In addition, the Loc_Notes field indicates the tree species and stream 

bank where the tag is located. 

During habitat typing surveys, each stream habitat unit is assigned a sequential basinwide habitat 

unit code representing the stream location, unit number, and year. For example, the basinwide 

unit code RW-01-244-2007-H indicates that this stream unit is on the Redwood Creek Mainstem 

(stream code RW-01), is the 244th stream habitat unit from the downstream survey start point, 

and is from the 2007 field season. The basinwide unit code is again recorded if and when the unit 

is re-visited 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 fish 

between snorkel surveys and electrofish surveys or compare unit measurements (length, width, 

depth) recorded during separate field events. 

Habitat Typing Data: Records for each habitat typing survey during the summer monitoring 

season are stored separately in the summer database. It may take several surveys to completely 

habitat type one of the stream fish study streams. Habitat typing event data is stored in tblEvents

and tblHabitatTypeSurveys. A SubProject value of HABITAT_TYPE in tblEvents indicates that 

a related record exists in tblHabitatTypeSurveys. Very little information is stored in 

tblHabitatTypeSurveys, including the general start and end points of the survey and the name of 

person who recorded the data. 

TblSummerHabitats stores separate records for each stream habitat unit (scour pool, flatwater, 

riffle, etc.) documented during the habitat typing survey. Each habitat unit, and therefore each 

record, is referenced to a stream section code and assigned a basinwide unit code. Measurements 

for each habitat unit include length, estimated width, measured width (if applicable), estimated 

surface area, measured surface area (if applicable), and maximum depth. In addition, counts of 

woody debris are conducted within each habitat unit, both instream and on the adjacent stream 

banks. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.15 

Electrofishing Data: Records for each stream unit electrofished during the summer monitoring 

season are stored separately in the summer database. Electrofishing event data is stored in 

tblEvents and tblEfishSurveys. SFAN I&M staff may conduct electrofishing work in the network 

parks for a variety of monitoring and management reasons, which are indicated in the tblEvents 

SubProject field. SubProject values that indicate related records in tblEfishSurveys include 

EFISH_INDEX, EFISH_BASIN, EFISH_GSS, RESCUE, and RESTORATION. Each 

SubProject value is defined in the look-up table tluProjects. The section code, basinwide unit 

code, index reach and unit number (if applicable), stream unit measurements (length, width, 

depth), water quality measurements, and habitat data for each stream unit electrofished are stored 

in tblEfishSurveys. 

TblSummerPasses contains information about each electrofishing pass conducted in the stream 

unit, including the pass time, volts, and current setting. Because stream units are sometimes 

initially cleared of fish with one or more seine passes before electrofishing commences, 

tblSummerPasses also has a pass type field. 

TblSummerCounts catalogs the counts of each species captured through each pass of the 

electrofisher. Both the pass number and pass type are indicated in tblSummerCounts. For some 

species, it is essential that separate count records are entered for each life stage of the species 

captured. For example, separate fish count records should be entered for steelhead young of year 

(YOY) versus older year classes (1+). The count record for each species/life stage is divided into 

the live count and dead count. The total number of fish caught for each species/life stage can be 

calculated by summing the Count plus Mortality fields. The field Species uses codes to denote 

the species captured, which is linked to the look-up table tluSpecies. TluSpecies indicates 

scientific name, common name, and TSN for each species. 

Not all fish that are captured during electrofishing are measured (see summer SOPs), but records 

of those fish that are measured, and the pass number during which they were captured, are 

entered into tblSummerMeasurements. The table stores individual fish fork length and fish 

weight (TotalWeight-BagWeight). Check boxes note if the measured fish was injured or dead. 

For ease of summarizing and reporting, each fish is assigned a numeric length category based on 

fork length. The field LengthCat is linked to tluLengthCategory, in which each LengthCat value 

is defined by a 5 mm length range. For example, a fork length of 108 mm is assigned a length 

category of 19, which indicates a length range of 106-110 mm. At times, bulk weights of 

unmeasured fish are recorded. For this reason, the field NumberOfFish indicates the number of 

fish that each data record corresponds to. Finally, each record in the fish measurements table is 

assigned a numeric FishID value, a simple AutoNumber field. The FishID helps to keep the 

records listed in the order in which they were entered, which is essential for error-checking the 

data. 

For each species/life stage collected in an electrofished stream unit, a population estimate for the 

stream unit is calculated following methods developed by the U.S.D.A. Forest Service for 

Microfish 3.0, a software product designed for fisheries biologists and resource managers for the 

purpose of analyzing fisheries data (Van Deventer and Platts 1985, 1989). Among other 

calculated values, data stored in tblCalculatedValues include the basinwide unit code, species 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.16 

and life stage, total catch, population estimate, population estimate confidence intervals, standard 

error, and fish density. 

Snorkeling Data: Records for each stream unit snorkeled during the summer monitoring season 

are stored separately in the summer database. Snorkeling event data is stored in tblEvents and 

tblSnorkelSurveys. A SubProject value of SNORKEL in tblEvents indicates that a related record 

exists in tblSnorkelSurveys. The section code, basinwide unit code, index reach and unit number 

(if applicable), unit type, and number of snorkel counts (or passes) for each stream unit are stored 

in tblSnorkelSurveys. 

TblSummerPasses contains information about each snorkel pass conducted in the stream unit, 

including the pass time and visibility. The pass type is by default always set to “Snorkel”. 

TblSummerCounts catalogs the counts of each species observed during each snorkel pass. Both 

the pass number and pass type are indicated in tblSummerCounts. For some species, it is 

essential that separate count records are entered for each life stage of the species captured. For 

example, separate fish count records should be entered for steelhead young of year (YOY) versus 

older year classes (1+). The field Species uses codes to denote the species observed, which is 

linked to the look-up table tluSpecies. TluSpecies indicates scientific name, common name, and 

TSN for each species. 

Index Habitat Data: Although not intended for long-term trend analyses at this point, the SFAN 

fisheries staff collects ancillary habitat data on each stream index reach monitored during the 

summer field season. The data is nevertheless housed in the summer monitoring database. Index 

habitat data is stored in tblEvents and tblIndexHabitat. A SubProject value of 

INDEX_HABITAT in tblEvents indicates that a related record exists in tblIndexHabitat. The 

index reach number, woody debris tally, vegetation cover values, and stream bank condition 

assessment for each index reach are stored in tblIndexHabitat. 

User Interface and Data Entry 

Habitat Typing Data 

Database users enter habitat typing data into the form frmHabitatSurveys (figure SOP 8.8). 

Because habitat typing data is stored in both tblEvents and tblHabitatTypeSurveys, the control 

source for the habitat typing data entry form is the query qryHabitatTypeDataEntry, which 

passes data into the appropriate tables. So that the query only returns and then displays habitat 

typing records in the data entry form, the query limits records to those with a tblEvents 

SubProject value of HABITAT_TYPE. 

 

Two subforms embedded within frmHabitatSurveys are used for entering stream habitat units 

and observer records. The subforms are respectively titled sbfSummerUnits and sbfObservers. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.17 

Figure SOP 8.6. Habitat typing data entry form. 

The observers subform passes data through the query qryObserver_DataEntry, which allows for 

display of the full name of the corresponding OBSCODE in the data entry window. 

The macro titled mcrHabitatForm runs a few actions within the snorkeling data entry form. First, 

once the watershed and stream names are entered, the WatershedID, StreamID, and StreamCode 

fields in tblEvents are automatically generated by looking up these related values in 

tluWatershed and tluStreamNames. In addition, the macro opens frmObservers when the “Add 

New Observer” button is clicked. Once the user has entered the new observer name and contact 

information into the form, the macro requeries the OBSCODE drop-down list in the observer 

subform. 

Within sbfSummerUnits, each stream unit documented in the field is entered in numerical 

sequence. For each stream unit, the macro mcrHabitatForm creates the correct SectionCode 

based on the StreamCode and Section# values. The macro generates the correct basin wide unit 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.18 

code for the habitat unit based on the stream code, basin wide unit number, and field season. 

Finally, the macro calculates average width, estimated surface area, measured surface area, and 

residual pool depth based on data collected for each stream unit. 

Electrofishing Data 

Database users enter electrofishing data into the form frmEfishSurveys (figure SOP 8.9). 

Because electrofishing survey data is stored in both tblEvents and tblEfishSurveys, the control 

source for the electrofishing data entry form is the query qryEfishDataEntry, which passes data 

into the appropriate tables. So that the query only returns and then displays electrofishing records 

in the data entry form, the query limits records to those with the following tblEvents SubProject 

values: EFISH_INDEX, EFISH_BASIN, EFISH_GSS, RESCUE, and RESTORATION. 

Five subforms embedded within frmEfishSurveys are used for entering pass information, fish 

counts, fish measurements, fish population estimates, and observer records. The subforms are 

respectively titled sbfElectrofishPasses, sbfElectrofishCounts, sbfSummerMeasurements, 

sbfCalculatedValues, and sbfObservers. The observers subform passes data through the query 

qryObserver_DataEntry, which allows for display of the full name of the corresponding 

OBSCODE in the data entry window. 

The macro titled mcrEfishForm runs a few actions within the electrofishing data entry form. 

First, once the watershed and stream names are entered, the WatershedID, StreamID, and 

StreamCode fields in tblEvents are automatically generated by looking up these related values in 

tluWatershed and tluStreamNames. For each stream unit electrofished, the macro creates the 

correct SectionCode based on the StreamCode and Section# values. The macro generates the 

correct basin wide unit code for the electrofished habitat unit based on the stream code, basin 

wide unit number, and field season. The macro also calculates the habitat unit’s surface area and 

volume based on the length, average width, and average depth. Finally, the macro opens 

frmObservers when the “Add New Observer” button is clicked. Once the user has entered the 

new observer name and contact information into the form, the macro requeries the OBSCODE 

drop-down list in the observer subform. 

Selecting the “Enter Transect Data” button in the electrofishing data entry form opens a subform, 

sbfTransectDepths, for entering stream unit depth measurements along separate transects (figure 

SOP 8.10). The user enters the transect width, depth measurements across each transect, and the 

number of depth measurements per transect, and then the macro mcrEfishForm calculates the 

average depth for each transect. Although none of the data values in sbfTransectDepths are 

permanently stored in the database, mcrEfishForm will use them to calculate the stream unit 

average width and average depth by clicking the corresponding buttons. These values are stored 

in tblEfishSurveys. 

Selecting the “Enter Substrate Tallies” button in the electrofishing data entry form opens a 

subform, sbfSubstrateTally, for entering stream unit substrate tallies collected at each depth 

measurement point along separate transects (figure SOP 8.11). Substrate tallies are not entered 

for each transect, but for all transects combined. Clicking the “Calculate Substrate Percentages” 

button, however, will calculate the percentage of each substrate category observed in the stream 

unit and store these values in tblEfishSurveys. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.19 

Figure SOP 8.7. Electrofishing data entry form. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.20 

Figure SOP 8.8. Transect width and depth data entry subform. 

Figure SOP 8.9. Substrate tally data entry subform. 

Visual Basic code embedded in the fish measurements subform performs two operations. First, 

the FishWeight value is calculated by subtracting the BagWeight from the TotalWeight. Second, 

the appropriate LengthCat (length category) code is generated based on the ForkLength value. 

Selecting the “Microfish Calculations” button generates population estimate values for all fish 

captured within the stream unit and stores the values in tblCalculatedValues. Clicking the button 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.21 

executes Visual Basic code that performs the calculations following methods developed by the 

U.S.D.A. Forest Service for Microfish 3.0, a software product designed for fisheries biologists 

and resource managers for the purpose of analyzing fisheries data (Van Deventer and 

Platts 1985, 1989). In order for the population estimate to calculate correctly, a fish count record 

must be entered for each fish species/life stage and each fish pass, even if no fish were captured 

and the count was zero. 

Snorkeling Data 

Database users enter snorkeling data into the form frmSnorkelSurveys (figure SOP 8.12). 

Because snorkeling survey data is stored in both tblEvents and tblSnorkelSurveys, the control 

source for the snorkeling data entry form is the query qrySnorkelDataEntry, which passes data 

into the appropriate tables. So that the query only returns and then displays snorkeling records in 

the data entry form, the query limits records to those with a tblEvents SubProject value of 

SNORKEL. 

Three subforms embedded within frmSnorkelSurveys are used for entering pass information, fish 

counts, and observer records. The subforms are respectively titled sbfSnorkelPasses, 

sbfSnorkelCounts, and sbfObservers. The observers subform passes data through the query 

qryObserver_DataEntry, which allows for display of the full name of the corresponding 

OBSCODE in the data entry window. 

The macro titled mcrSnorkelForm runs a few actions within the snorkeling data entry form. First, 

once the watershed and stream names are entered, the WatershedID, StreamID, and StreamCode 

fields in tblEvents are automatically generated by looking up these related values in 

tluWatershed and tluStreamNames. For each stream unit snorkeled, the macro creates the correct 

SectionCode based on the StreamCode and Section# values. The macro generates the correct 

basin wide unit code for the electrofished habitat unit based on the stream code, basin wide unit 

number, and field season. Finally, the macro opens frmObservers when the “Add New Observer” 

button is clicked. Once the user has entered the new observer name and contact information into 

the form, the macro requeries the OBSCODE drop-down list in the observer subform. 

Within the fish count subform, the database user must enter fish count records for each pass for 

those species/life stages for which a basinwide population estimate will be calculated following 

methods outlined in Dollof et al. (1993). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.22 

Figure SOP 8.10. Snorkeling data entry form. 

Index Habitat Data 

Database users enter index habitat data into the form frmIndexHabitat (figure SOP 8.13). 

Because index habitat data is stored in both tblEvents and tblIndexHabitat, the control source for 

the index habitat data entry form is the query qryIndexHabitatDataEntry, which passes data into 

the appropriate tables. So that the query only returns and then displays index habitat records in 

the data entry form, the query limits records to those with a tblEvents SubProject value of 

INDEX_HABITAT. 

 

For entering observer records, one subform, sbfObservers, is embedded within frmIndexHabitat. 

The observers subform passes data through the query qryObserver_DataEntry, which allows for 

display of the full name of the corresponding OBSCODE in the data entry window. 

The macro titled mcrIndexHabitatForm runs a few actions within the index habitat data entry 

form. First, once the watershed and stream names are entered, the WatershedID, StreamID, and 

StreamCode fields in tblEvents are automatically generated by looking up these related values in 

tluWatershed and tluStreamNames. Finally, the macro opens frmObservers when the “Add New 

Observer” button is clicked. Once the user has entered the new observer name and contact 

information into the form, the macro requeries the OBSCODE drop-down list in the observer 

subform. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.23 

Figure SOP 8.11. Index habitat data entry form. 

Basinwide Habitat and Population Estimates

A series of queries have been developed within the summer database that follows the guidelines 

developed by Dollof 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 long-term 

trend analyses. 

Before performing any calculations, it is essential that the data be thoroughly error-checked and 

prepped for analysis. The following data preparations are required: 

• Within tblSummerHabitats, all backwater, side channel units, and units outside of the 

study area must be excluded from analysis by checking the Exclude_BW check box field. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.24 

• Habitat units that were electrofished for the purposes of basinwide population estimates 

should have the CalibrationPool check box checked in tblEfishSurveys or 

frmEfishSurveys. 

• Those calibration pools which were electrofished but must subsequently be excluded 

from analysis must have the Exclude_BW check box field checked in tblEfishSurveys or 

frmEfishSurveys. 

• Snorkel units in which the bounded count method was performed using several snorkel 

counts should have the Bounded_Count check box checked in tblSnorkelSurveys or 

frmSnorkelSurveys. 

• Snorkel units in which the initial snorkel count was calibrated using the bounded count 

method should have the Calibration_Pool check box checked in tblSnorkelSurveys or 

frmSnorkelSurveys. 

• Snorkel units that must be excluded from analysis should have the Exclude_BW check 

box checked in tblSnorkelSurveys or frmSnorkelSurveys. 

• Basin wide unit code values in tblSummerHabitats, tblSnorkelSurveys, and 

tblEfishSurveys must be properly generated. 

• Snorkel fish count records must be entered for each pass and for each species/life stage 

for which a basinwide population estimate will be calculated. 

• Electrofishing fish count records must be entered for each species/life stage captured and 

each pass. 

• All values in tblCalculatedValues must be properly and accurately calculated. 

Once the data has been prepared with approval from the SFAN Data Manager, records in 

tluBasinWide are created that dictate which basinwide analyses the database is capable of 

performing. Fields in tluBasinWide are stream name, field season, species, and life stage. For 

example, if the database is prepped for calculating a basinwide population estimate for coho 

young-of-year in 2008 on the Olema Creek Mainstem, these are the values in tluBasinWide that 

would be entered for species, life stage, field season, and stream name, respectively. For streams 

and years for which only basinwide habitat calculations will be performed, the species and life 

stage fields should be left blank. 

In order to run the basinwide calculations, the database user must open frmBasinWide (figure 

SOP 8.14). Several features in the form prevent the user from attempting to make calculations 

for which the database is not prepared. First, the drop-down menus for stream name, field 

season, species, and life stage are generated from tluBasinWide and are limited to values based 

on the previous fields’ selection. For example, if the user selects Bear Valley Creek, coho will 

not be an option for analysis since this species does not exist in this stream and there is no 

corresponding coho species value for Bear Valley Creek in tluBasinWide. Second, if one of the 

fields in the form is changed, from Olema Creek Mainstem to Redwood Creek Mainstem for 

example, all subsequent fields will be cleared and re-queried. Finally, calculations are not 

possible unless all of the correct fields are filled in. Instead, a message box is displayed alerting 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.25 

the user that all fields must be complete. Actions that help accomplish these control measures are 

built into the macro mcrBW_Form. 

Figure SOP 8.12. The basinwide calculation initiation form. 

The steps required to run the basinwide fish population and habitat calculations are outlined 

below. 

Fish Population Calculations: 

1. Open frmBasinWide and fill in values for stream name, field season, species, and life 

stage. 

2. Click the “Fish Correlations” button to view all stream units incorporated into the 

analysis. These units were snorkeled and then electrofished for calibration, and the 

corresponding number of fish from snorkel surveys (MaxCount) and electrofishing 

surveys (BW_Pop) for each unit are displayed. The query that is opened is titled 

BW_FishCount_Compare. Inspect the data for potential errors. 

3. Click the “Check df” button to determine the degrees of freedom used in the analysis. 

The value will be one minus the number of records just viewed in the query 

BW_FishCount_Compare. The form that is opened is titled frmFish_DF (figure SOP 

8.15). 

4. Use a Student's t Distribution table to look up the t-value for this degrees of freedom in 

the column for p = 0.025 (one-tailed probability). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.26 

5. Click the “Get Fish #s” button and enter the t-value when prompted. The calculated fish 

values will be displayed in the form frmBWFish_Report (figure SOP 8.16). The control 

source for the form is the query BWFish_Report. 

Figure SOP 8.13. Degrees of freedom form for fish population calculations. 

Figure SOP 8.14. Basinwide fish population estimate results form. 

Habitat Calculations: 

1. Open frmBasinWide and fill in values for stream name and field season. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.27 

2. Click the “Area Correlations” button to view all stream units incorporated into the 

analysis. Stream measurements for these units were both estimated and measured for 

calibration, and the corresponding estimated and measured surface areas for each unit are 

displayed. The query that is opened is titled HABS. Inspect the data for potential errors. 

3. Click the “Check df” button to determine the degrees of freedom used in the analysis. 

The value will be one minus the number of records just viewed in the query HABS. The 

form that is opened is titled frmHabitat_DF (figure SOP 8.17). 

4. Use a Student's t Distribution table to look up the t-value for this degrees of freedom in 

the column for p = 0.025 (one-tailed probability). 

5. Click the “Get Hab #s” button and enter the t-value when prompted. The calculated 

habitat values will be displayed in the form frmHabitat_Report (figure SOP 8.18). The 

control source for the form is the query HABS_Report. 

Figure SOP 8.15. Degrees of freedom form for fish population calculations. 

Look-up Table Database 

Several look-up tables are essential to all three stream monitoring databases. For ease of 

maintenance and to ensure that the look-up table records are identical in all three databases, these 

tables are stored and managed in a separate stream fish look-up table database. The database is 

titled StreamFish_LU_Tables.mdb. The look-up tables are established as linked tables within 

each of the monitoring databases. All of the tables in the look-up database have been described 

previously, and include: 

• tluLengthCategories 

• tluObservers 

• tluSpecies 

• tluStreamNames 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.28 

• tluStreamTags 

• tluWatershed 

The only table intended for editing via the monitoring databases is tluObservers, which is most 

easily accessed through the form frmObservers. The other tables should only be edited or added 

to by the SFAN Data Manager or the Project Leader. 

Figure SOP 8.16. Basinwide habitat results form. 

Annual Data Work Flow 

The master monitoring databases 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 Point Reyes National Seashore 

(PORE). The satellite data tables are blank in each of the databases, but the look-up tables are 

populated and ready for use. The SFAN Data Manager updates all default values, such as field 

season, prior to distribution. The databases are provided in MS Access XP format. 

Satellite databases should be backed up regularly during the course of the season. CDs are a 

good option for back-ups. Databases can be also be regularly copied to an archive on the 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.29 

network, to a hard drive, or both. File names of back-up databases should include the date of the 

back-up, such as: Smolt08_Satellite_050108_BackUp. 

At the end of each season, the stream fish 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. The Data Manager works with the Project Lead and the field staff to 

complete any final edits or additions to the seasonal dataset. See Section 4.0 Data Verification 

and Validation Procedures for more information. 

Once certified, the Data Manager imports the satellite data into the master database, appends the 

data to the appropriate tables, and archives the satellite database within the I&M directory. A 

copy of the final satellite database and a new copy of the master database are provided to the 

stream fish staff at PORE. 

Quality Assurance and Quality Control 

The success of the stream fish 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 stream fish 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. 

Data Collection 

Attention to detail during the data collection phase is crucial to overall data quality. Unlike a 

typographical error that occurs during data entry, an incorrect observation in the field is not 

easily corrected. The stream fish monitoring program adopts the following guidelines regarding 

data collection that affect data quality: 

• Field crews will receive proper training in data collection and recording. 

• Field equipment will be regularly maintained and calibrated. 

• Data will be recorded on pre-formatted, project-specific datasheets that reflect the overall 

design of the project and are designed to minimize the amount of writing necessary to 

effectively record observations. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.30 

• The format of field datasheets will be reflected in the computer data entry interface to 

help ensure all relevant information is recorded and subsequent data entry errors are 

minimized. 

• Field forms will be reviewed for completion and errors each day in the field. 

Data Entry 

Data entry is the process whereby the raw data collected in the field are transferred from paper 

field forms into the project databases. The stream fish field staff performs all data entry into 

seasonal satellite databases. The goal of data entry is to transcribe field observations into a 

computer database with 100% accuracy, although errors are unavoidable. Several QA/QC 

practices help to reduce errors during the data entry phase: 

• Data will be entered as soon as reasonably possible after collection 

• Data entry will be completed by someone familiar with data collection. The Project 

Leader or SFAN Data Manager must ensure that data entry staff is familiar with the 

database software, database structure, and any standard codes in the databases. At a 

minimum, data entry technicians should know how to open a data entry form, create a 

new record, edit an existing record, and exit the database properly. They must also learn 

how to correct mistakes made while typing. 

• Data will be entered into pre-designed database forms that resemble field sheets to the 

greatest extent possible. Data entry forms maximize error control wherever possible, 

include the use of default values, limiting data entry domains to values in drop-down 

menus, and auto-generating certain codes (i.e., StreamID, SectionCode, 

BasinWideUnitCode). 

• Data will be entered, one logical "set" at a time. Paper forms are initialed and dated when 

completed to avoid confusion about what has been entered and what has not. 

Data Verification 

Following data entry, subsequent data verification is conducted to ensure that the raw data on the 

paper datasheets matches the entered data. The stream fish field staff verifies all data in the 

seasonal satellite databases before forwarding on to the SFAN Data Manager. The following 

steps occur during the data verification phase: 

• Data verification is carried out by staff thoroughly familiar with data collection and entry 

• A visual review after data entry is performed with one person reading aloud from the 

original datasheets while a second person checks the corresponding entered data in the 

database. 

• Errors in the data are immediately corrected once discovered. 

• When complete, the Verified check-box in the database record is checked and the paper 

datasheet is initialed and dated. 

• All records (100%) are verified against the original source data. 

• A subset of randomly selected records (10%) should be reviewed after initial verification 

by the Project Leader. If errors are found, the entire data set should be verified again. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.31 

Data Validation 

Data verification checks that the digitized data match the source data, while data validation 

checks that the data make sense. Although data entry and verification can be handled by 

personnel who are less familiar with the data, validation requires in-depth knowledge about the 

data. The SFAN Data Manager performs all data validation procedures on the seasonal satellite 

databases before integrating the data into the master databases. The Data Manager consults with 

the Project Lead, the field staff, or directly reviews the datasheets to correct any errors that are 

discovered. 

During the data validation phase, the Data Manager checks all three monitoring databases for the 

following and makes corrections as needed: 

• Verified checkbox checked for all data records. 

• Erroneously generated records with no actual data. 

• Orphaned records within the sub-tables (i.e., no link back to tblEvents). 

• Data outliers: applies to both numerical and date/time values. 

• Logic errors (i.e., start time is after the end time, more fish measured than were actually 

counted in the smolt trap). 

• Accurate generation or calculation of automated fields (i.e., stream ID, basinwide unit 

code, fish length category, measured surface area). 

• Correct values for fields with fixed domains (i.e., species codes, unit types, fish mark 

codes). Complete data entry for all required fields (i.e., section code, life stage value for 

all salmonids, redd species). 

In addition to the above, the Data Manager regularly checks the seasonal satellite databases for 

elements specific to each database type. 

Smolt Database: 

• FishWeight value is equal to TotalWeight-BagWeight. 

• The number of marked fish in the measurement table is equal to the marked fish in the 

count table. 

• LiveTotal+DeadTotal is equal to New+Recaptured. 

• The number of fish count records is equal to or greater than the fish measurement 

records. 

Spawner Database: 

• ReddArea equals ReddLength*ReddWidth. 

• Fish species observed on redd corresponds to redd type and fish observation records. 

• Weight values not entered for live fish. 

Summer Database: 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.32 

• Basin wide unit code values equal between tblEfishSurveys and related records in 

tblCalculatedValues. 

• Check to see if duplicate habitat measurement, snorkel or electrofish records exist for 

unique basin wide unit codes. 

• Set wood counts from habitat typing and index habitat surveys from null to 0. 

• Count records for each species/pass combination are at least equal to the sum of the 

associated measured fish records. 

• Count records for each species/pass combination are equal to the sum of the 

NumberOfFish values in the associated measured fish records. 

• Index Reach/Unit values consistently entered in electrofish and snorkel forms for same 

basin wide unit code. 

• SectionCode values consistently entered for same stream units in habitat, electrofish, and 

snorkel forms. 

• Pass type values consistent between tblSummerPasses and tblSummerCounts. 

• Pass number is equal to the number of related pass records for electrofish and snorkel 

surveys. 

• Pass number value reported in tblSummerMeasurements is within the number of passes 

for the unit. 

• Check that there are no duplicate pass counts for the same species/life stage. 

• Check that there are no duplicate pass numbers accounted for in the pass table for a single 

stream unit. 

• Prepare all data for basinwide fish population and habitat calculations as described 

previously (User Interface and Data Entry (Summer Database) – Basinwide Habitat and 

Population Estimates). 

Version Control Guidelines and Database History 

Version control guidelines for the stream fish 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 

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 ...). With proper controls and 

communication, versioning ensures that only the most current database version is used for 

queries and analyses. Significant database re-design may require approval by the project 

manager, review by other data management staff, and revisions to this data management SOP. 

The database version number should be included in the file title of the database, for example, 

Smolt_MasterXP_v1_00. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.33 

The Data Manager maintains history logs of each of the stream fish 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 located at: 

Inpgogamahe1\Divisions\Network I&M\Individual Vital Signs\Streamfish Assemblages\ 

data\databases 

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 is 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. 

The database history may also be used each year to summarize anything that was unique or 

changed about the year’s methodology and is therefore reflected in the annual dataset. Notes on 

techniques for collection and review of data are also very helpful. 

Metadata Procedures 

The NPS GIS Committee requires all NPS GIS data layers 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 stream 

fish 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 stream fish 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. 

The metadata records for the stream fish monitoring databases will initially be developed in 

Dataset Catalog v3.0, an MS Access metadata development and catalog tool developed by the 

NPS I&M Program. Dataset Catalog is currently the preferred tool to begin metadata records for 

MS Access databases because of its ability to harvest entity and attribute information from this 

database format. 

The metadata records will be exported from Dataset Catalog as XML files and completed in NPS 

Metadata Tools and Editor v1.1 (NPS MTE), thus allowing for all NPS-specific elements in the 

metadata records to be completed. When completed, metadata records, but not the data 

themselves, 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 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.34 

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). 

The NPS Data Store can be accessed at: 

http://science.nature.nps.gov/nrdata/

Data Storage and Archival Procedures 

Golden Gate National Recreation Area 

All master data files for the stream fish monitoring project are housed at Golden Gate National 

Recreation Area (GOGA). The SFAN I&M Program office and the SFAN Data Manager are 

stationed at GOGA. The master databases, all currently in version 1_00, reside within the 

Master_Databases folder at: 

Inpgogamahe1\Divisions\Network I&M\Individual Vital Signs\Streamfish Assemblages\ 

data\databases 

Inpgogamahe1\Divisions\Network I&M must always be mapped as the Z drive. The following 

folders reside within the above “databases” directory: 

Master_BackUps: Back-up copies of the active master databases should be stored here. File 

names of back-up databases should include the date of the back-up, such as: 

Smolt_MasterXP_050108_BackUp. 

Fish_Dbase_Archives: When a master database is converted to a new version number, the final 

previous database version should be archived here. Final seasonal satellite databases and all 

project legacy databases are also stored in this archive directory. There are separate folders for 

smolt, spawner, and summer monitoring databases. 

Lookup_Dbase: This folder stores the look-up table database, StreamFish_LU_Tables.mdb. All 

stream fish databases at GOGA that link to the look-up table database must be pathed to this 

directory. 

Point Reyes National Seashore 

The stream fish 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 stream fish 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 

Inppore05\Resources must always be mapped as the U drive. The following folders reside within 

the above directory: 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.35 

Master_Databases: Copies of the active master smolt, spawner, and summer master databases are 

stored here. The SFAN Data Manager provides copies of the master databases to PORE each 

time they are updated. 

Working_Databases: Active seasonal satellite databases are stored here. The field staff may also 

place copies of the master databases or final satellite databases here for creating queries or data 

summaries. 

Lookup_Dbase: This folder stores the look-up table database, StreamFish_LU_Tables.mdb. All 

stream fish databases at PORE that link to the look-up table database must be pathed to this 

directory. 

Data Distribution 

In order for the stream fish monitoring program to inform park management and to share its 

information with other organizations and the general public, guidance documents, reports, and 

data must be easily discoverable and obtainable. 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/

Although the stream fish monitoring database will not be posted for public download, as 

previously mentioned, 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 online 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. The public version of NatureBib is in development by the NPS I&M program. 

All documents produced by the stream fish monitoring program will be published in either the 

Natural Resource Report Series or the Natural Resource Technical Report Series following 

guidance from the NPS Natural Resource Program Center in Fort Collins, Colorado. The Natural 

Resource Publications Management home page hosts a list of all documents published in the 

NRR and NRTR Series. The home page can be found at: 

http://www.nature.nps.gov/publications/NRPM/

Literature Cited 

National Park Service (NPS). 2006. Natural Resource Database Template Version 3.1 

documentation. Natural Resource Program Center, Office of Inventory, Monitoring, and 

Evaluation, Fort Collins, Colorado. Online. 

(http://science.nature.nps.gov/im/apps/template/index.cfm). Accessed 5 February 2010.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 8.36 

National Park Service (NPS). 2008. Data management guidelines for inventory and monitoring 

networks. Natural Resource Report NPS/NRPC/NRR—2008/035. National Park Service, 

Fort Collins, Colorado. Online. (https://science1.nature.nps.gov/naturebib/biodiversity/2009-

1-28/National_DM_Plan_v1.1.pdf). Accessed 15 January 2010. 

 

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. 

Press, D. T. 2005. Data management plan for the San Francisco Bay Area Network Inventory 

and Monitoring Program. National Park Service, San Francisco, California. 

Van Deventer, J. S., and W. S. Platts. 1985. A computer software system for entering, managing, 

and analyzing fish capture data from streams. Research Note INT-352, Intermountain Forest 

and Range Research Station. USDA Forest Service, Ogden, Utah. 

Van Deventer, J. S., and W. S. Platts. 1989. Microcomputer software system for generating 

population statistics from electrofishing data: Users guide for Microfish 3.0. General 

Technical Report INT-254. USDA Forest Service, Intermountain Forest and Range 

Experiment Station, Ogden, Utah. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.1 

SOP 9. Sampling Site Descriptions 

Version 1.2 

Revision History Log 

Prev. Version 

# 

Revision 

Date 

Author Changes Made Reason for 

Change 

New 

Version #

 January 

2007 

Marcus 

Koenen 

Excerpted from 

other SOP 

Clarification 1.0 

 1.0 March 

2007 

Michael 

Reichmuth 

Review of SOP Update SOP to 

current project 

status 

1.01 

1.01 May 2008 Sarah 

Carlisle 

Changes 

suggested by 

MR 

 1.1 

1.1 July 2008 Sarah 

Carlisle, 

Marcus 

Koenen 

Added in maps 

of monument 

tags and tables of 

locations. Edited 

 1.11 

1.12 August 

2008 

Michael 

Reichmuth 

Reviewed and 

made minor edits

Clarification 1.12 

1.13 September 

2008 

Michael 

Reichmuth 

Add GPS 

Coordinates 

Update SOP 1.13 

1.13 September 

2008 

Dawn 

Adams 

Formatting For peer review 1.14 

1.14 November 

2008 

Michael 

Reichmuth 

Remove 

Presence/Nondetect 

Update 1.15 

1.15 December 

2008 

Michael 

Reichmuth 

Minor edits For peer review 1.16 

1.16 November 

2009 

Michael 

Reichmuth 

Added Lit Cited Peer review 

response 

1.17 

1.17 February 

2010 

Michael 

Reichmuth 

Final edits for 

final submittal 

Response to 

editors and 

internal review 

comments 

1.2 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.2 

Figures 

Page 

Figure SOP 9.1. Olema Creek mainstem spawner reach 2 with monument tags and 

index sites included. ............................................................................................................. SOP 9.8

Figure SOP 9.2. Olema Creek mainstem spawner reach 3 with monument tags and 

index reaches included. ........................................................................................................ SOP 9.9

Figure SOP 9.3. Olema Creek mainstem spawner reach 4 with monument tags and 

index reaches included. ...................................................................................................... SOP 9.10

Figure SOP 9.4. Olema Creek mainstem spawner reach 5 with monument tags and 

index reaches included. ...................................................................................................... SOP 9.11

Figure SOP 9.5. Olema Creek mainstem spawner reach 6 with monument tags and 

index reaches included. ...................................................................................................... SOP 9.12

Figure SOP 9.6. Pine Gulch Creek spawner survey reaches (also shows index 

reaches). ............................................................................................................................. SOP 9.14

Figure SOP 9.7. Redwood Creek mainstem spawner reach 1 with monument tags 

and index reaches included. ............................................................................................... SOP 9.16

Figure SOP 9.8. Redwood Creek mainstem spawner reach 2 with monument tags 

and index reaches included. ............................................................................................... SOP 9.17

Figure SOP 9.9. Redwood Creek mainstem spawner reach 3 with monument tags 

and index reaches included. ............................................................................................... SOP 9.18

Figure SOP 9.10. Cheda Creek and Devil's Gulch (no longer surveyed) spawner 

survey reaches. ................................................................................................................... SOP 9.19

Figure SOP 9.11. Location of smolt traps on SFAN streams in Marin County, 

California. .......................................................................................................................... SOP 9.22

Figure SOP 9.12. Basinwide GSS Survey reach for Olema Creek. ................................... SOP 9.24

Figure SOP 9.13. Basinwide GSS Survey reach for Pine Gulch. ...................................... SOP 9.25

Figure SOP 9.14. Basinwide GSS Survey reach for Redwood Creek. .............................. SOP 9.26

Figure SOP 9.15. Location of eight index reaches in Olema Creek Watershed. ............... SOP 9.31

Figure SOP 9.16. Locations of six site index reaches in the Pine Gulch Creek 

Watershed. ......................................................................................................................... SOP 9.33

Figure SOP 9.17. Locations of seven index reaches in the Redwood Creek 

Watershed. ......................................................................................................................... SOP 9.35
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.3 

Tables 

Page 

Table SOP 9.1. Index reach locations for Olema Creek .................................................... SOP 9.27

Table SOP 9.2. Index reach locations for Pine Gulch ....................................................... SOP 9.28

Table SOP 9.3. Index reach locations for Redwood Creek ............................................... SOP 9.29
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.4 

Overview 

Monitoring efforts will focus primarily on watersheds in Golden Gate National Recreational 

Area (GOGA), Muir Woods National Monument (MUWO), and Point Reyes National Seashore 

(PORE), that contain coho salmon (Oncorhynchus kisutch) and steelhead trout (O. mykiss). 

These watersheds represent the majority of salmonid-bearing streams in Marin County, 

California, and support the southernmost stable populations of coho salmon on the western 

Pacific Coast. SFAN park streams and associated tributaries in Marin County which currently 

contain populations of both coho and steelhead include Redwood Creek, Pine Gulch Creek, 

Olema Creek, and Lagunitas Creek. This standard operating procedure (SOP) describes all of the 

sampling sites for this monitoring project. 

Monument Tags 

Permanent, sequentially numbered monument tags are located at 100-m intervals along the 

mainstems of Olema Creek, Pine Gulch, and Redwood Creek (Appendix L). These tag locations 

were marked using GPS during the summer of 2007 and are used to identify sampling sites. 

The markers are aluminum tags with plastic survey flagging that have been attached to trees 

along the stream bank. In areas without trees, the tags were placed on steel “rebar” stakes and 

driven into the bank. Each tag is imprinted with a unique code that describes the watershed, 

stream, and distance from the stream mouth. More specifically, the identification scheme is a set 

of three separate two- or three-digit codes. These tags were spatially located using UTM 

coordinates. 

XX-##-## 

The first code is the watershed designation. The two-letter abbreviations are: 

Lagunitas Creek LG 

Olema Creek OL 

Pine Gulch Creek PG 

Redwood Creek RW 

The second numerical code identifies the specific stream within a watershed. The mainstem is 

always designated as 01. The tributary codes are listed on maps for each watershed and will be 

provided by the PORE and GOGA staff. 

The third numerical code identifies the stream segment and corresponds with the measured linear 

distance upstream from the mouth. The beginning point for each of the segmented streams has 

been labeled as 00 (meter 0). The first 100-m segment receives the code 01. The 15th segment 

(1500 m upstream from the mouth) receives the code 15. For example, a monument tag may 

appear as: 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.5 

The translation is Olema Creek watershed, mainstem, 4,800 m. 

Replacing Tags 

During summer basinwide habitat surveys, any missing tags will be noted on the datasheet. At 

the end of the summer monitoring season or prior to the start of winter spawner surveys, field 

crews will make a return visit to the locations of the missing tags. Using the GPS coordinates, 

they will locate where the tag is supposed to be. If intensive searching reveals the tag to be truly 

missing, then the tag will be replaced. If the object to which the tag was attached is no longer 

there, then the nearest comparable object will be used in its place. This new location will be 

marked using either a Trimble or Garmin GPS unit, and the coordinates along with location 

descriptions will be downloaded and added to the database upon returning to the office. 

In order to make new tags for replacing those that are lost, take a blank aluminum tag and the 

stamping kit located in the PORE fish garage; stamp the tag code into the aluminum tag. These 

tags can be affixed to any large permanent object, preferably a tree, as close to the stream as 

possible. Place the tag in an obvious spot on the tree and back it with flagging so as to make 

spotting it on subsequent surveys as easy as possible. Permanent objects include posts or trees. 

Most often the tag is affixed to an alder; however, redwoods, bays, and fir trees are generally 

more preferable due to their longevity. 

Sampling Sites 

Spawner Reaches 

The spawner surveys are conducted along spawner reaches which are 2–4 km sections of 

streams. Teams of 2–4 observers walk upstream along creek margins and banks where possible, 

and look for live fish, carcasses, and redds. 

Olema Creek: A large section (17.6 km) of the mainstem of Olema Creek has been surveyed 

since 1993. The section is currently divided into 7 survey reaches starting 1 km above the 

confluence with Lagunitas Creek and ending at the Highway 1 culvert at milepost 19.94 (figures 

SOP 9.1–5). Reaches are delineated to facilitate sampling based on access, length, and the 

existence of permanent landmarks for reach boundaries. 

• Spawner reach 1: Is rarely surveyed. It goes from 1 km above the confluence with 

Lagunitas Creek to the Bear Valley Road Bridge in the town of Olema (1.6 km). Access 

the reach through the marsh below the house at Olema Marsh. Drive through the gate to 

 

 OL 01 48 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.6 

the park residence. Enter the stream by crossing the wetland below the house and 

following the trail to the creek. The reach ends at the Bear Valley Road Bridge. 

• Spawner reach 2: Goes from the Bear Valley Bridge to the confluence with Truttman 

Creek (3.2 km). Park at the pullout next to the bridge, and access the creek on the 

upstream side of the bridge. The reach ends at the confluence with Truttman Creek. Exit 

the creek by back tracking approximately 50 m to a spot flagged on the right bank of the 

stream. There is a steep trail that goes up the ridge to the Truttman house. 

• Spawner reach 3: Goes from Truttman Creek to the horse trail crossing at the Stewart 

Ranch (2.6 km). It starts at the Truttman Creek confluence with Olema Creek mainstem. 

Pull out and park at the Truttman house. Access is via a path that starts below the barn 

and ends at the creek. This path follows the fence line for a time before going downhill 

into the creek, and is flagged. The reach ends at the horse crossing at Stewart Ranch. Exit 

the creek by climbing the left bank and finding the Rift Zone Trail. Follow Rift Zone 

Trail back to the Stewart Horse Camp. 

• Spawner reach 4: Goes from the Stewart Ranch at the horse trail crossing to the first 

Hwy. 1 bridge at Five Brooks (1.3 km). Park at the Stewart Horse Camp and follow Rift 

Zone Trail downstream until reaching the horse crossing at the Ranch itself. The reach 

ends at the first Highway 1 bridge at the Five Brooks turnoff. Exit the stream by climbing 

the right bank into the open field beyond the confluence of Giacomini Gulch. 

• Spawner reach 5: Goes from the Highway 1 bridge next to the Five Brooks to the 

abandoned Lime Kilns (2.8 km). Turn off into the pullout just past Giacomini Gulch and 

before John West Fork. Access the creek by crossing the open grassy area and moving 

downstream along the shoreline before putting in at the bridge. The reach ends at the 

abandoned Lime Kilns. Exit the stream at the Lime Kilns and climb the hill to Highway 

1. 

• Spawner reach 6: Goes from the Lime Kilns to the abandoned Randall ranch house (1.7 

km). 

• Park at the pull out on Highway 1 between mile markers 22.22 and 22.07, at the top of 

the hill beyond John West Fork. Walk down the hill towards the stream, angling 

upstream. When you hit the stream, walk upstream until coming to the abandoned lime 

kilns, at the start of the survey reach. The reach ends at the old Randall house. To exit, 

follow one of the paths near the Randall Gulch confluence with Olema Creek mainstem 

up to Highway 1. 

• Spawner reach 7: Goes from the Randall house to the Hwy. 1 culvert at milepost 19.94 

(4.1 km). Pull out in front of the Randall house and park. Cross Highway 1 to Olema 

Creek and enter at the confluence of Randall Gulch and Olema Creek mainstem. The 

reach ends at the Highway 1 culvert crossing at mile post 19.94. Exit the stream there and 

climb to the road side. This survey reach is rarely surveyed due to unsafe stream 

conditions and a decrease in spawning activity upstream of the Randall Gulch 

confluence. 

In addition to the mainstem of Olema Creek, surveys are often conducted on some of the larger 

tributaries as personnel and flow conditions allow. In particular John West Fork Creek should be 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.7 

surveyed on the same day as the mainstem of Olema Creek to provide a more accurate PLD 

count for the watershed. For each tributary, survey reaches start at the mouth and generally 

continue upstream as long as no passage barriers exist. The tributaries, many of them unnamed 

on U.S. Geological Survey (USGS) 7.5 minute maps, are listed in order of survey priority: 

1. John West Fork located 10.9 km above the mouth of Olema Creek at Hwy. 1 milepost 

22.67. (survey reach from tributary mouth to 2 km upstream) 

2. Quarry Gulch located close to the Olema Cemetery 4.1 km above the mouth of Olema 

Creek at Hwy. 1 milepost 25.35. 

3. Giacomini Gulch located 10.8 km above the mouth of Olema Creek at Hwy. 1 milepost 

22.78 

4. Horse Camp Gulch located 9.6 km above the mouth of Olema Creek at Hwy. 1 milepost 

23.26. 

The headwaters of Olema Creek (considered a tributary for the purposes of the survey due to its 

physical characteristics) beginning at Hwy.1 milepost 19.94. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.8 

Figure SOP 9.1. Olema Creek mainstem spawner reach 2 with monument tags and index sites included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.9 

Figure SOP 9.2. Olema Creek mainstem spawner reach 3 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.10 

Figure SOP 9.3. Olema Creek mainstem spawner reach 4 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.11 

Figure SOP 9.4. Olema Creek mainstem spawner reach 5 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.12 

Figure SOP 9.5. Olema Creek mainstem spawner reach 6 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.13 

Pine Gulch: Since 1997, the NPS has conducted surveys along a 9-km section of the mainstem of 

Pine Gulch Creek. Coho salmon were first spotted during surveys in the winter of 2000–2001. 

Due to private property access issues and the nature of the watershed, the survey reaches are 

longer than normal (figure SOP 9.6). This requires a solid day to conduct the survey with two 

teams. Additional surveyors are required to complete the McCurdy tributary. 

The spawner surveys start at the Olema-Bolinas Road Bridge and extend upstream to at-least the 

Teixeira Ranch. Complete surveys should extend up the mainstem to the Pacific Coast Learning 

Center/Hagmaier complex. The section encompasses most of the stream length that would be 

potentially used by coho salmon. 

• Spawner reach 1. Starts at the Olema-Bolinas Road Bridge and goes to the Teixeira 

Ranch (6.0 km). Park at the pullout after the bridge and access the creek on the upstream 

side of the bridge. The end of the reach is at the Teixeira Ranch. 

• Spawner reach 2: The reach begins at the Teixeira Ranch (upstream beyond Teixeira) and 

goes to approximately monument marker 100 (3.5 km). Turn off of Highway 1 at the 

Teixeira Ranch entrance. Continue across the bridge to the barns, and park next to the 

smaller barn. Access the creek through the fence alongside the barn. The end of reach 

two is at monument tag 100. The field crew must hike back down the creek in order to 

exit. 

• Spawner reach 3 (McCurdy Reach): This reach is McCurdy Creek and it is rarely 

sampled. It goes from Teixeira Ranch up McCurdy Creek tributary (2 km). McCurdy 

Creek is the most likely tributary to support a significant population of coho salmon and 

steelhead trout. Fish passage in McCurdy is limited by a culvert under Hwy 1, 

approximately 130 m from the mouth, which has been identified as one of the highest 

priority barriers in Marin County (Taylor and Associates 2003). Monitoring would be 

conducted to quantify response. The survey reach extends 2 km upstream from the 

confluence with Pine Gulch Creek, to a series of steep cascades 1 km upstream. To 

access it, park at the pullout for the Olema Valley Trail. Follow the trail until it is parallel 

to the large stand of eucalyptus before heading towards Pine Gulch Creek. Stay to the left 

of the eucalyptus grove. Upon hitting Pine Gulch Creek, head downstream until the 

reaching the confluence of McCurdy Creek and Pine Gulch Creek mainstem. The 

McCurdy reach starts there. Head upstream, approximately 2 km. To exit the stream, 

retrace the route taken in. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.14 

Figure SOP 9.6. Pine Gulch Creek spawner survey reaches (also shows index reaches). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.15 

Redwood Creek: Since 1994, the NPS has conducted annual surveys along a 7.4 km section of 

the mainstem of Redwood Creek (figures SOP 9.7–9) between the Pacific Way Bridge and a 

small waterfall within Mt Tamalpais state park just upstream of monument tag #74. The section 

encompasses most of the stream length used by coho salmon. To facilitate sampling, the section 

is divided into three reaches: 

• Spawner reach 1: Starts at the Pacific Way Bridge and goes to the Kent Creek confluence 

in Mt. Tamalpais State Park (2.7 km). Access to the creek is on the upstream side of the 

bridge. The reach goes to the Kent Creek confluence with Redwood Creek mainstem, 

within Mt. Tamalpais State Park. Exit the creek by following the trail out of the creek up 

to the footbridge and up to the road. 

• Spawner reach 2: Starts at the confluence between Kent Creek and Redwood Creek 

mainstem and goes to Bridge 1 in MUWO (2.4 km). Park at the pullout closest to the 

footbridge on Redwood Creek Trail in Mt. Tamalpais State Park. Access is on the 

upstream side of the footbridge. The reach goes to Bridge 1 in MUWO. Exit by climbing 

out of the creek and walking back along the boardwalk. 

• Spawner reach 3: Starts at Bridge 1 in MUWO and continues to approximately 500 m 

above Bridge 4 at monument tag 74. Access the creek by parking at the visitor center 

parking lot and following the boardwalk up to the first bridge. Exit the creek by climbing 

out of the creek and following the Bootjack Trail back to the parking lot. 

Portions of Fern and Kent Creeks, the two largest Redwood Creek tributaries, will also be 

sampled. The reach on Kent Creek extends from the confluence with Redwood Creek to a water 

fall, approximately 1 km upstream that is impassable to migrating adults. The Fern Creek section 

has been surveyed since 1994 and extends between the Redwood Creek confluence and a series 

of steep cascades 1 km upstream. The upstream limit of surveys on Redwood Creek and the high 

gradient cascade on Fern Creek are not impassable barriers for steelhead. However, neither coho 

salmon adults nor juveniles have been observed above these points and they are assumed to be 

coho barriers. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.16 

Figure SOP 9.7. Redwood Creek mainstem spawner reach 1 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.17 

Figure SOP 9.8. Redwood Creek mainstem spawner reach 2 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.18 

Figure SOP 9.9. Redwood Creek mainstem spawner reach 3 with monument tags and index reaches 

included. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.19 

Cheda Creek: Cheda Creek (figure SOP 9.10), a Lagunitas Creek tributary, has been surveyed 

since 1996–1997 to detect the presence or absence of coho. The NPS completed a fish passage 

project in the fall of 2000, coho salmon spawning in the upper part of the creek above the fish 

passage project site was detected for the first time during the 2004–2005 spawning season. A 

total of about 1.2 km is typically surveyed, including a 0.8 km reach below the fish passage 

improvement and 0.4 km above. 

Figure SOP 9.10. Cheda Creek and Devil's Gulch (no longer surveyed) spawner survey reaches. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.20 

Smolt Trapping Sites 

 Smolt trapping is conducted by placing traps at the downstream end of the watershed to gain an 

accurate smolt productivity index for the entire watershed upstream of the trap. Smolt trapping is 

conducted at Olema, Pine Gulch, and Redwood Creek. Both Pine Gulch and Redwood Creeks 

are first order streams and thus an accurate production estimate can be obtained through 

downstream migrant trapping. Although Olema Creek is not a first order stream, the proximity of 

its confluence with Lagunitas Creek is relatively close to Tomales Bay and is thus an acceptable 

trapping location. 

The location of the trap and watershed size plays a role in the equipment used to conduct smolt 

trapping. Smolt traps are located as far downstream as possible on the sampled watersheds or 

sub-watersheds, preferably near the mouth of the stream. Sites are selected based upon channel 

character, accessibility, and protection. Sites should also be reasonably accessible to facilitate 

equipment transport, and stream channel gradient should be suitable for type of trap being used. 

Sites must have adequate vertical gradient to push water through the pipe. This is easier in 

smaller and steeper watersheds. We have found with operation of traps at the lower end of 

mainstream systems, that performance is closely linked to spring runoff conditions. The trap 

operations may be washed over, and consideration should be taken to construct traps that readily 

open for high flow conditions. 

Procedures for selecting smolt sample locations: Sites are selected based upon channel character, 

accessibility, and protection. The sites have adequate vertical gradient to push water through the 

pipe. At the existing Pine Gulch Creek site and other low gradient sites, the trap requires 

significant sand bagging around the weir as hydraulic head is necessary to push water into the 

trap. Inadequate head in the system results in very low flow through the pipe and inefficient 

trapping. 

 

Accessibility and security are also important aspects of the trapping site. The structure should be 

located in an area where equipment can be easily carried to the site. In addition, it is important 

that the trap be located in a place where vandalism is not likely to occur. Trap locations should 

be assessed on an annual basis prior to trap construction. If the channel morphology changes to a 

state that is no longer conducive smolt trapping, a new location should be located as close to the 

previous trapping location as possible. New trapping locations will be spatially located using 

UTM coordinates. 

Location of Traps: See figure SOP 9.11. 

• Olema Creek: The Olema Creek smolt trap is located on NPS lands approximately 1.9 

km upstream of the mouth of the creek, approximately 60 m upstream of tag 15. Due to 

high flow failure and the capture of California red-legged frog tadpoles in the trap box, 

we relocated the site to an area upstream of the potential red legged frog breeding habitat. 

To access the site, enter the Olema pasture on the right side of Bear Valley Road at the 

top of the hill above the park administration offices. Follow the ranch road along the 

ridge. Take the right hand fork and follow it down the hill. Turn right again at the pond 

and follow the road to the creep feeder at the bottom of the hill and park there. The smolt 

trap site is on the other side of the cattle fence. 

• Pine Gulch: The location of the Pine Gulch trap site is determined in large part by access, 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.21 

since the lower 4.5 km of the mainstem is on mostly private lands. The current location is 

about 2 km above the mouth and was chosen with the cooperation of the landowner in 

Paradise Valley (see Appendix M: Landowner access agreement). The original trap 

location in 1999, on public lands 300 m upstream of the mouth, was subject to high 

public access and vandalism. In order to reach the trap site, take Bolinas Road towards 

Bolinas. After passing a long stand of cypress trees, take the dirt road to the right that 

follows the line of cypress. Follow this road until it forks, and stay to the left. Go past 

two houses and pull in beneath the fruit tree next to the intern housing (a collection of 

small travel trailers). The trap site is slightly downstream of this pull out. 

• Redwood Creek: The Redwood Creek mainstem site is situated approximately 400 m 

upstream of the mouth of the creek adjacent to the Muir Beach picnic area. The trap is 

downstream of all tributaries to Redwood Creek thus providing an accurate estimate of 

the watershed production. To access the site, drive down to the Muir Beach Parking Lot 

and park alongside the picnic tables. Cross the cable fence and walk across the restoration 

area to the creek. The smolt trap site starts below the end of the willows on the upstream 

side of the restoration area. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.22 

Figure SOP 9.11. Location of smolt traps on SFAN streams in Marin County, California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.23 

Basinwide GSS Surveys 

Basinwide GSS surveys are conducted along the mainstems of Olema, Redwood, and Pine Gulch 

Creeks. Survey reaches were delineated to capture the majority of the summer juvenile coho 

habitat found within each of the three creeks. Survey reaches may be adjusted on each creek on 

an annual basis to reflect the current water year. 

• Olema Creek: A large section (11.5 km) of the mainstem of Olema Creek has been 

surveyed since 2003. The section currently starts 3.5 km above the confluence with 

Lagunitas Creek at the Vedanta Bridge and ending at the confluence of Randal Gulch 

with Olema Creek (figure SOP 9.12). 

• Pine Gulch: Since 2001, the NPS has conducted surveys along a 10-km section of the 

mainstem of Pine Gulch Creek. Coho salmon were first spotted during surveys in the 

winter of 2000–2001. The section currently starts approximately 1.0 km above the 

confluence with Bolinas Lagoon at the Bolinas Road bridge and ending 2.5 km above the 

Texeira ranch (figure SOP 9.13). 

• Redwood Creek: Since 2004, the NPS has conducted continuous annual surveys along a 

7.4 km section of the mainstem of Redwood Creek (SOP 9.14) between the Pacific Way 

Bridge and a small waterfall within Mt Tamalpais state park just upstream of monument 

tag #74. The section encompasses most of the stream length used by coho salmon. 

Index Reaches 

Index reaches are located in the Olema, Pine Gulch, and Redwood Creeks. Index reaches were 

selected based upon general conditions including Rosgen channel type (Rosgen 1994), land use 

patterns, other habitat characteristics, and professional judgment and knowledge of the 

watersheds to encompass appropriate fish habitats including a combination of pools, riffle, and 

runs (Beamish 2000). Because habitats change dynamically, the index reach boundaries may be 

adjusted slightly from year to year to incorporate this variability. The lengths of individual index 

sites will range from over 100 m for the lower reaches of the mainstems to 70–100 m on the 

upper mainstem reaches. Each index reach is designed to include at least two meander lengths 

(roughly 35–40 mean stream widths) so that at least three riffle-pool sequences are included 

(Simonson et al. 1994). Within the high priority streams in the network there are 23 index 

reaches (tables SOP 9.1–3 and figures SOP 9.15–17) of which 21 index reaches are currently 

being sampled on an annual basis. 

Several steps are taken to facilitate the relocation of each index reach. The upstream and 

downstream ends of each site are marked with flagging and labeled aluminum tree tags. The 

location of the nearest permanent 100-m monument tag is recorded, and digital photos are taken 

and archived electronically. UTM coordinates will be recorded for the downstream and upstream 

ends of all index reaches for inclusion in a GIS database. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.24 

Figure SOP 9.12. Basinwide GSS Survey reach for Olema Creek. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.25 

Figure SOP 9.13. Basinwide GSS Survey reach for Pine Gulch. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.26 

Figure SOP 9.14. Basinwide GSS Survey reach for Redwood Creek. 
SOP 9.27 

Table SOP 9.1. Index reach locations for Olema Creek (coordinates from Garmin backpack unit, *= no differential correctio

# 

Name/ Location 

Reach ID (stream km) Description 

Dec deg downstream Dec deg up

lat long lat 

1 Olema Flat 1.2 Downstream of riparian gap in Olema Flat 

2 Vedanta 3.7 ~30 m upstream of Vedanta vehicle bridge 38.02170 -122.471 38.02146 3 Cemetery 

Pond 

4.9 ~100 m downstream of Cemetery Pond in 

Stewart’s pasture 

38.01477 -122.471 38.01461 

4 Truttman 6.3 At Truttman Gulch confluence w/ Olema 

mainstem 

5 Bldg 

168/Shook’s house 

7.6 ~70 m downstream of Park Quarters # 168 38.00599 -122.462 38.00587 

6 Horse Camp 9.4 ~200 m downstream of Stewart’s Horse Camp 38.00195 -122.455 38.00173 7 5 Brooks 10.8 At Giacomini Gulch confluence w/ Olema 

mainstem 

*37.59491 -122.452 *37.59479 

8 Lime 

Kilns/Upper Olema 

13.0 ~200 m downstream of Lime Kilns *37.59249 -122.450 *37.59234 
SOP 9.28 

Table SOP 9.2. Index reach locations for Pine Gulch (coordinates from Garmin backpack unit, *= no differential correction)

# 

Name/ Location 

Reach ID (stream km) Description 

Dec deg downstream Dec deg u

lat long lat 

1a MCOSD (Open 

Space) 

0.3 Downstream of dredge pool in Open Space 37.55150 -122.412 37.55152 

1b Murch’s 0.4 By stream gauge @ Murch’s footbridge 37.55107 -122.413 37.55110 1c Weber’s 0.7 ~50 m upstream of Bolinas Rd. bridge 37.55061 -122.414 37.55055 2 Paradise 

Valley 

2.8 By lone redwood at entrance road to Paradise 

Valley 

37.55340 -122.422 37.55353 

3 Gorge 3.9 Downstream end of gorge at end of 

Martinelli’s road 

37.55517 -122.424 37.55520 

4 BPUD pasture 5.1 Downstream end of (former) BPUD pasture 5 lower Teixeira 6.8 ~50 m downstream of Olema Valley Trail 

lower xing 

37.56545 -122.425 37.56566 

6 upper Teixeira 7.8 ~20 m upstream of Olema Valley Trail upper 

xing 

37.57160 -122.430 37.57166 
SOP 9.29 

Table SOP 9.3. Index reach locations for Redwood Creek (coordinates from Garmin backpack unit, *= no differential correc

# 

Name/ Location 

Reach ID (stream km) Description 

Dec deg downstream Dec deg up

lat long lat 

7 Pacific Way 

Bridge 

0.1 J. Smith site #7, below Pacific Way bridge 4190845.6

20 

530 

6 Banducci 0.8 J. Smith site #6, sampled by NPS 4191377.3

30 

536859.000 

4191434.650 

530 

5 Frank Valley 

Road Bridge 

1.9 J. Smith site #5, above Frank Valley Road 

bridge in Mt. Tam State Park 

4192072.780 

536751.220 

4192148.190 

530 

4 Kent Creek 2.9 J. Smith site #4, above Kent Creek confluence 

in Mt. Tam State Park 

4192688.690 

537271.220 

4192777.510 

530 

3 Miwok Trail 

Crossing 

3.8 J. Smith site #3, below Miwok Trail Crossing 4193098.5

10 

537770.520 

4193143.200 

530 

2 MUWO 

restroom 

5.2 J. Smith site #2, sampled by NPS 4193946.3

40 

537612.890 

4194030.370 

530 

1 MUWO 

boardwalk 

6.3 by boardwalk above MUWO bridge 3 4194790.4

10 

537150.140 

4194863.830 

530 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.30 

Olema Creek: There are 8 reaches on Olema Creek (figure SOP 9.15). 

• Index reach 1: is no longer sampled on Olema Creek, due to impossible access. 

• Index reach 2: is located immediately upstream of the Vedanta vehicle bridge. After 

turning off of Highway 1 at the Vedanta Retreat road, field crews should cross the bridge 

and pull out alongside the road on the left. A trail leads down to the stream channel. 

• Index reach 3: is located near Cemetery Pond on Stewart Ranch. Access is through the 

gate on the right side of Highway 1, after passing the cemetery and crossing Quarry 

Gulch. Follow the ranch road through the gate and into the second pasture to the right. 

Continue on the ranch road until you pass the wetland area, and then turn to the left and 

drive across the pasture until coming to the fence. The index is across the fence and 

downstream approximately 50 m, below the large woody debris jam. 

• Index reach 4: is located at the Truttman Creek confluence with the Olema Creek 

mainstem. Turn off of Highway 1 into the Truttman House complex and park near the old 

dairy barn. Follow the path that starts downhill from the barn, down to Olema Creek. The 

path is marked with flagging, and intersects with the creek approximately 50 m 

downstream from the bottom of the index reach. The index reach’s upstream end is 

covered by an extremely large woody debris jam. 

• Index reach 5: is located downstream of one of the park residences. Turn off of Highway 

1 into the driveway of Building 168 and pull off to the side of the driveway. The path 

starts at the gate below the house and continues down to the creek, letting out into the 

middle of the index reach. The index reach’s bottom is approximately 30 m downstream. 

• Index reach 6: is located near the Stewart Horse Camp. Pull off of Highway 1 at the 

Stewart Horse Camp entrance and park close to the Rift Zone Trail entrance. Follow the 

Rift Zone Trail up to the top of the hill and continue down the trail for approximately 75 

m. A small deer trail will split off to the right, heading downhill to the creek. Follow this 

trail downhill until reaching the creek. Index reach 6 is located approximately 200 m 

downstream of the Horse Camp. 

• Index reach 7: is located near the Giacomini Gulch confluence with the Olema Creek 

mainstem. Pull into the pullout area upstream of the Giacomini Gulch Highway 1 

crossing, across from the Giacomini Ranch house. Cross the open area, heading back 

towards Giacomini Gulch, and go down to the creek. Index reach 7 is located 

approximately 30 m upstream of the confluence with Giacomini Gulch. 

• Index reach 8: is located downstream of the old Lime Kilns along Olema Creek. Go up 

the hill beyond John West Fork and pull off of Highway 1 at the pullout between mile 

markers 22.22 and 22.07. Head down the hill towards the creek. The index is 

approximately 30 m upstream of tag 129. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.31 

Figure SOP 9.15. Location of eight index reaches in Olema Creek Watershed. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.32 

Pine Gulch Creek: There are 8 reaches on Pine Gulch Creek (figure SOP 9.16). 

• Index reach 1a: is located within the Marin County Open Space property. Pull out and 

park at the Murch’s farm and head downstream. It is downstream of the dredge pool, and 

located at about tag 1. 

• Index reach 1b: is located by the stream gauge placed just downstream of the Murch’s 

footbridge. As with index 1a, park at the Murch’s farm and walk down to the footbridge. 

Access is to the side of the footbridge. The index starts just downstream of the 

footbridge, close to the stream gauge. 

• Index reach 1c: is located approximately 50 m upstream of the creek crossing at the 

Bolinas Road Bridge. Pull off of the road at the pull out just beyond the bridge. Access 

this site by walking up the Star Route Farms driveway to the right and walk towards the 

creek and go past the farm house. A small path will lead toward the creek behind the farm 

house. Once you reach the creek the downstream end of the index reach will start 

immediately upstream of the trail entrance. The index starts at approximately 20 m below 

tag 6. 

• Index reach 2: is located in Paradise Valley. Take Bolinas Road towards Bolinas. After 

passing a long stand of cypress trees, take the dirt road to the right that follows the line of 

cypress. Follow this road until it forks, and stay to the right. After crossing a cattle guard, 

continue around the first bend in the road and pull off in the large grassy area on the left 

side of the road. Move down into the creek. The index is below the only redwood in the 

line of trees along the creek. The index starts at approximately 30 m upstream of tag 24. 

• Index reach 3: is located at the downstream end of the gorge at the end of the Martinelli’s 

road. Follow the road past the pullout for index 2 and continue past the Martinelli farms. 

Follow the road up the hill, staying to the right whenever roads branch off. Pass through 

the gate and turn to the left. Go past the pond and turn left again, going through the gate; 

park at the end of that ranch road. Follow the creek upstream until reaching the 

downstream end of the gorge. The index starts just past the large woody debris jam, 

approximately 20 m upstream of tag 35. 

• Index reach 4: This index reach is currently not sampled due to private property access 

issues. 

• Index reach 5: is located near the Olema Valley Trail lower crossing. Follow Olema 

Valley Trail from Hwy 1 towards the lower crossing. Follow the deer trail to the left 

approximately 30 m upstream of the stream crossing. Index reach is approximately 15 m 

downstream of tag 64. 

• Index reach 6: is located near the Olema Valley Trail upper crossing. Follow the trail to 

the upper crossing and head upstream. The index reach is approximately 20 m upstream 

of the crossing and 80 m upstream of tag 72. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.33 

Figure SOP 9.16. Locations of six site index reaches in the Pine Gulch Creek Watershed. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.34 

Redwood Creek: There are 7 reaches on Redwood Creek (figure SOP 9.17). Unlike Olema and 

Pine Gulch Creeks, Redwood Creek’s index reaches start in the upper portion of the watershed 

with reach 1 and move downstream.

• Index reach 1: is located within MUWO, above Bridge 3. Park in the parking lot and 

follow the boardwalk upstream until reaching the third bridge. The index starts 

approximately 12 m above tag 63. 

• Index reach 2: is located within MUWO, by the visitor restrooms next to the first parking 

lot. The index starts approximately 50 m below tag 54. 

• Index reach 3: is located below the Miwok Trail Crossing. Use the pullout closest to the 

bridge and follow the creek downstream from the bridge. Index 3 starts approximately 40 

m below tag 38. 

• Index reach 4: is located just upstream of the Kent Creek confluence with Redwood 

Creek mainstem. Use the pullout closest to Kent Creek, near the footbridge where 

Redwood Creek Trail crosses the stream. Move upstream of the footbridge. The index is 

at tag 29. 

• Index reach 5: is located above the Frank Valley Road Bridge. Pull out at the Frank 

Valley camping area and go across the road to the creek. The index reach starts at 

approximately 30 m upstream of tag 18 and approximately 100 m upstream of the road 

bridge. 

• Index reach 6: is located near the Banducci restoration site. Park in the pull out beneath 

the eucalyptus trees approximately 250 m up Muir Woods Road from the Highway 1 

turn-off. Access the creek by the path that leads from the pull out down to the creek. 

• Index reach 7: is located below the Pacific Way Bridge. The index reach starts 

approximately 120 m below the bridge. To reach it, park at the Muir Beach Parking lot, 

and walk up the road until reaching the index, which is directly alongside the road. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.35 

Figure SOP 9.17. Locations of seven index reaches in the Redwood Creek Watershed. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 9.36 

Literature Cited 

Beamish, S. S. 2000. Determining the significance of habitat on coho salmon and steelhead trout 

in the Olema Creek watershed. Masters project. Nicholas School of the Environment, Duke 

University, Durham, North Carolina. 

Rosgen, D. 1994. Applied river morphology. Wildland Hydrology, Pagosa Springs, Colorado. 

Simonson, T. D., J. Lyons, and P. D. Kanehl. 1994. Guidelines for evaluating fish habitat in 

Wisconsin streams. General Technical Report NC-164. USDA Forest Service, North Central 

Forest Experiment Station, St. Paul, Minnesota.

Taylor and Associates. 2003. Marin County stream crossing inventory and fish passage 

evaluation: Final report. County of Marin, Department of Public Works, San Rafael, 

California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.1 

SOP 10. Data Summaries and Analysis 

Version 3.9 

Revision History Log 

Previous 

Version 

# 

Revision 

Date 

Author Changes Made Reason for Change New 

Version 

# 

 January 

2007 

Marcus 

Koenen 

Created this SOP to focus 

on Data Analysis only. 

Reduce redundancy 

among protocols 

and SOP 

3.2 

 3.2 March 2007 Michael 

Reichmuth 

Review of new SOP Update protocol to 

current 

methodology 

3.2 MR 

3.2MR May 2008 Erin Brown 3.3 

3.3 June 2008 Sarah 

Carlisle 

Added in smolt power 

analysis 

 3.31 

3.31 June 2008 Sarah 

Carlisle 

Linked data analysis and 

summaries with 

objectives and questions 

 3.32 

3.32 June 2008 Sarah 

Carlisle 

Updated all figures and 

graphs 

 3.33 

3.33 June 2008 Sarah 

Carlisle 

Added Escapement and 

Juvenile power analyses 

 3.34 

3.34 July 2008 Michael 

Reichmuth 

Reviewed and revised, 

combined with SOP 11 

Clarification 3.4 

3.4 August 2008 Michael 

Reichmuth 

Addressed comments 

received from Marcus 

Clarification 3.5 

3.5 August 2008 Brannon 

Ketcham 

 Document Review 

for final draft 

3.6 

3.6 August 2008 Leigh Ann 

Starcevich 

 Document Review 

for final draft 

3.6 

3.6 September 

2008 

Michael 

Reichmuth 

Address Leigh Ann’s 

comments 

Clarification 3.7 

3.7 November 

2008 

Michael 

Reichmuth 

Address Darren Fong 

comments 

Clarification, minor 

edits 

3.8 

3.8 November 

2008 

Dawn 

Adams 

Formatting For peer review 3.81 

3.81 December 

2008 

Michael 

Reichmuth 

Minor edits For peer review 3.82 

3.82 November 

2009 

Michael 

Reichmuth 

Added Lit Cited Peer review 

response 

3.83 

3.83 February 

2010

Michael 

Reichmuth

Final edits for final 

submittal

Response to 

editors and 

internal review 

comments

3.9 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.2 

Figures 

Page 

Figure SOP 10.1. A conceptual model used to represent the flow of information 

through the monitoring programs reporting process. ....................................................... SOP 10.10

Figure SOP 10.2. Correlation between electrofishing estimates and snorkel counts 

for 23 pools: Olema Creek, 2007. .................................................................................... SOP 10.13

Figure SOP 10.3. Coho histogram for fish measured in the seven Redwood Creek 

index reaches, 2007. ......................................................................................................... SOP 10.16

Figure SOP 10.4. Coho weight-length relationships for fish measured in the seven 

Redwood Creek index reaches, 2007. .............................................................................. SOP 10.16

Figure SOP 10.5. Redwood Creek watershed, coho salmon PLD Index 

Escapement results winter 1994–1995 through winter 2006–2007. ................................ SOP 10.25

Figure SOP 10.6. PLD measures by cohort for Cheda, Olema, Pine Gulch, and 

Redwood Creeks. ............................................................................................................. SOP 10.26

Figure SOP 10.7. Coho redd density per 100 m within Olema Creek and John 

West Fork. ........................................................................................................................ SOP 10.30

Figure SOP 10.8. Live coho fish, carcass, and redd observations by kilometer 

during spawner year 2006–2007 on the Olema Creek mainstem. ................................... SOP 10.31

Figure SOP 10.9. Redds per km measures by cohort for all four watersheds. ................ SOP 10.31

Figure SOP 10.10. Representation of rainfall totals and coho adult escapement 

survey results on Olema Creek mainstem, including live fish, carcasses, and 

redds, observed during surveys in 2006–2007. ................................................................ SOP 10.33

Figure SOP 10.11. Percent of total coho smolts captured by Julian week for 

Olema Creek in 2007 compared to the running average 2004–2007. .............................. SOP 10.34

Figure SOP 10.12. DARR output graph of smolt outmigration by week for traps 

requiring mark/recapture operation. ................................................................................. SOP 10.35

Figure SOP 10.13. Coho smolt and fry fork lengths in 10 mm increments for 

Olema Creek, 2007 .......................................................................................................... SOP 10.36

Figure SOP 10.14. Fork length of coho salmon smolts in Olema Creek, 2004–

2007.................................................................................................................................. SOP 10.36

Figure SOP 10.15. Weight-length comparison between coho smolts of Olema 

Creek in 2007 compared to the average from years 2004–2007. .................................... SOP 10.37
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.3 

Figure SOP 10.16. Survival rate between monitored life stages in Olema, Pine 

Gulch, and Redwood Creeks for spawner year 2003–2004. ............................................ SOP 10.39
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.4 

Tables 

Page 

Table SOP 10.1. Summary of reporting and communication products. ............................ SOP 10.6

Table SOP 10.1. Summary of reporting and communication products (continued). ......... SOP 10.6

Table SOP 10.2. Habitat composition of Olema Creek coho survey area, 2007. ............ SOP 10.12

Table SOP 10.3. Summary of coho snorkel counts in Olema Creek, 2007. .................... SOP 10.13

Table SOP 10.4. Coho density and population estimates: Olema Creek coho 

survey area, 2007. ............................................................................................................ SOP 10.14

Table SOP 10.5. Mean length, weight, and K factor calculated for coho, steelhead 

young of year (SH YOY), and steelhead 1+ (SH 1+) measured and weighed in the 

seven Redwood Creek index reaches, 2007. .................................................................... SOP 10.15

Table SOP 10.6. Summary of habitat composition; shows extent of area sampled 

and variation between reaches; Redwood Creek 2007. ................................................... SOP 10.19

Table SOP 10.7. Summary of total catch for coho salmon (CO) and steelhead 

(SH) along with steelhead young of the year (YOY) by reach within Redwood 

Creek mainstem index reach sample locations, 2004–2007. ........................................... SOP 10.20

Table SOP 10.8. Summary of population and density estimates for each coho 

salmon (CO), steelhead young of the year (SHYOY) and steelhead >1 year old 

(SH 1+) by index reach on Redwood Creek, summer 2007. ........................................... SOP 10.21

Table SOP 10.9. Summary of population and density estimates from 

electrofishing surveys for coho salmon by index reach habitat unit on Redwood 

Creek, 2004–2007. ........................................................................................................... SOP 10.22

Table SOP 10.10. Summary of live adults, carcasses, and redds found on Olema 

Creek mainstem, winter sampling season 2006–2007. .................................................... SOP 10.23

Table SOP 10.11. Coho salmon run timing, total monthly rainfall (Bear Valley 

rain gage, PORE), and Redwood Creek Peak Live plus Cumulative Dead (PLD), 

total carcasses and redds documented in the surveys for spawner years 1998–1999 

through 2006–2007 within Redwood Creek mainstem. .................................................. SOP 10.24

Table SOP 10.12. Coho salmon spawning survey including Peak Live plus 

Cumulative Dead (PLD) Index tally of total carcasses, and total redds for 

Redwood Creek. ............................................................................................................... SOP 10.24

Table SOP 10.13. Coho salmon spawning survey Area Under the Curve (AUC) 

estimates for Redwood Creek, 1997–1998 through 2006–2007. ..................................... SOP 10.27
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.5 

Table SOP 10.14. Density information (per kilometer) for parameters measured or 

estimated during spawner surveys for Olema Creek, winters 1997–1998 through 

2003–2004........................................................................................................................ SOP 10.27

Table SOP 10.15. Sex ratios and size of live coho (visually estimated) and 

carcasses (measured) within Redwood Creek, 1997–2007. ............................................. SOP 10.29

Table SOP 10.16. Seven day total rainfall per Julian week, average water clarity, 

and the number of coho redds, carcasses, and live adults observed in 2006–2007 

on Olema Creek mainstem. .............................................................................................. SOP 10.32

Table SOP 10.17. Summary of salmonid information for Olema, Redwood, and 

Pine Gulch Creeks trap operations, 1999–2006 ............................................................... SOP 10.34

Table SOP 10.18. Mean and median coho smolt length, weight, and K factor 

calculated for the trapping location at Olema Creek 2004–2007. ................................... SOP 10.37

Table SOP 10.19. A comparison of multiple life stage observations of coho 

salmon within the Olema Creek mainstem from the SY 2002–2003 to SY 2006–

2007.................................................................................................................................. SOP 10.40
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.6 

Overview 

This SOP provides guidance for a variety of reports, publications, and outreach material 

generated through the salmonid monitoring program (table SOP 10.1). To increase efficiency, 

reports are designed to build on previous reports, starting with smaller seasonal summaries and 

building to comprehensive annual and long term trend reports (figure SOP 10.1). At the end of 

each field season, brief one- to two-page summaries are generated for park managers and project 

volunteers. After the completion of the seasonal update, each season’s data will be validated and 

finalized following the procedures in SOP 8 (Data Management). Once the database has been 

finalized it can be used to generate the information needed for the seasonal summary reports. 

These reports focus solely on each individual field season (winter spawner surveys, spring smolt 

trapping, and summer/fall basinwide GSS surveys and index reach surveys) and provide a more 

extensive summation of the season’s results. 

The next reporting step involves compiling the information from each progress report into one 

annual report. The annual monitoring report is generated to summarize the results of a full year 

of monitoring efforts. In addition, annual permitting reports documenting monitoring-associated 

take are produced for National Marine Fisheries Service (NMFS; Section 10 permit 1046) and 

the California Department of Fish and Game (CDFG) Scientific Collection Permit. Both of these 

reports have specific guidelines and information these agencies desire which is extracted from 

the seasonal summary reports and compiled into a single report (SOP 6). 

Every nine years, a Synthesis and Analysis Report will be developed that builds on the annual 

reports by including statistical analyses to detect trends. Scientific publications will also be 

pursued to focus on key findings and other topics of interest to the scientific community. 

Table SOP 10.1. Summary of reporting and communication products. 

Table SOP 10.1. Summary of reporting and communication products (continued). 

Communication 

Product 

Lead Audience Schedule Summary 

Coho Spawner 

Survey Update 

Fishery 

Biologist 

NPS Staff, 

Program 

Volunteers, 

Interested Parties 

December –

February 

(Weekly) 

Highlight raw results of field work. 

Document important field 

incidents. Increase 

communication within the park 

and network 

Coho Smolt 

Trapping Update 

Fishery 

Biologist 

NPS Staff, 

Program 

Volunteers, 

Interested Parties 

April–June 

(Weekly) 

Highlight raw results of field work. 

Document important field 

incidents. Increase 

communication within the park 

and network. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.7 

Table SOP 10.1. Summary of reporting and communication products (continued). 

Communication 

Product 

Lead Audience Schedule Summary 

Coho Juvenile 

Survey Update 

Fishery 

Biologist 

NPS Staff, 

Program 

Volunteers, 

Interested Parties 

July–October 

(Monthly) 

Highlight raw results of field work 

Document important field 

incidents. Increase 

communication within the park 

and network 

Coho Spawner 

Report 

Fishery 

Biologist/Field 

Staff 

CDFG, NPS 

Resource 

Management 

March Highlight finalized results of field 

work. Document important field 

incidents, technical problems 

Increase communication within 

the park and network. 

Examples: Manning 1999, 

Ketcham et al. 2004, Del Real et 

al. 2007. 

Coho Smolt 

Report 

Fishery 

Biologist/Field 

Staff 

CDFG, NPS 

Resource 

Management 

October Highlight results of field work. 

Document important field 

incidents, technical problems 

Increase communication within 

the park and network. 

Examples: Ketcham et al. 2004 

Del Real et al. 2007. 

Coho Juvenile 

Report 

Fishery 

Biologist/Field 

Staff 

CDFG, NPS 

Resource 

Management 

December Highlight results of field work. 

Document important field 

incidents, technical problems 

Increase communication within 

the park and network. 

Example: Del Real et al. 2008. 

Annual Reports 

(Olema, 

Redwood, Pine 

Gulch) 

Fishery 

Biologist/Field 

Staff 

CDFG, NPS 

Resource 

Management 

June Summarize and compare results 

on all three watershed. 

Example: Carlisle et al. 2008. 

Annual Section 10 

permit reports 

Fishery 

Biologist 

NMFS May Meet permit requirements. 

Example: Brown et al. 2004. 

Bi-annual CDFG 

scientific 

collection permit 

report 

Each Principal 

Investigator 

CDFG 2 years Summarize take of species by 

principal investigator. 

Reports vary depending on permit 

limitations for each permitted 

principal investigator. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.8 

Table SOP 10.1. Summary of reporting and communication products (continued). 

Communication 

Product 

Lead Audience Schedule Summary 

Analysis and 

Synthesis Report 

PORE 

Hydrologist 

Park Resource 

Managers 

9 years Determine patterns and trends. 

Discover correlations among 

resources being monitored. 

Analyze data to determine the 

level of change that can be 

detected using the existing 

sampling scheme. 

Provide context, interpret data for 

the park within a multi-park, 

regional, or national context. 

Recommend changes to 

management practices. 

Program and 

Protocol Reviews 

I&M Program 

Manager 

Program Lead, 

Water Quality 

Steering 

Committee, I&M 

Technical 

Steering 

Committee, Water 

Resource Division 

5 years Periodic formal reviews of 

operations and results. 

Review of protocol design and 

product to determine if changes 

are needed. 

Part of the quality assurance – 

peer- review process. 

Executive Briefing Fishery 

Biologist + 

I&M Program 

Manager 

Program 

Managers, 

Superintendents, 

Front line 

interpretation staff 

Annually 

(upon 

completion of 

annual 

report) 

Two-page summary that lists 

monitoring objectives and 

questions, discusses annual 

results, and provides a regional 

context. 

 

Vital Sign Report 

Card 

I&M Program 

Manager 

Program 

Managers, 

Superintendents, 

Front line 

interpretation staff 

9 years 

(upon 

completion of 

Analysis and 

Synthesis 

Report 

Two-page summary that 

aggregates trend data into an 

index. 

Web Site Intranet Network 

Website 

Manager 

Park Staff Annually or 

as needed 

Post all completed reports. 

Web Site Internet Network 

Website 

Manager 

Park Staff, 

General Public 

Annually or 

as needed 

Post all Executive Briefings. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.9 

Table SOP 10.1. Summary of reporting and communication products (continued). 

Communication 

Product 

Lead Audience Schedule Summary 

Park 

Presentations 

Fishery 

Biologist 

Park Staff, 

Volunteers, 

General Public 

as needed Provide presentations to park 

staff during senior staff, all 

employee meetings, division 

meetings, and/or outreach events 

at each park upon request. Gives 

staff, volunteers, and general 

public an opportunity to ask 

questions about the program. 

IM Update Fishery 

Biologist 

Park Staff Quarterly This one-page monthly e-mail 

provides park staff with a short 

update on vital signs projects. 

Text should be no more than one 

paragraph. 

Photos Fishery 

Biologist 

For all reports 

and publication 

Continuous High quality publication quality 

photo are needed to support all 

communication products. For 

digital photos: 300 pixels per inch 

resolution in a plain or 

compressed TIF format. 

Specialists should make every 

effort to document ongoing work, 

special incidents, site visits for 

communication purposes. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.10 

Figure SOP 10.1. A conceptual model used to represent the flow of information through the monitoring 

programs reporting process. Dashed lines represent information contributing to non-programatic reports. 

Seasonal Updates 

At the end of each monitoring season (summer, winter, and spring), seasonal updates will be 

provided to all park staff, program volunteers, and other interested parties. These reports are 

brief two page summaries which provide a subjective overview of each field season using only 

raw data sources. The focus of the updates is on field conditions and incidents, as well as, the 

observed trends. These updates are intended to provide 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. 

The most recent example of a seasonal update can be viewed at 

http://science.nature.nps.gov/im/units/sfan/vital_signs/fish/fish.cfm

Summary Progress Reports 

Summary progress reports are designed as a summary of finalized (QA/QC) data for each field 

season. Summary reports are intended for both park resource managers and the CDFG as a final 

synopsis of each field season. At the end of each monitoring season (summer, winter, and spring) 

data will be summarized into a progress report by the fishery biologist and technicians. These 

reports will compile data that pertains only to each individual monitoring season. Formats follow 

the same general outline including standard sections briefly describing background and 

introduction, study area, methods, results, and discussion. The reports follow the Natural 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.11 

Resource Publications Management format 

(http://www.nature.nps.gov/publications/nrpm/finalreport.cfm). 

Examples of the most recent reports (Ketcham et al. 2005; Reichmuth et al. 2005, 2006) can be 

viewed at the following website: 

http://www1.nature.nps.gov/im/units/sfan/vital_signs/stream_fish.cfm. 

An explanation of the content which is covered in each of the seasonal summaries is presented 

below. 

Summary Report–Juvenile Report 

The Summer Juvenile Summary Report provides information about coho juvenile population 

changes along with stream habitat changes, as well as population distribution. Data are collected 

through Basinwide GSS surveys and stream index reach surveys. 

Summer Juvenile Summary Reports address the following monitoring objectives: 

• Conduct summer surveys at Olema, Pine Gulch, and Redwood Creeks by conducting 

basinwide snorkel surveys (general systematic surveys [GSS]) to determine long-term 

trends in distribution and abundance of juvenile coho salmon. 

• Conduct summer surveys at Olema, Pine Gulch, and Redwood Creeks at preexisting 

index reaches to determine long term trends in density, size, and age composition of coho 

salmon at preexisting index reaches. 

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

during summer/fall surveys. 

Basinwide General Systematic Survey: Analyses provided in the summary Basinwide GSS 

report section are generated completely within the Salmonid Summer Database Module (See 

SOP 8). The summary results are dependent on the results of correlation analyses which compare 

visual estimates with measured results, to develop a calibration factor (raw count to calibrated 

count). The reported results are calibrated using the correlation factor before population 

estimates are determined using a ratio estimator. The following summary tables are developed 

within the database and reported in the summary progress report. 

• summary of habitat metrics (table SOP 10.2) 

• summary of snorkel counts (table SOP 10.3) 

• summary of density and population estimates for target species (table SOP 10.4) 

• analysis of fish condition (length and length-weight) to indicate fitness (table SOP 10.5, 

figures SOP 10.3–4) 

Also see Del Real et al. (2008) for recent examples of summary tables and graphs. 

Habitat Metrics: Habitat summaries will focus on the habitat composition of the watersheds 

surveyed. The metrics will be used to answer questions that relate to habitat composition and 

constraints that might influence salmonid populations and recovery efforts. It should be noted in 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.12 

some cases that the habitat survey length exceeds the snorkel survey length due to water quality 

conditions. Results in table SOP 10.2 represent habitat survey length. Habitat unit numbers and 

survey length in table SOP 10.3 represent the habitat conditions within the actual area snorkeled. 

Table SOP 10.2. Habitat composition of Olema Creek coho survey area, 2007. 

Unit type 

2007 

# of units Length of units (m) % 

Pool 406 8,217 65 

Flatwater 217 2,184 17 

Riffle 307 2,297 18 

 Total 930 12,698 100 

Survey length* 12.7 km 

*Survey lengths are based on established monument tags for comparison between years. 

Snorkel Survey Habitat Units and Pools: Refer to table SOP 10.3 below for a detailed example of 

how data will be reported for basinwide juvenile coho estimates. Although stream length is 

provided for comparison of length of stream surveyed between years, it is not used for 

calculating the actual population estimate. The number of pools snorkeled are provided with the 

number that contain coho as an indicator of distribution between pool habitats. A raw snorkel 

count for all sampled units is provided as minimum count for each creek (Dolloff et al. 1993). 

All subsequent basinwide population estimate formulas were extracted directly from Dolloff et 

al. (1993). 

Calibrated Coho per Pool: A ratio is created using the estimated number of juvenile coho 

observed while snorkeling and the actual number of juvenile coho calculated by multiple pass 

electrofishing (figure SOP 10.2). The calibration ratio (R

)

) is calculated by dividing the total 

number of fish estimated by multiple pass removal electrofishing (yi) by the total number of fish 

counted by the diver in the habitat unit (xi; Dollof et al. 1993). 

n' = number of units sampled both by the diver and by electrofishing. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.13 

y = 1.1505x + 0.307

R2

 = 0.8828

n = 23

calibration ratio = 1.154851

0

50

100

150

200

250

0 50 100 150 200

coho-dive counts

coho-electrofishing estimates

Figure SOP 10.2. Correlation between electrofishing estimates and snorkel counts for 23 pools: Olema 

Creek, 2007. 

Table SOP 10.3. Summary of coho snorkel counts in Olema Creek, 2007. 

Year 

Total snorkel 

survey stream 

length (km) 

Total number 

of habitat 

units 

Number of Pools Coho Counted 

Total Snorkeled w/ Coho Raw 

Calibration 

Ratio 

2007 11.8 917 368 89 86 6,688 1.155 

Juvenile Coho Density per Pool: The raw juvenile coho density per pool (table SOP 10.4) is 

calculated by dividing the total raw snorkel count (x ̄; table SOP 10.3) by the number of pool 

units snorkeled (n; table SOP 10.3). The calibrated juvenile coho density per pool (y ̄dr ; table 

SOP 10.4) is calculated by multiplying the calibration ratio (R

)

; table SOP 10.3) by raw snorkel 

count (x ̄; table SOP 10.3) and dividing the product by the number of pool units snorkeled (n; 

table SOP 10.3; Dollof et al. 1993). 

Juvenile Coho Density (coho/m and coho/m2

): Juvenile coho density per meter (SOP 10.4) is 

derived from the total calibrated coho count, calculated above, divided by the total length of pool 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.14 

habitat sampled (derived from macro in MS Access database). Juvenile coho density per square 

meter (SOP 10.4) is derived from the total calibrated coho count, calculated above, divided by 

the total surface area of pool habitat sampled (derived in MS Access database). Juvenile density 

by meter or square meter is a common density metric to compare salmonid production between 

watersheds. 

Juvenile Coho Population Estimate and 95% Confidence Interval: The juvenile coho population 

estimate (SOP 10.4) is a ratio estimation derived from the product of the calibrated average coho 

per pool (y ̄dr ; table SOP 10.4) by the total number of pools in the survey area (N; SOP 10.3). 

A more complicated estimator of variance (V^(y ̄dr)) is used to determine a 95% confidence 

interval. A sample based estimator of uncertainty is provided from Dollof et al. 1993 to 

determine the 95% confidence interval for the calculated juvenile coho population estimate (table 

SOP 10.4). 

Once an estimator of variance is determined for the sample habitat type an estimator of variance 

for the total number of fish in all pool habitat units can be determined and a 95% confidence 

interval can be constructed. 

Table SOP 10.4. Coho density and population estimates: Olema Creek coho survey area, 2007. 

Year 

Avg. Coho per pool Juvenile Coho Density Juvenile Coho 

Population 

Estimate 

95% confidence 

Interval Raw Calibrated coho/m Coho/m2 

2007 75.15 86.78 4.247 1.295 31,936 ± 4,122 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.15 

Fish Condition: Fish condition will be calculated from weight-length data that will be collected 

at each systematically selected calibration unit. All provided examples for fish condition are 

displayed using index reach data as systematic calibration unit data will not be available until the 

2009 field season. Although future tables and figures will use systematic calibration unit data, 

the provided information will remain the same in both format and content. 

Fish condition can be assessed using Fulton’s condition factor and weight-length power function 

(Anderson and Gutreuter 1983). Fulton’s condition factor (K) is represented by: 

100 ,000

( )

( )

3 x

Length mm

Weight g K =

Mean K can then be calculated for each species/age class within a reach or habitat type. Table 

SOP 10.5 shows an example of the mean length, weight, and K factor for all coho and steelhead 

measured during the electrofishing surveys. Typically, “plumper” fish have higher K values than 

“skinny” fish. 

Table SOP 10.5. Mean length, weight, and K factor calculated for coho, steelhead young of year (SH 

YOY), and steelhead 1+ (SH 1+) measured and weighed in the seven Redwood Creek index reaches, 

2007. 

Year Species 

Sample 

Size 

Mean 

Length 

(mm) 

Length 

Standard 

Deviation 

Mean 

Weight 

(g) 

Weight 

Standard 

Deviation 

Mean KFactor 

K-Factor 

Standard 

Deviation 

2007 coho 294 73.73 8.38 4.15 1.49 1.00 0.08 

2007 SH YOY 548 63.56 9.66 2.76 1.31 1.00 0.11 

2007 SH 1+ 78 122.15 26.21 19.54 13.13 0.95 0.11 

In addition to fish condition, fish measurement data can be further summarized graphically to 

represent the condition or size distribution (figure SOP 10.3). A bimodal distribution indicates 

the presence of multiple age classes and shows the approximate size break between classes. 

Figure SOP 10.4 shows fish length plotted against weight, and the power function curve from 

which the equation W = aLb (where W=weight, L=length, and a and b are parameters) is 

calculated (Anderson and Gutreuter 1983). This equation provides an idea of the fitness of the 

sample of measured fish, with higher b values indicating plumper fish, and can also be used to 

calculate weights of individual fish from their measured length. These data are used to answer 

larger questions about long-term trends within fish condition. Long-term trends in fish condition 

will be assessed using a mixed linear model of VanLeeuwen et al. (1996) and Piepho and Ogutu 

(2002) which is modified to reflect the cohort structure of coho salmon. Refer to Trend Model 

section below for an example of the trend model to be used to analyze fish condition. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.16 

Coho Fork Length Frequency, Redwood Creek 2007

0

10

20

30

40

50

60

70

80

90

31-3536-4041-4546-5051-5556-6061-6566-7071-7576-8081-8586-9091-95

96-100

101-105106-110111-115

Fork Length (mm)

Frequency

Length2007 n=312

AvgLength n=27420

Figure SOP 10.3. Coho histogram for fish measured in the seven Redwood Creek index reaches, 2007. 

Historical averages (1998–2006) are shown for comparison. Fork length is represented in 5 mm bins.

Coho Weight-Length, Redwood Creek 2007

Coho 2007

y = 1E-05x2.9419

R2 = 0.9451

Coho All Years

y = 2E-05x2.9086

R2 = 0.9326

0

2

4

6

8

10

12

14

16

0 20 40 60 80 100 120

Fork Length (mm)

Fish Weight (g)

CohoAllYears

Coho2007

Power (Coho2007)

Power (CohoAllYears)

Figure SOP 10.4. Coho weight-length relationships for fish measured in the seven Redwood Creek index 

reaches, 2007. Historical relationships added for comparison (1998–2006). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.17 

Index Reach Survey 

Index reach monitoring will be maintained as a legacy dataset. Many other monitoring programs 

in the region conduct similar index reach monitoring, and our dataset would be available for 

comparative purposes. Data summaries of index reach surveys will include the following: 

• Summary of the habitat area sampled and characteristics of each index reach (SOP 10.6) 

• Summary of total number of fish captured during index reach sampling (table SOP 10.7) 

• Summary of population estimates and associated densities for each species by index 

reach and habitat type (tables SOP 10.8–9) 

• Analysis of temporal changes in fish densities (fish/meter) per habitat type (tables SOP 

10.8–9) 

• Analysis of fish densities (fish/meter) per index reach and per year (tables SOP 10.8–9) 

Habitat Characteristics: Summaries of habitat characteristics will be used to detect major stream 

alterations and help explain changes in fish densities (table SOP 10.6) 

Habitat Summaries: These summaries will be used to answer questions that relate to habitat 

composition and constraints that might influence salmonid populations and recovery efforts. 

Total Number of Fish: For habitat units sampled by multiple pass electrofishing, MicroFish 

software is used to analyze data. The software is based on removal-depletion methods to account 

for detection error. The program calculates a maximum likelihood estimate of the population 

total for each unit sampled and provides a variance estimate for the model adjustment of raw 

counts. This Microfish abundance estimate applies to the population within each index reach unit 

within a basin. 

From Starcevich and Irvine (2008): 

 

Total abundance and the associated variance estimate for each index reach will be 

calculated as follows: 

1

ˆ ˆ

n

b i

i

T t == ∑ , 

where ˆ

i t is the estimate of total juveniles in habitat unit i, n is the number of habitat units 

within the index reach, and ˆTb is the estimate of juvenile abundance within an index 

reach. Assuming independence among habitat unit counts within a reach, the variance of 

ˆTb is then: 

( ) ( ) 2

11 1

ˆ ˆ ˆ ˆ nn n

b i ii

ii i

Var T Var t Var t σ == =

⎛ ⎞ = == ⎜ ⎟ ⎝ ⎠ ∑ ∑ ∑ , 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.18 

where 

2 ˆσ i is the estimated variance of estimated juvenile abundance at habitat unit i. The 

assumption of independence among habitat unit counts within an index reach is likely 

tenuous, and estimated variances may underestimate the true variance if pool counts are 

positively correlated in space. 

Fish population estimates and confidence intervals by species/age class will be calculated for 

each index reach unit sampled. Table SOP 10.7 shows the total number of fish captured during 

index reach sampling and can be quickly compiled from the raw data for an initial summary of 

sampling results. It provides a general sense of the annual variation in fish numbers within and 

distribution between index reaches monitored since 1999 (e.g., higher coho numbers in 2001 and 

2002). These data can be used to answer questions relating to densities and population trends 

along index reaches over time. Total catch will also be used as the population estimate for 

species with poor multiple pass depletions or no captures after the first pass, and in units sampled 

with a single pass. 

Fish Density: The database automatically calculates density estimates of each species by stream 

length (fish/m) and surface area (fish/m2

)for each habitat unit (See SOP 8 for calculation 

details). Fish densities are calculated from the length and surface area of the habitat units that are 

actually sampled. See tables SOP 10.6–8. Such data can be used for answering questions related 

to fish densities within index reaches over time. 

Density Among Habitat Types: Densities based on habitat unit type can be used to answer 

questions related to both density trends and habitat constraints on salmonid populations. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.19 

Table SOP 10.6. Summary of habitat composition; shows extent of area sampled and variation between 

reaches; Redwood Creek 2007. 

Index 

Reach 

Habitat 

Type 

 Length Surface Area 

# of Units Sampled (m) % of total Sampled (m2) % of total 

 Pool 3 39.9 36.2% 145.3 40.4% 

1 Riffle 3 46.2 42.0% 144.3 40.1% 

 Flatwater 2 24.0 21.8% 69.9 19.5% 

 Total 8 110.1 100.0% 359.6 100.0% 

 Pool 3 42.1 40.0% 209.9 52.5% 

2 Riffle 2 25.1 23.8% 65.7 16.5% 

 Flatwater 2 38.1 36.2% 124.1 31.0% 

 Total 7 105.3 100.0% 399.7 100.0% 

 Pool 4 59.2 79.4% 224.2 86.6% 

3 Riffle 2 15.4 20.6% 34.7 13.4% 

 Flatwater 0 0 0.0% 0 0.0% 

 Total 6 74.6 100.0% 258.9 100.0% 

 Pool 4 57.9 69.9% 211.2 81.7% 

4 Riffle 2 9.7 11.7% 11.8 4.6% 

 Flatwater 2 15.2 18.4% 35.6 13.8% 

 Total 8 82.8 100.0% 258.6 100.0% 

 Pool 3 74.2 68.9% 323.8 72.3% 

5 Riffle 1 4.2 3.9% 5.3 1.2% 

 Flatwater 1 29.3 27.2% 119.0 26.6% 

 Total 5 107.7 100.0% 448.0 100.0% 

 Pool 3 78.1 92.1% 273.3 95.7% 

6 Riffle 1 6.7 7.9% 12.4 4.3% 

 Flatwater 0 0 0.0% 0 0.0% 

 Total 4 84.8 100.0% 285.7 100.0% 

 Pool 2 32.4 41.0% 84.5 46.9% 

7 Riffle 2 3.8 4.8% 4.1 4.4% 

 Flatwater 3 42.9 54.2% 91.6 50.9% 

 Total 7 79.1 100.0% 180.2 102.2% 

 Pool 18 383.8 59.6% 1472.1 67.2% 

 Total Riffle 13 111.1 17.2% 278.3 12.7% 

 Flatwater 10 149.5 23.2% 440.2 20.1% 

 Total 41 644.4 100.0% 2190.6 100.0% 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.20 

Table SOP 10.7. Summary of total catch for coho salmon (CO) and steelhead (SH) along with steelhead 

young of the year (YOY) by reach within Redwood Creek mainstem index reach sample locations, 2004–

2007. 

Year Species 

Index Reach 

1 2 3 4 5 6 7 Total 

2004 

CO 

Not 

sampled 

42 95 74 159 71 

not 

sampled 

441 

SH YOY 6 22 19 24 4 75 

SH 1+ 19 8 17 15 13 72 

2005 

CO 23 59 77 93 164 236 338 990 

SH YOY 44 38 41 70 77 178 81 529 

SH 1+ 5 12 12 10 14 9 4 66 

2006 

CO 6 21 21 38 3 9 0 98 

SH YOY 38 78 26 20 5 17 4 188 

SH 1+ 2 24 21 20 11 20 1 99 

2007 

CO 54 138 215 120 146 89 8 770 

SH YOY 90 161 305 170 212 392 144 1474 

SH 1+ 8 43 10 11 7 11 7 97 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.21 

Table SOP 10.8. Summary of population and density estimates for each coho salmon (CO), steelhead 

young of the year (SH YOY) and steelhead >1 year old (SH 1+) by index reach on Redwood Creek, 

summer 2007. 

Index Species Population Estimate Density 

Reach (age) # of Fish 95% CI Fish/m 95% CI Fish/m2 95% CI 

 

 CO 54 ±38 0.49 ±0.35 0.15 ±0.11 

1 SH YOY 98 ±83 1.57 ±0.15 0.41 ±0.04 

 SH1+ 8 ±65 0.07 ±0.59 0.02 ±0.18 

 

 CO 138 ±35 1.31 ±0.33 0.35 ±0.09 

2 SH YOY 165 ±15 1.57 ±0.15 0.41 ±0.04 

 SH1+ 43 ±47 0.41 ±0.44 0.11 ±0.12 

 

 CO 215 ±18 2.88 ±0.25 0.83 ±0.07 

3 SH YOY 305 ±8 4.09 ±0.10 1.18 ±0.03 

 SH1+ 10 ±44 0.13 ±0.59 0.04 ±0.17 

 

 SH YOY 125 ±56 1.51 ±0.68 0.48 ±0.22 

4 SH1+ 179 ±43 2.16 ±0.52 0.69 ±0.16 

 SH (1+) 11 ±63 0.13 ±0.76 0.04 ±0.04 

 CO 146 ±22 1.36 ±0.21 0.33 ±0.05 

5 SH YOY 215 ±18 2.00 ±0.17 0.48 ±0.04 

 SH (1+) 7 ±38 0.06 ±0.35 0.02 ±0.08 

 

 CO 89 ±15 1.05 ±0.18 0.31 ±0.05 

6 SH YOY 396 ±10 4.67 ±0.12 1.39 ±0.04 

 SH (1+) 11 ±34 0.13 ±0.40 0.04 ±0.12 

 

 CO 8 ±52 0.10 ±0.65 0.04 ±0.29 

7 SH YOY 155 ±42 1.96 ±0.53 0.86 ±0.23 

 SH (1+) 7 ±61 0.09 ±0.78 0.04 ±0.34 

Average 

Densities 

CO 1.20 ±0.36 0.35 ±0.10 

SH (0+) 2.35 ±0.34 0.69 ±0.10 

SH (1+) 0.15 ±0.55 0.04 ±0.16 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.22 

Table SOP 10.9. Summary of population and density estimates from electrofishing surveys for coho 

salmon by index reach habitat unit on Redwood Creek, 2004–2007. 

Year 

Habitat 

Type 

# of 

Habitat 

Units 

Population 

Estimate Density 

# of 

Fish 95% CI Fish/m 95% CI Fish/m2 95% CI 

 

2004 Pool 13 428 ±38 1.81 ±0.16 0.46 ±0.04 

Riffle *Not Surveyed 

Flatwater 4 23 ±5 0.40 ±0.08 0.16 ±0.03 

 

2005 Pool 19 977 ±362 2.02 ±0.75 0.48 ±0.18 

Riffle 5 22 ±80 0.24 ±0.88 0.12 ±0.44 

Flatwater 3 12 ±27 0.24 ±0.55 0.11 ±0.25 

 

2006 Pool 22 103 ±149 0.25 ±0.37 0.07 ±0.10 

Riffle 13 0 N/A 0 N/A 0 N/A 

Flatwater 6 0 N/A 0 N/A 0 N/A 

 

2007 Pool 16 761 ±51 1.98 ±0.13 0.52 ±0.03 

Riffle 6 2 ±109 0.02 ±0.98 0.01 ±0.39 

Flatwater 3 12 ±69 0.08 ±0.46 0.03 ±0.16 

*Riffles were not surveyed in 2004 due to low flow conditions. 

The Spawner Summary Report 

The Spawner Summary Report provides information about the adult coho population changes. 

The main objective to be addressed in this report is: 

• Conduct winter survey at Olema, Pine Gulch, Redwood, and Cheda Creeks by counting 

numbers of spawners, carcasses, and redds along spawner reaches to determine long-term 

trends in distribution and abundance, size (length and weight) of spawning coho salmon 

within reaches. 

For each stream, the report should clearly describe the: 

• Total number of live fish, redds, and carcasses observed during each survey (table SOP 

10.10); 

• Population estimates based on Peak Live Dead (PLD) Index (tables SOP 10.11–12, 

figures SOP 10.5–6) and Area Under the Curve (AUC) Index estimates (tables SOP 

10.13–14); 

• Spawner population density (table SOP 10.14); 

• Sex ratios of live fish and carcasses with total numbers of jacks; (table SOP 10.15) 

• Total number and spatial distribution of redds (figures SOP 10.7–9) 

• Environmental conditions during each survey including flow or gage data, 

weather, and water clarity (table SOP 10.16, figure SOP 10.10) 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.23 

Numbers of Spawners: The analysis of spawner survey data is complicated by annual variability 

in environmental conditions and run characteristics. Table SOP 10.10 presents data collected 

during the spawner surveys. Accurate abundance estimates are difficult to generate without 

counting weirs or other intensive sampling techniques (Irvine et al. 1992). The NPS monitoring 

program is, nonetheless, interested in developing precise indices of abundance. Two techniques, 

Peak Live plus cumulative Dead (PLD) and Area Under the Curve (AUC) are used to compute 

index values (Beidler and Nickelson 1980; Johnston et al. 1987). In addition to calculating the 

indices, we summarized the live fish, redd, carcass, and environmental data for each stream. 

Table SOP 10.10. Summary of live adults, carcasses, and redds found on Olema Creek mainstem, winter 

sampling season 2006–2007. 

Survey 

Date 

# of Coho Redds 

# of Adult Coho 

Total 

Adults 

# of Live Adult Coho # of Coho Carcasses 

Definite Possible Male Female Unknown Male Female Unknown 

11/22/06 0 0 0 0 0 0 0 0 0 

12/18/06 34 1 21 36 1 4 1 0 63 

12/31/06 21 1 18 24 2 1 8 2 55 

1/10/07 10 0 6 11 0 2 3 1 23 

1/24/07 5 0 2 1 0 2 2 3 1 

2/16/07 0 0 0 0 0 0 0 0 0 

The PLD and AUC estimates provide different types of information. While the PLD index 

produces a minimum instantaneous estimate, the AUC method is used to calculate a total 

population estimate. 

Peak Live Dead (PLD): The PLD index is computed using the sum of live fish observed during a 

single day of the spawning season and the cumulative number of unmarked carcasses observed 

prior to that date. Live numbers may only be added from separate survey dates when the survey 

interval is greater than 20 days between peak live fish counts and the residence time of spawning 

coho are assumed to be less than 20 days long (Irvine et al. 1992). Redd count and location is 

used to describe spawning density, spawner success, and spatial distribution. Data collected 

during the spawner surveys are used to detect any changes in timing, distribution of salmon 

spawning, adult sex ratios, and escapement in estimates in the streams surveyed. Tables SOP 

10.11–12 show PLD indices along with other survey results, run timing, and survey information. 

Figure SOP 10.5 provides a summary of the PLD indices for coho in the Redwood Creek 

watershed. The three year classes are represented as different patterns to show relationships 

between spawning runs. Other creeks are presented in figure SOP 10.6. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.24 

Table SOP 10.11. Coho salmon run timing, total monthly rainfall (Bear Valley rain gage, PORE), and 

Redwood Creek Peak Live plus Cumulative Dead (PLD), total carcasses and redds documented in the 

surveys for spawner years 1998–1999 through 2006–2007 within Redwood Creek mainstem. 

Spawner 

Year (SY) Run Timing 

Total Monthly Rainfall 

(in) Redwood Creek PLD 

 Nov Dec Jan Feb Nov Dec Jan Feb 

Survey 

Area (km)

PLD 

Index 

Total 

Carcasses

Total 

New 

Redds 

1998–1999 3.28 1.49 5.27 8.47 9.4 39 10 58 

1999–2000 2.72 0.59 5.95 0.00 8.4 10 1 7 

2000–2001 0.00 0.00 4.39 6.07 9.4 49 13 35 

2001–2002 0.00 0.00 0.83 3.56 9.4 105 63 47 

2002–2003 2.18 13.04 1.23 1.83 9.4 24 3 7 

2003–2004 2.62 3.45 7.21 6.38 9.4 67 25 43 

2004–2005 0.8 7.59 3.66 3.09 9.4 171 76 93 

2005–2006 2.19 12.57 0.00 3.48 9.4 27 5 12 

2006–2007 2.58 4.27 0.63 3.63 9.4 28 6 21 

Table SOP 10.12. Coho salmon spawning survey including Peak Live plus Cumulative Dead (PLD) Index 

tally of total carcasses, and total redds for Redwood Creek. 

Year 

Number of 

Surveys 

Survey Area 

(km) PLD Index 

Total 

Carcasses Total Redds

1969** 1 3.2 24 4 -- 

1977–1978*** 1 3.2 36 3 -- 

1985–1986** 1 7.2 50 -- -- 

1994–1995 5 8.4a

 58 22 -- 

1995–1996 5 8.4a

 27 18 -- 

1996–1997 6 8.4a

 57 15 -- 

1997–1998 7 9.4b

 65 30 80 

1998–1999 11 9.4b

 3 c 10 58 

1999–2000 6 8.4a

 10 1 7* 

2000–2001 5 9.4a

 49 13 35 

2001–2002 5 9.4b

 105d 63 47 

2002–2003 5 9.4b

 24e 3 7* 

2003–2004 6 9.4b

 67 25 43 

2004–2005 7 9.4b

 171f 76 93

2005–2006 5 9.4b

 27e 5 12 

2006–2007 9 9.4b

 28g 6 21 a

Includes the main stem of Redwood Creek and Fern Creek 

b

Includes the main stem of Redwood Creek, Fern Creek, and Kent Creek 

c

Includes two peaks, 7 weeks apart 

d

Includes two peaks, 22 days apart 

e

Includes two peaks, 33 days apart 

f

Includes two peaks, 25 days apart 

g

Includes three peaks, 26 and 24 days apart 

*Poor survey conditions resulted in low observer efficiency 

**CDFG 1986 

***CDFG 1978 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.25 

1 1 1

1

2 1

2

2

2

3

3

3 3

0

50

100

150

200

250

1994-95

1995-96

1996-97

1997-98

1998-99

1999-00

2000-01

2001-02

2002-03

2003-04

2004-05

2005-06

2006-07

Spawner Year

PLD Minimum Escapement Estimate

Year Class 1 Year Class 2 Year Class 3

Figure SOP 10.5. Redwood Creek watershed, coho salmon PLD Index Escapement results winter 1994–

1995 through winter 2006–2007. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.26 

Figure SOP 10.6. PLD measures by cohort for Cheda, Olema, Pine Gulch, and Redwood Creeks. 

Area Under Curve 

The AUC estimate (table SOP 10.3) is calculated using the total number of live fish observed 

during each survey and the average life of fish on the spawning grounds (residence time). 

Calculating the area under the curve created by plotting the live fish observations for each 

survey, produces a quantity termed total fish-days. The area under the escapement curve was 

given by: 

AUC = 0.5 { ∑ (tI – tI-1) (pI + p I-1)} 

where tI is the number of days since the first fish entered the survey area and pI is the total 

number of fish observed on the ith day (Irvine et al. 1992). Dividing the total number of fish days 

by the residence time gives the population estimate. Because we did not estimate residence time, 

separate AUC estimates were computed using the range of values, 8 to 17 days, presented in the 

literature (Moring and Lantz 1975; Johnston et al. 1987; Irvine et al. 1992). Data collection 

typically stops after repeated surveys no longer indicate the presence of live coho. High flows 

prevented us from conducting surveys during significant portions of some spawner seasons. If 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.27 

fish were observed during the last survey of the season, the last date used for calculating the 

AUC estimate was arbitrarily set at 10 days after the final survey date. AUC estimates are 

provided as a more liberal estimate of coho escapement but are not used for trend analysis at this 

time due to the inconsistency in the ability to make an AUC estimate in any given year. 

Table SOP 10.13. Coho salmon spawning survey Area Under the Curve (AUC) estimates for Redwood 

Creek, 1997–1998 through 2006–2007. 

Year

Number 

of 

Surveys 

Date of 

Entry 

Mean 

Survey 

interval 

(days) 

Survey 

Length 

(km) 

AUC Range 

100% OE

RT 8–17 days

AUC Range 

50% OE 

RT 8–17 days

AUC Range 

70–80% OE 

RT 11–13 

days 

Redwood 

Creek 

PLD 

1997–1998 7 23 Nov 97 7.5 9.4 89–188 177–376 145–195 65 

1998–1999 11 29 Nov 98 8.6 9.4 39–83 78–167 64–87 39

1999–2000 6 01 Jan 00 11.8 8.4 8–17 16–35 13–18 10 

2000–2001 5 15 Dec 00 13.0 9.4 74–157 148–314 121–163 49 

2001–2002 5 07 Dec 01 11.3 9.4 116–247 233–494 190–257 105

2002–2003 5 10 Dec 02 14.0 9.4 22–46 43–92 35–48 24

2003–2004 6 11 Dec 03 6.3 9.4 43–91 86–182 70–94 67 

2004–2005 7 06 Dec 04 8.3 9.4 169–359 338–718 276–373 171

2005–2006 5 01Dec 05 9.6 9.4 28–59 55–117 45–61 27 

2006–2007 9 13 Nov 06 10.4 9.4 24–50 46–98 39–51 29 

Spawner Density: To facilitate comparisons between years and with other watersheds where 

survey areas may be considerably different, survey results will be also be expressed as # per 

kilometer. Table SOP 10.14 shows an example of # of live fish (based on PLD and AUC 

estimates), carcasses, and redds per km for multiple years. 

Table SOP 10.14. Density information (per kilometer) for parameters measured or estimated during 

spawner surveys for Olema Creek, winters 1997–1998 through 2003–2004. Survey areas used to 

calculate PLD, carcass and redd densities may be different from the survey area used to calculate the 

AUC estimate. 

Year 

Density (# / km) 

PLD 

Index 

AUC 

OE=80% 

RT=13 days 

AUC 

OE=70% 

RT= 11 days 

Total 

Carcasses Total Redds 

1997–1998 7 20 27 2.9 9.4 

1998–1999 4 5 7 1.1 3.6 

1999–2000*

 1* 1.3 1.4 

2000–2001 9 11 14 5.6 7.4 

2001–2002 8 15 20 2.4 5.0 

2002–2003*

 2* 1.5 0.4 

2003–2004 12 20 26 2.9 7.6 

*Survey data for mainstem not adequate to develop AUC estimate 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.28 

Sex Ratio: Sex ratios are reported for both live coho and carcasses (table SOP 10.15). 

Mean fork lengths are also provided on the relative number of two year old spawners and 

female fecundity. Males less than 50 cm fork length are considered jacks (2-year-old 

males; Shapovalov and Taft 1954), and their relative numbers can indicate the amount of 

exchange between year classes. Sizes are summarized for both carcasses and live fish 

lengths. Live fish lengths represent visual estimates only while carcass lengths are 

measured to the nearest centimeter. 

Redd Density and Distribution: Figure SOP 10.7 shows a GIS map of coho redd density (# redds 

per 100 m). Figure SOP 10.8 shows a graph with similar information at a lower resolution (per 

km instead of per 100 m) but with live coho and carcasses observed in addition to redds. Because 

power analysis indicated that results are most meaningful expressed by cohort and watershed 

data are presented as in figure SOP 10.9. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.29 

Table SOP 10.15. Sex ratios and size of live coho (visually estimated) and carcasses (measured) within 

Redwood Creek, 1997–2007. 

 Live Coho Carcasses 

Year Month # % Mean FL FL SD # % Mean FL FL SD

1997–

1998 

 M 12 26% 57.9(n=12) 5.42 6 25% 56.0(n=3) 6.56 

 F 24 52% 56.9(n=24) 4.85 7 29% 54.8(n=6) 4.07 

 J 4 9% 40.0(n=4) 0.00 4 17% 39.7(n=7) 1.25 

 Unk 6 13% 53.3(n=6) 4.08 7 29% 60(n=2) 7.07 

All 46 100% 24 100% 

1998–

1999 

 M 8 22% 61.3(n=8) 3.54 2 14% 62.0(n=2) 2.83 

 F 16 44% 53.8(n=16) 3.87 6 43% 52.3(n=6) 2.58 

 J 6 17% 36.7(n=6) 5.16 5 36% 42.2(n=5) 2.59 

 Unk 6 17% 55.0(n=6) 4.47 1 7% 

All 36 100% 14 100% 

1999–

2000 

 M 3 33% 56.7(n=3) 11.55 0 0 

 F 4 44% 62.5(n=5) 11.90 1 100% 55.0(n=1) 

 J 0 0 0 0 

 Unk 2 22% 67.5(n=2) 3.54 0 0 

All 9 100% 1 100% 

2000–

2001 

 M 4 9% 60.0(n=4) 7.07 3 23% 62.5(n=2) 3.54 

 F 14 30% 55.0(n=14) 4.39 6 46% 66.8(n=5) 2.94 

 J 28 61% 39.1(n=28) 4.31 3 23% 42.7(n=3) 4.62 

 Unk 0 0 1 8% 55.0(n=1) 

All 46 100% 13 100% 

2001–

2002 

 M 52 56% 59.2(n=51) 8.25 19 37% 70.1(n=19) 6.31 

 F 31 33% 56.7(n=30) 6.34 20 38% 65.4(n=20) 5.28 

 J 1 1% 45.0(n=1) 0 0 

 Unk 9 10% 57.1(n=7) 6.99 13 25% 64.9(n=7) 4.6 

All 93 100% 52 100% 

2002–

2003 

 M 2 13% 65.0(n=2) 7.07 0 0 

 F 10 67% 53.6(n=7) 3.78 1 20% 50.0(n=1) 

 J 2 13% 42.5(n=2) 3.54 4 80% 36.5(n=4) 8.19 

 Unk 1 7% 55.0(n=1) 0 0 

All 15 100% 5 100% 

2003–

2004 

 M 19 32% 62.0(n=19) 6.96 10 36% 63.8(n=8) 7.32 

 F 26 43% 59.6(n=25) 4.55 13 46% 64.2(n=12) 5.39 

 J 13 22% 35.4(n=13) 6.91 2 7% 40.5(n=2) 0.71 

 Unk 1 2% 55.0(n=1) 3 11% 64.0(n=2) 1.41 

All 59 99% 28 100% 

2004–

2005 

 M 69 40% 65.1(n=68) 5.50 18 26% 67.2(n=15) 4.68 

 F 82 48% 60.1(n=78) 5.13 40 58% 63.3(n=40) 4.78 

 J 9 5% 38.3(n=9) 2.50 1 1% 70.0(n=1) 

 Unk 11 6% 60.6(n=8) 6.23 10 14% 49.0(n=1) 

All 171 100% 69 100% 

2005–

2006 

 M 8 21% 69.4 (n= 8) 14.7 2 40% 57 (n=2) 1.4 

 F 13 34% 60.4 (n=12) 5.8 3 60% 62 (n=3) 1.7 

 J 12 32% 38.7 (n=12) 4.8 0 

 Unk 5 13% 57 (n=5) 2.7 0 

All 38 100% 5 100% 

2006–

2007 

 M 13 30% 63.4 (n=13) 4.7 0 

 F 26 59% 60.4 (n=26) 3.7 4 66% 66 (n=4) 5.8 

 J 1 2% 45 (n=1) 1 17% 44 (n=1) 

 Unk 4 9% 57.5 (n=4) 2.89 1 17% 62 (n=1) 

All 44 100% 6 100% 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.30 

Figure SOP 10.7. Coho redd density per 100 m within Olema Creek and John West Fork.
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.31 

Olema Creek Coho per Kilometer

0

5

10

15

20

25

30

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15

Kilometers

Observations

Redds per km

Live Fish per km

Carcasses per km

Figure SOP 10.8. Live coho fish, carcass, and redd observations by kilometer during spawner year 

2006–2007 on the Olema Creek mainstem. 

Figure SOP 10.9. Redds per km measures by cohort for all four watersheds. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.32 

Ancillary Data: Weather and Water Clarity: Table SOP 10.16 shows the weekly rainfall and 

water clarity during the winter surveys, as well as the raw results for those surveys. During the 

winter months stream conditions can change rapidly with increased stream flows caused by 

winter storm events. Winter storm events with subsequent increased stream flows may lower 

water clarity which in turn lowers observer efficiency. Figure SOP 10.10 shows the results of 

each survey in graphical format. These data, while ancillary, are useful in answering possible 

questions about environmental conditions, spawner timing, and data confidence. For example 

during the 2006–2007 spawner season on Olema Creek, spawning activity was observed 

following rain events. However, rain events also reduce water clarity which can decrease the 

detection of spawning by the surveyor. If water clarity remains low throughout the spawner 

season, then the reported PLD and total redd count are likely to be lower than the actual 

escapement size. 

Table SOP 10.16. Seven day total rainfall per Julian week, average water clarity, and the number of coho 

redds, carcasses, and live adults observed in 2006–2007 on Olema Creek mainstem. 

Julian 

Week Survey Date 

Survey 

Reaches 

Calendar 

Day 

7 Day Rainfall 

during Julian 

Week 

(in) 

Average 

Survey Water 

Clarity 

(cm) 

Coho 

Redds 

Coho 

Carcass Live Coho

46 13 Nov 06 1.65 

47 21 Nov 06 1–3 325 0.14 70 0 0 0 

48 1.16 

49 1.86 

50 2.65 

51 18 Dec 06 2–6 352 0.84 95 34 5 58 

52 2.28 

53 31 Dec 06 2–6 365 0 88 20 12 43 

1 0.67 

2 10 Jan 07 2–6 10 0.02 100 9 5 17 

3 0.03 

4 24 Jan 07 2–6 24 0.37 100 3 4 3 

5 0 

6 5.54 

7 16 Feb 07 2–6 47 0.68 52 0 1 0 

8 2.59 

 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.33 

Olema Spawners vs Cumulative Rainfall

0

10

20

30

40

50

60

70

11/21/2006

12/18/2006

12/31/2006

1/10/2007

1/24/2007

2/16/2007

Survey Dates

Observations

0

5

10

15

20

25

Cumulative Rainfall (inches)

Coho Redds

Live Coho

Coho Carcasses

Cumulative Rainfall

Figure SOP 10.10. Representation of rainfall totals and coho adult escapement survey results on Olema 

Creek mainstem, including live fish, carcasses, and redds, observed during surveys in 2006–2007. 

Summary Report: Spring Smolt 

The Spring Smolt Report provides information about the adult coho population changes. The 

main objective to be addressed in this report is: 

• Conduct spring surveys at Olema, Pine Gulch, and Redwood Creeks by smolt trapping 

near creek mouths of Olema, Pine Gulch, and Redwood creeks to determine long-term 

trends in abundance of smolt coho salmon. 

For each stream, the report should clearly describe the: 

• Summary of trap operation dates (table SOP 10.17) 

• Summary of total number of smolts captured, population estimates during smolt trapping 

(table SOP 10.17, figures SOP 10.11–12) 

• Summary of outmigration timing and peaks (figures SOP 10.11–12) 

• Analysis of fish condition (length and weight-length) to indicate fitness (table SOP 10.18, 

figures SOP 10.13–15) 

For an example of a Spring Smolt Report see Del Real (2007). 

Because the spring monitoring period is subject to high flow events, there are some periods 

where the traps are not operable or are blown out. In such cases traps are reinstalled as soon as 

feasible. Because of the highly variable response observed in outmigration patterns, we have not 

attempted to estimate fish numbers for the period of time when the trap is out. Evaluation of 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.34 

multiple years of data may allow us to develop estimates based on flow and smolt emigration 

rates for each year. 

Operation Period: Smolt trapping dates and locations are presented in table SOP 10.17. 

Number of Smolt Captured: Coho smolt and fry along with steelhead juvenile and adult captured 

are presented in table SOP 10.17 and figure SOP 10.11. 

Table SOP 10.17. Summary of salmonid information for Olema, Redwood, and Pine Gulch Creeks trap 

operations, 1999–2006 

Watershed Year

Trap Operation 

Dates 

Steelhead

Coho 

Coho Production 

Juvenile Adult Estimate 

from 

to 

smolt parr fry resident

oceanrun smolt fry estimate SD 

Olema 

Creek 

2004 30 Mar 28 May 13 5 140 0 0 229 32 831 ± 167 

2005* 1 Apr 9 May 9 8 1,218 0 1 87 14 1,296 ± 724 

 2006 10 Apr 9 Jun 6 19 497 0 0 368 51 10,544 ± 8,399 

Redwood 

Creek 

2005 27 Mar 31 May 1 1 344 0 0 301 535 2,481 ± 616 

2006 18 Apr 9 Jun 18 0 24 0 0 1,048 27 3,253 ± 542 

Pine Gulch 1999 16 Apr 24 May 62 42 65 1 0 0 0 N/A N/A 

2002 28 Mar 29 May 27 27 240 0 5 249 0 N/A N/A 

2003 28 Mar 30 May 282 120 235 1 1 576 1 N/A N/A 

2004 25 Mar 28 May 49 50 57 0 0 149 0 737 ± 144 

2005 31 Mar 31 May 28 10 200 0 0 8 0 N/A N/A 

2006 26 Apr 9 Jun 11 7 2 0 0 93 1 368 ± 76 

Coho and steelhead presmolts are included in the coho smolt totals. 

*Trapping discontinued May 9 due to high flows. Trap was not reinstalled. 

0

5

10

15

20

25

30

11 12 13 14 15 16 17 18 19 20 21 22 23

Julian week

percentage of total smolts

average 2004-2007

2007

Figure SOP 10.11. Percent of total coho smolts captured by Julian week for Olema Creek in 2007 

compared to the running average 2004–2007. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.35 

The result of the Darroch Analysis with Rank Reduction (DARR) modeling exercise (figure SOP 

10.12) is an estimate of smolt production and confidence interval for the watershed. DARR 

modeling uses the stratified mark/recapture data from each survey week to determine capture 

efficiencies for each survey period. Using a stratified Peterson estimator, a series of algorithms 

are performed on the stratified mark/recapture data set to aggregate the survey periods to produce 

a reasonable estimate of smolt abundance and subsequent confidence intervals (Bjorkstedt 2005). 

Figure SOP 10.12. DARR output graph of smolt outmigration by week for traps requiring mark/recapture 

operation. Shows # of fish captured (bars), estimated total # of fish (solid line with o’s), and estimated 

capture efficiency (dotted line with x’s) for each week, Olema Creek, 2007. 

Fish Condition: Trends in fish condition can be tracked using fork length frequencies (figures 

SOP 10.13–14) and weight-length relationships (figure SOP 10.15), as well as Fulton’s condition 

factor (K factor), as shown in table SOP 10.18. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.36 

Olema Creek Smolt Trap 2007

1 1 2

7

16

39

87

63

32

11

5 5 7 5 2 2 5

56

11

46

81

68

27

8

0

10

20

30

40

50

60

70

80

90

100

<20mm

26-30mm

36-40mm46-50mm

56-60mm66-70mm

76-80mm86-90mm

96-100mm

106-110mm

116-120mm126-130mm136-140mm

146-150mm156-160mm166-170mm

Fork Length (mm)

Frequency

coho smolts and presmolts, n=284

coho fry, n=302

Figure SOP 10.13. Coho smolt and fry fork lengths in 10 mm increments for Olema Creek, 2007 

Olema Creek Watershed Coho Smolt Fork Length (mm) 

2004-2007

80

90

100

110

120

130

140

2004 2005 2006 2007

Fork Length (mm) 

90th Percentile

10th Percentile

25th Percentile

75th Percentile

Median

Mean

Legend

Figure SOP 10.14. Fork length of coho salmon smolts in Olema Creek, 2004–2007. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.37 

2007

y = 1E-05x2.8954

R2 = 0.9263

2004-2007

y = 5E-05x2.6722

R2 = 0.8978

0

5

10

15

20

25

30

35

40

45

60 80 100 120 140 160 180

Fork Length (mm)

Weight (grams)

2004-2007 coho smolts

2007 coho smolts

Power (2007 coho smolts)

Power (2004-2007 coho smolts)

Figure SOP 10.15. Weight-length comparison between coho smolts of Olema Creek in 2007 compared to 

the average from years 2004–2007. 

Table SOP 10.18. Mean and median coho smolt length, weight, and K factor calculated for the trapping 

location at Olema Creek 2004–2007. 

Year

 Sample 

Size 

Mean 

Length 

(mm) 

Length 

Standard 

Deviation 

Median 

Length 

(mm) 

Mean

Weight 

(g) 

Weight

Standard 

Deviation 

Median 

Weight (g) 

Mean 

K-Factor 

K-Factor

Standard 

Deviation 

2004 169 114.31 9.30 113 15.11 4.02 14.5 0.99 0.08 

2005 37 116.05 9.53 116 15.95 3.89 14.98 1.01 0.13 

2006 203 98.94 9.56 98 10.28 3.06 9.56 1.04 0.11 

2007 191 116.43 10.99 115 14.72 4.73 13.64 0.91 0.07 

Total 

Average

750 109.89 12.69 13.40 4.56 0.98 0.10 

Annual Reports 

Annual summary reports are designed as a compilation of the three seasonal reports that include 

standard sections such as an introduction, study area, methods, results, and discussion. The intent 

of the annual report is to provide resource managers with a status review of goals met, 

comparison of trends observed between watersheds, and the current recovery stage for 

salmonids. Data presented in annual reports are the same as those discussed in the summary 

reports (above). The annual reports provide more meaningful discussion of unique findings for 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.38 

the year and interpret their significance to managers. Annual reports will also interpret annual 

findings relative to other years and relative to the other year classes. These reports will focus on 

presenting multi year and creek summaries for key metrics including: 

• Abundance of coho salmon (juvenile, spawning, and smolt) (tables SOP 10.4, 10.11–14, 

figures SOP 10.10–11) 

• Distribution of coho salmon (juvenile, spawning) (tables SOP 10.3, figures SOP 10.7–8) 

• Condition (length) and sex ratio of spawning coho salmon (table SOP 10.5) 

• Juvenile and smolt coho condition (length, weight) and age composition. (tables 

SOP 10.5 and 10.8, figures SOP 10.3–4, 10.13–15) 

• Juvenile coho salmon density along index reaches (tables SOP 10.7–9) 

• Juvenile steelhead trout density, condition (length, weight), age composition along index 

reaches (tables SOP 10.7–8) 

• Changes in ratios of habitat types (pool:riffle) (table SOP 10.2) 

• Analysis of multiple life-stages (table SOP 10.9, figure SOP 10.16) 

Carlisle et al. (2008) provide the most recent example available and was the basis of the graphs 

shown above in the summary reports. Annual reports are peer reviewed by other NPS staff and 

follow the Natural Resource Technical Report (NRTR) format (see: 

http://www.nature.nps.gov/publications/nrpm/). Annual reports are generally completed between 

the smolt sampling season and the summer sampling season. 

Analysis of Multiple Life Stages 

Data from coho spawner surveys can be combined with juvenile coho data from summer surveys 

and spring smolt trapping to allow for comparison of trends within a cohort, as well as between 

cohorts in the same or different year classes. Figure SOP 10.16 shows the survival rate between 

life stages between watersheds while table SOP 10.19 tracks each cohort across multiple, life 

stages and gives a rough idea of survivorship between life stages within the individual 

watershed. By tracking survivorship between life stages the NPS will be able to determine 

potential limiting factors that currently inhibit the recovery of coho salmon in each watershed. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.39 

1

10

100

1000

10000

100000

1000000

SY 2003-04 Adults

Egg estimate

Juvenile Estimate

Smolt Production

Returning Adults

Number of Fish

Redwood Creek

Olema Creek

 Pine Gulch Spring Emergence and Rearing

Winter Rearing

Ocean and Estuary Rearing

Upstream Migration and Spawning

*It should be noted that the Olema Creek smolt trap was removed approximately one month early during the spring of 2005 and 

therefore the 2005 smolt production estimate is likely much smaller than the true production. 

Figure SOP 10.16. Survival rate between monitored life stages in Olema, Pine Gulch, and Redwood 

Creeks for spawner year 2003–2004. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.40 

Table SOP 10.19. A comparison of multiple life stage observations of coho salmon within the Olema 

Creek mainstem from the SY 2002–2003 to SY 2006–2007. 

Olema Creek mainstem 

(watershed)* 

Spawner Year (SY) 

2002–2003 2003–2004 2004–2005 2005–2006 2006–2007 

PLD Index 20 138 184 12 80 

Redds 

(Watershed Redd total)* 

10a 

(22) 

88 

(109) 

92 

(137) 

6a 

(10) 

66 

(95) 

Average Female Fork 

Length 

64b 66.3 65.7 58.7 65.3 

Estimated Number of 

Eggs 

23,580c

 230,202c 234,317c 10,973c 165,106c

Basinwide Juvenile 

Estimate

11,926 

±3,244 

25,857 

±1,499 

27,423 

±7,772 

1,793±869 31,936 

±4,122 

Estimated Survival Rate 

Egg to Juvenile 

50.6% 11.2% 11.7% 16.3% 19.3% 

Watershed Smolt 

Production Estimate 

831±167 1,296±724d

 10,544 

±8,399 

1,098±116 - 

Mean Smolt Length (mm) 114.31 116.05 98.94 116.43 

Mean Smolt Weight (g) 15.11 15.95 10.28 14.72 

Estimated Survival Rate 

Juvenile to Smolt 

7.0% 5.0% 38.4% 61.2% - 

Estimated Survival Rate 

Egg to Smolt 

3.5% 0.6% 4.5% 30.0% - 

Estimated Survival Rate 

Smolt to Adult e 2.40% 14.66%d

 SY2007–2008 SY2008–2009 SY2009–2010

*Includes John West Fork redd count 

a

Due to poor observer efficiency, the PLD index was used to estimate the Olema mainstem redd count based on two 

spawners per redd. 

b

Average female length based on female carcass lengths on Olema Creek for spawner years 2003–2004 thru 2006–

2007. 

c

Estimated number of eggs using Shapovalov and Taft (1954) formula based on average female fork length. 

d

The Spawner Year 2003–2004 watershed production estimate is artificially low since trapping operations were 

suspended early due to the capture of Red-legged frog tadpoles. The actual watershed production estimate was 

likely four to five times higher based on regional smolt production estimates. For these reasons, the smolt to 

adult survival rate is likely artificially high. e

 Estimated smolt to adult calculated by dividing number of adult spawners (estimated based on 2 times the total 

watershed redd count (in parentheses)) divided by the estimated number of outmigrating smolts for previous 

cohort 

Other Annual Reports 

NMFS Section 10 Permit Reports 

The Endangered Species Act Section 10 permit reports are required annually by NMFS, as well 

as a final report which is to be submitted at the end of each Section 10 permitting period. All 

reports are due to the NMFS on the first of May. For complete details provided by the NMFS for 

final, annual and special reporting requirements please refer to SOP 6 (Permit Requirements). 

The most recent Section 10 annual report can be viewed online 

(http://science.nature.nps.gov/im/units/sfan/vital_signs/fish/fish.cfm). 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.41 

Annual USFWS Section 10 Permit Report 

An annual report of activities shall be submitted to the Recovery Permit Coordinator at the 

Sacramento U.S. Fish and Wildlife Service (USFWS) office by January 31 of each year. The 

report should include: 1) an introduction addressing the reasons and objectives for taking the 

species; 2) methodologies used for data collection and analysis; 3) a results section that 

summarizes the data collected on any federally listed species wile conducting monitoring efforts 

under this permit; and 4) a conclusion that provides recommendations for the recovery of the 

species. 

Other Reporting Documents and Components 

Bi-annual CDFG Scientific Collection Permit Report 

The CDFG requires that a Report of Specimens Collected or Salvaged (RSCS) be submitted 

within 30 days of the expiration of the scientific collection permit (SCP). Permits are valid for 2 

years; therefore, reports will be submitted on a bi-annual basis. Each individual to whom a SCP 

is issued must provide their own RSCS. Even if the SCP holder is not renewing a permit, CDFG 

still requires a final report to be submitted within 30 days of the expiration of the SCP. For 

detailed directions on how to fill out a RSCS refer to the CDFG website: 

http://www.dfg.ca.gov/licensing/pdffiles/SC_REPT.xls. The CDFG also requires that a record of 

field observations of Threatened, Endangered, or Special Concern species is submitted to the 

California Natural Diversity Data Base. The California Native Species Survey Form and 

instructions for completing it are posted on our web page at 

www.dfg.ca.gov/whdab/html/animals.html. 

Executive Briefing 

The executive briefing is submitted to the park superintendent, program management, and park 

interpretation staff after the completion of the annual report. This is a two-page summary that 

lists monitoring objectives and questions and discusses annual results. It is intended to provide a 

regional context for the information that is collected through the fisheries monitoring programs 

Web Sites 

Websites are used to provide information to both park staff and the general public. Information 

will be updated both annually and as new reports and updates are completed. Posted items 

include all seasonal and annual reports, Executive Briefings, and the Vital Signs Report Card. 

Park Presentations 

Presentations may be preformed for NPS staff, volunteers, and the general public at different 

times for a variety of different purposes. Presentation may be preformed at senior staff meetings, 

all employee meetings, and division meetings. This opportunity gives staff a chance to hear 

about the monitoring program and ask questions. Other outreach presentations may be performed 

for volunteers and the general public at different times upon request at any of the SFAN network 

parks. 

I&M Update 

The I&M Program Manager will prepare a one-page monthly e-mail to park staff with a short 

update on vital signs projects in order to keep park staff informed about the program. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.42 

Photos 

High quality publication photos are needed to support all of the program’s communication 

products. For digital photos this means 300 pixels per inch resolution in a plain or compressed 

TIF format. Program participants should make every effort to document ongoing work, special 

incidents, site visits for communication purposes. 

Outreach Materials 

A variety of products are developed or updated regularly that are directed at lay audiences but 

include park staff. These include 2-page Executive Briefings, Vital Sign Report Cards, I&M 

Updates. Content on existing websites including internet and intranet will also be updated to 

ensure that the most recent information is available to the public. 

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. Analysis and synthesis reports are intended 

to provide a benchmark for park management in their mission to preserve and protect our stream 

resources for future generations. These reports will focus on presenting trend analyses on key 

metrics including: 

• Abundance of coho salmon (juvenile, spawning, and smolt) 

• Distribution of coho salmon (juvenile, spawning) 

• Condition (length) and sex ratio of spawning coho salmon 

• Juvenile and smolt coho condition (length, weight) and age composition. 

• Juvenile coho salmon density along index reaches 

• Juvenile steelhead trout density, condition (length, weight), age composition along index 

reaches 

• Changes in ration of habitat types (pool:riffle) 

• Analysis of multiple life-stages 

Along with comparing trends between watersheds and year-classes, trend and synthesis reports 

will compare trends reported by other research programs or agencies. The analyses include a 

synthetic look at multiple life stages. Discussions will include recommendations for changes in 

management practices that will help increase coho salmon populations to their optimal 

sustainable population. General content and format will follow the annual reports with the 

addition of a population trend analysis. 

Population Trend Analysis 

The following trend analysis will be performed on abundance data for juvenile, smolt, and adult 

coho salmon data sets. Distribution, condition, and habitat data will be used as covariate 

information and will therefore be after an initial trend analysis is performed. Methods for 

analyzing covariate information will be determined following tend analysis results. 

Trend Model Selection: Piepho and Ogutu (2002) parameterize year as both a fixed effect for 

testing linear trend and as a random effect to account for annual variation in the outcome. The 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.43 

fixed effect of year, referred to as WYear in their paper, is defined as an integer starting at 0 and 

increasing each year by one. Because SFAN personnel want to interpret three-year multiplicative 

changes in outcomes, the fixed effect for year is parameterized as 0, 0, 0, 3, 3, 3, 6, 6, 6, ... to 

account for the coho return schedule. This fixed effect for year is referred to here as CCYear, for 

creek-cohort year. 

A mixed linear model of VanLeeuwen et al. (1996) and Piepho and Ogutu (2002) is modified to 

reflect the cohort structure of coho salmon. 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). 

Trend Model: The mixed linear model of VanLeeuwen et al. (1996) and Piepho and Ogutu 

(2002) is modified to reflect the cohort structure of coho salmon. Assuming one population 

estimate per watershed per year, the modified linear mixed model is given by: 

ln(yijk) = bj + αi +wjβ + wj ti + γκ+ φik+wj dk + eijk 

where i = 1,..., ma indexes watershed; 

j = 1, ..., mb indexes year; 

k= 1,2,3 indexes the cohort; 

ma = the number of watersheds surveyed for juveniles (ma = 3); 

mb = the number of years of sampling; 

yijk = Basinwide population estimate for juveniles in watershed i, year j, and cohort k.

bj =random intercept of the j

th year, iid as N(0, σ2

b ); 

αi = the fixed intercept of the i

th watershed; 

β = fixed slope of the linear time trend; 

wj = is a constant representing the j

th cohort-by-watershed year; 

t i = random slope of i

th watershed, iid as N(0, σ2

t); 

γk = fixed intercept of k

th cohort;

φik = the fixed interaction between the i

th watershed and kth cohort; 

dk = random slope for the k

th cohort, iid as N(0, σ2

d ); and 

eijk = unexplained error, iid as N(0, σ

2

e ). 

This linear model forms the basis of the power analysis for the test of the fixed effect for 

CCYear. Tests will be performed at the α=0.10 level. Simulations will be conducted in R to 

generate random effects and assess the power to detect actual trends over time. The two-sided 

hypothesis test of no trend will be calculated for three-year multiplicative decreases of 2.5%, 

10%, 25%, 50%, and 75%. 

Program and Protocol Revision 

A formal review of the monitoring program and protocols will take place on a 6-year cycle or 

two life cycles. The review will ensure that the most sound and up to date methodologies for 

collecting and analyzing fisheries data are being used. All protocols require editing as new 

sample collection, analysis, and data management information becomes available. Required edits 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.44 

should be made as soon as they are deemed necessary and as appropriate reviews are conducted. 

See SOP 7 for details on protocol revisions. 

Literature Cited 

Anderson, R. O. and S. J. Gutreuter. 1983. Length, weight, and associated structural indices. 

Pages 283–300 in L. A. Nielsen and D. L. Johnson, editors. Fisheries techniques. American 

Fisheries Society, Bethesda, Maryland. 

Beidler, W. M. and T. E. Nickelson. 1980. An evaluation of the Oregon Department of Fish and 

Wildlife standard spawning fish survey system for coho salmon. Oregon Department of Fish 

and Wildlife Information Report Series, Fisheries Number 80-9, Portland, Oregon. 

Bjorkstedt, E. P. 2000. DARR (Darroch Analysis with Rank-Reduction): A method for analysis 

of stratified mark-recapture data from small populations, with application to estimating 

abundance of smolts from outmigrant trap data. Contribution 116. Administrative Report SC00-02. National Marine Fisheries Service, Southwest Fisheries Science Center, La Jolla, 

California. Online. (http://swfsc.noaa.gov/textblock.aspx?Division=FED&id=3346). 

Accessed on 20 January 2010. 

Brown, G. G., and B. J. Ketcham. 2002. Documentation of coho salmon in Pine Gulch Creek, 

Marin County, California. Coho Salmon and Steelhead Trout Restoration Project. PORENRWR-02/02. Point Reyes National Seashore, Point Reyes, California. 

California Department of Fish and Game (CDFG). 1978. Silver salmon and steelhead survey of 

 Redwood Creek, Marin County. Internal memo to Fisheries Management, Region 3. CDFG, 

Bay Delta Region, Napa, California. 

 

California Department of Fish and Game (CDFG). 1981. Fish and Game report – Stream survey. 

Internal memo to NPS. CDFG, Region 3, Bay Delta Region, Napa, California. 

Carlisle, S., M. Reichmuth, E. Brown, and S. C. Del Real. 2009. Long-term coho salmon and 

steelhead trout monitoring in coastal Marin County 2007: annual monitoring progress report. 

Natural Resource Technical Report NPS/SFAN/NRTR—2009/269. National Park Service, 

Fort Collins, Colorado. 

Del Real, S. C., M. Reichmuth, and B. J. Ketcham. 2007. Long-term coho salmon and steelhead 

trout monitoring program in coastal Marin County – Summer 2006 monitoring progress 

report. Report to California Coastal Conservancy. San Francisco Bay Area Inventory and 

Monitoring Program, Point Reyes Station, California. 

Del Real, S. C., S. Carlisle, M. Reichmuth, E. Brown, and B. J. Ketcham. 2008. Summer 2007 

monitoring progress report. Natural Resources Technical Report NPS/SFAN/NRTR2008/002. National Park Service, San Francisco Bay Area Inventory and Monitoring 

Program, Point Reyes Station, California. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.45 

Dolloff, C. A., D. G. Hankin, and G. H. Reeves. 1993. Basinwide estimation of habitat and fish 

populations in streams. General Technical Report SE-83. USDA Forest Service Southeastern 

Forest Experiment Station, Asheville, North Carolina. Online. 

(http://www.srs.fs.usda.gov/pubs/gtr/gtr_se083.pdf). Accessed 10 November 2009. 

Gurka, M. J. 2006. Selecting the best linear mixed model under REML. The American 

Statistician 60(1):19–26. 

Irvine, J. R., R. C. Bocking, and K. K. English, and M. Labelle. 1992. Estimating coho salmon 

(Oncorhynchus kisutch) escapements by conducting visual surveys in areas selected using 

stratified random and stratified index sampling designs. Canadian Journal of Fisheries and 

Aquatic Sciences 49:1972–1981. 

 

Johnston, N. T., J. R. Irvine, and C. J. Perrin. 1987. Instream indexing of coho salmon 

(Oncorhynchus kisutch) escapement in French Creek, British Columbia. Canadian Technical 

Report of Fisheries and Aquatic, No. 1573. 

Ketcham, B. J., G. G. Brown, and O. G. Wolff. 2004. 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. 

Ketcham, B.J., M. Reichmuth, and K. L. Leising. 2005. Long-term coho salmon and steelhead 

trout monitoring program in coastal Marin County – summer 2005 monitoring progress 

report. Report to California Department of Fish and Game, contract #P0330431. 

Manning, D. J. 1999. Coho and steelhead restoration project annual coho salmon spawner survey 

report: 1997–1998. Coho and Steelhead Restoration Project. PORE-NR-WR-99/01. Point 

Reyes National Seashore, Point Reyes, California. 

Moring, J. R., and R. L. Lantz. 1975. The Alsea watershed study: Effects of logging on the 

aquatic resources of three headwater streams of the Alsea River, Oregon. Part I- biological 

studies. Oregon Department of Fish and Wildlife, Fishery Research Report 9:1–39. 

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. 

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, California. 

Online. (http://science.nature.nps.gov/im/units/sfan/vital_signs/fish/docs/2004-

05%20Coho%20Escapement%20Summary%20Report%20Final%201205.pdf). Accessed 20 

January 2010. 

Reichmuth, M., C. Del Real, and B. J. Ketcham. 2006. Smolt trapping program summary: Olema 

Creek, Pine Gulch, and Redwood Creek, Marin County, California. 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, 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 10.46 

California. Online.

(http://science.nature.nps.gov/im/units/sfan/vital_signs/fish/docs/2006%20Annual%20smolt

%20trapping%20summary%20v2.2%20final.pdf). Accessed 20 January 2010. 

Shapovalov, L., and A. C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo 

gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with specific reference to 

Waddell Creek, California, and recommendations regarding their management. California 

Department of Fish and Game Fish Bulletin 98. 

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, California. Online. 

(http://science.nature.nps.gov/im/units/sfan/vital_signs/fish/docs/JuvenileStatusTrend.pdf). 

Accessed 20 January 2010. 

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. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.1 

SOP 11. Personnel Training and Safety 

Version 1.5 

Revision History Log 

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1.5 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.2 

Tables 

Page 

Table SOP 11.1. Examples of diseases potentially hazardous to field personnel. ............. SOP 11.8

Table SOP 11.2. First aid, CPR, and AED training options ............................................ SOP 11.11

Table SOP 11.3. Wilderness First Aid training options. .................................................. SOP 11.13

Table SOP 11.4. Typical field and/or fisheries related injuries. ...................................... SOP 11.13

Appendixes 

Page 

Appendix SOP 11A. Fisheries Job Hazard Analysis ....................................................... SOP 11.17 

Appendix SOP 11B. Volunteer Agreement Form ........................................................... SOP 11.26 

Appendix SOP 11C. Checklists for Standard Safety Equipment .................................... SOP 11.30 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.3 

Overview 

This standard operating procedure (SOP) describes the training and safety measures required for 

staff and volunteers. Training and safety are handled in one SOP because they are tightly linked: 

thorough training must include proper safety coverage to ensure the well-being of employees and 

volunteers. This SOP discusses training for spawner surveys, smolt trapping, habitat typing, 

electrofishing, snorkeling, seining, and data management. The safety section addresses general 

field safety, defensive and safe driving, and CPR/AED and first aid training. Sample forms and a 

fisheries job hazard analysis (Appendix A) pertaining to safety protocol are also provided. 

Training Requirements for Staff 

Prior educational and field background is very important to implement this monitoring program. 

All program staff should review all pertinent reading material prior to engaging in any 

monitoring activities. 

The Fisheries Biologist (Program Lead) 

The project lead should have field experience working with smolt traps, snorkel surveys, 

electrofishing, and spawner surveys as well as experience leading field crews. Familiarity with 

statistics and report-writing is also useful. Field experience and some leadership background are 

required for the Field Crew Leader. Field Assistants and other technical staff should have some 

educational background in biology or aquatic sciences, with minimal field experience required. 

Crew Leaders and Crew Members 

All field staff including the Crew Leader and Crew Members should be familiar with the list of 

potentially occurring aquatic species either through past job experience, academic coursework, 

or by use of field guides for this region. The nature of the work described in the Salmonid 

Monitoring Protocol involves access through difficult terrain and working in potentially 

inclement weather. All staff should be aware of their physical limitations before conducting 

monitoring activities. 

Volunteers 

Volunteers will need less experience because they will always be going out with experienced 

staff. Once they are trained, however, they may take on the roles of Crew Members. All 

volunteers should be aware of their physical limitations before conducting monitoring activities. 

All volunteers are required to complete a volunteer agreement form (Appendix B) prior to 

participating in monitoring activities. Volunteer agreement forms will be verified and maintained 

by the program lead. 

Spawner Survey 

Crew Leader: Crew Leaders lead spawner surveys. Staff members and experienced 

volunteers can be trained as Crew Leaders by the Program Leader. Training will consist 

of reviewing identification materials and SOP 5 in the office and accompanying the 

Program Leader on spawner surveys in the field. Field training will continue until the 

Program Leader is confident in the trainee’s ability to consistently identify live fish and 

redds correctly, process a carcass, and lead a crew in the field. 

Crew Member: Crew Members accompany a Crew Leader on a spawner survey and 

consist of staff members and volunteers. Crew Members should review identification 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.4 

information prior to the survey. In the field, Crew Leaders should review distinguishing 

characteristics among the fish species and should point out examples of each to the Crew 

Members when seen. 

Smolt Trapping 

Staff members should review SOP 4 prior to going out in the field. Once in the field, the 

Program Leader or an experienced staff member should demonstrate how to set up, maintain, and 

take down the smolt trap. The Program Leader should also review how to operate the trap, 

process fish, and should demonstrate how to tag a fish with Passive Integrated Transponder (PIT) 

tags. After demonstrating, the Program Leader should supervise new staff members while PITtagging fish until the Program Leader feels they are competent. 

Volunteers need less extensive training because they will not be checking smolt traps without an 

accompanying staff member. In the field, the staff member can direct volunteers on how to assist 

with trap set-up, trap maintenance, and fish recording. 

Habitat Typing 

New staff members should review the section on habitat typing in SOP 1 prior to going out in the 

field. In the field, new staff members should be paired with an experienced staff member until 

the experienced staff member is confident in the new staff member’s ability to characterize 

habitat. Volunteers will not be involved with habitat typing.

Electrofishing 

Only staff members should be trained to operate the electrofisher and process fish. All field crew 

members, including volunteers and staff members, should be trained to net, pass, and record fish. 

Staff members should review the electrofishing section in SOP 3. The staff member leading the 

field crew should go over safety measures and procedures before starting work in the field. 

Electrofisher Operator: Only staff members will be trained to operate the electrofisher. 

Prior to going out in the field, staff members will review the Principles and Techniques of 

Electrofishing handbook to learn the fundamental techniques and safety precautions. 

Once in the field, the Program Leader will demonstrate how to use the electrofisher, 

explain how to fish around challenging areas like rootwads, undercut banks, woody 

debris, and deep holes. The Program Leader should also supervise a recently trained staff 

member during the first couple of times operating the electrofisher, offering suggestions 

and guidance. 

Netter: Netters flank the electrofisher operator and catch stunned fish. Once in the field, a 

staff member should demonstrate proper netting technique and how to transfer fish 

between nets and buckets. The staff member should remind netters to stay on either side 

of the electrofisher operator and not to get ahead of the operator, which could 

compromise visibility by stirring up sediment. 

Passer: In the field, a staff member should demonstrate proper technique for transporting 

and handling fish. Volunteers should be reminded to wet their hands and nets before 

handling fish. 

Processor: Only staff members should be trained to weigh and measure fish. In the office, 

staff should review identification techniques for the various species of fish. While in the 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.5 

field, the Program Leader should point out distinguishing features of fish specimens. All 

staff members should review the section Handling Captured Fish in SOP 3. 

Recorder: A staff member should ensure that all crew members are familiar with the data 

sheets, described in the section Handling Captured Fish in SOP 3. 

Snorkeling 

Only staff members will snorkel; accurately counting and identifying fish requires extensive 

experience. New staff members will be trained by the Program Leader or another staff member 

who is an experienced diver. Divers will be trained in the field for at least one season before 

becoming lead divers and leading surveys themselves. Before going out in the field, new divers 

should review the section on snorkeling in SOP 1 and should discuss with the lead diver 

techniques for counting fish and filtering them between divers. Once in the field, the lead diver 

should demonstrate how to dive and point out fish underwater to help the new staff member learn 

to identify fish underwater. 

Seining 

Staff members should review the section on seining in SOP 3. Once in the field, the Program 

Leader or other experienced staff member should demonstrate how to pull the seine net for new 

staff members and volunteers. 

Data management 

Staff members should familiarize themselves with SOP 8. An experienced staff member should 

lead new staff members through the process of using the database. Volunteers will not use the 

database. 

Safety 

General Field Safety 

Safety Circle: Prior to beginning any activity that is new to field personnel, the crew should 

gather for a safety talk. Additionally, a period of stretching to prepare the crew for physical 

activity is highly advisable and could potentially minimize risk for injuries. 

Safe Wading: Field personnel working in and near streams may encounter a number of 

hazards. Due to the often uneven streambeds containing slippery rocks of varying sizes, it is 

easy for field crew members to fall which can lead to injuries or drowning. To wade safely, 

enter a stream where water movement is slowest, taking short steps into the current, walk at a 

slight downstream angle in swifter waters and if you must turn, turn into the current. Waders 

should fit properly, with enough room to allow for mobility. Wading belts should also be 

worn with waders as they help prevent waders from filling if overtopped. Standard, rubber 

soled wading boots are suitable for slower-moving streams with mud, sand, or pebble beds. 

Using a wading staff is very helpful in maintaining balance while wading in swifter waters. If 

used, hold the staff on the upstream side, placing it firmly before taking a step. Personal 

flotation devices should always be worn when wading in large streams (Berry, Jr., 1996). 

Streams in the San Francisco Bay Area Network (SFAN) tend to be “flashy” due to the 

Mediterranean climate in the region. Flashy streams are characterized as having water levels 

that rise rapidly during storm events. If multiplying a stream’s velocity by its width results in 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.6 

greater than or equal to 10 ft2

/s, one should not attempt wading. Other hazards to be aware of 

during storms include the presence of flowing logs, debris, and falling trees (Cooprider & 

Carson, 2006). 

Electrofishing Safety: All field crew members should wear proper chest waders with no 

leaks. Crew members netting or operating the electrofisher should wear polarized glasses. 

Lineman’s gloves are advised. The electrofisher operator should review electrofishing 

methods and safety measures prior to starting field work. When the shocker is on, crew 

members should not put their hands in the water even if wearing gloves (Kolz et al, 1998). 

Netters and other crew members should alert the electrofisher operator if they need to touch 

the water or feel unbalanced so that the operator can stop shocking. People who are pregnant 

or have heart conditions, such as a pacemaker, should not participate in electrofishing 

fieldwork. Anyone operating the electrofisher should be CPR and First Aid Certified. If 

weather conditions turn stormy with continuous rain or thunder and lightning, the 

electrofisher operater should stop electrofishing. No one should be out in the field 

electrofishing alone. More detailed safety considerations are in chapter 12 of the Principles 

and Techniques of Electrofishing handbook. 

Fish Handling Safety: The risk for personal injury and disease from handling fish is often 

greatly underestimated among field personnel. Potential hazards include diseases or 

infections from contact with certain organisms, cuts, punctures, or abrasions from various 

parts of fish such as spines, gill rakers, teeth, or opercula (table SOP 11.1). The risk for 

contracting diseases is particularly elevated in polluted or organically enriched streams 

because these streams contain increased levels of pathogens and bacteria. Avoiding polluted 

areas as much as possible should be considered and contamination prevention by the 

consistent practice of wearing gloves should be emphasized. Punctures, and open wounds 

should of course be avoided but if they occur, prompt, thorough cleansing, disinfection, and 

bandaging of the wound after exposure is critical to prevent disease and infection. If wounds 

are sustained to bodily joints, medical care should be sought immediately as punctures to 

these areas of the body are more vulnerable to infection. Signs of infection include: 

ascending red marks, increased pain, and soreness in joint areas or above the sting area 

(Olmsted, 2008). 

Underwater and Diving Safety: All divers must be strong swimmers able to swim in fastmoving water. Divers should work in groups of at least two and should wear full wetsuits, 

including hood and gloves, and a snorkel. Before going in the field, divers should look at 

maps and aerial photos of the survey area to find good access points and possible evacuation 

points. Divers should not try to swim through cascades or under large logs and should instead 

exit the creek and walk around potentially hazardous obstacles. While underwater, divers 

must stay alert to avoid hitting hidden objects or becoming tangled in debris. All divers 

should be CPR and First Aid Certified and should know the signs of hyperthermia and 

hypothermia. On especially warm days, divers should take extra care to stay hydrated and 

cool, especially if there are long distances to hike between dive sites. Divers should not dive 

in areas known to have poor water quality and should use their judgment at sites where water 

quality is unknown but seems questionable. When possible divers should request water 

quality samples from the I&M Water Quality Specialist within 48 hours of the scheduled 

surveys. 
Salmonid Monitoring Protocol for the San Francisco Area Network: Standard Operating Procedurees 

SOP 11.7 

Plants: The most common plants throughout the SFAN that warrant hazard awareness are 

poison oak (Toxicodendron diversilobum), and stinging nettle (Urtica dioica). The safety 

briefing “Working in Poison Oak” (Brands-Maloney, 2001) provides an extensive review of 

poison oak identification, location, prevention, and treatment of contact dermatitis and can be 

consulted for details. Field personnel should review this BEFORE entering the field and 

should be familiar with the shape, color, and size of poison oak leaves twigs, vines, and, yes, 

shrubs. Stinging nettle is not a health threat but causes skin irritation which can be severe 

(though temporary) if in large amounts (Cooprider & Carson, 2006). 
SOP 11.8 

Table SOP 11.1. Examples of diseases potentially hazardous to field personnel. Table SOP 11.1. Examples of diseases potentially hazardous to field personnel (continued).Name Other Names Pathogen Carrier How transmitted 

Appearance on host Human symptoms 

Vibriosis Vibrio 

parahaemolyticus; 

V.vulnificus; V. alginolyticus 

Shellfish, crustaceans 

Cuts, open wounds. 

Not visible Acute diarrhea, 

abdominal cramps, fever, soft tissue destruction 

Erysipeloid or Erythema migrans 

Fish handler’s disease, fish poisoning, fish hand, sealer’s finger, whale finger blubber finger, diamond skin disease 

Erysipelothrix rhusiopathiae 

Fish, shellfish, marine mammals. 

Handling infected organisms or fecal waste with open wounds 

 Elevated lesions on 

skin (can be diamond-shaped), 

joint pain, fever, 

severe headaches; incubation 1-7 days

Crayfish Handlers Disease 

Sealer’s finger Erysipelothrix 

insidiosa, species of Vibrio 

Fish and shellfish Handling infected 

organisms with open wounds or abrasions 

Not visible Painful itching or 

burning; joint swelling, stiffness; lasts up to 3 weeks 

Fish TB Fish tank granuloma, 

swimming pool granuloma, tuburculosis, mycobacteriosis 

Mycobacterium marinum 

Fish Handling fish with 

open wounds 

 Skin, soft tissue 

destruction; small purple lesions that gradually enlarge; incubation period 2 weeks–2 years; can mimic carpal tunnel syndrome 

Salmonellosis Salmonella Salmonella 

sandiego, S. java, S. Pomona, S. Miami 

Turtles, newts, frogs, toads, other reptiles and amphibians 

Direct contact and indirect (unwashed clothes). 

Not visible Diarrhea, abdomina

cramping, fever 

Swimmer’s Itch Schistosome 

cercarial dermatitis 

Waterfowl and humans-adult phase; aquatic snails –intermediate 

Swimming or contact with waters infested with the flatworm 

 Skin rashes and 

bumps (papulae) within 30 min of exposure 
SOP 11.9 

Table SOP 11.1. Examples of diseases potentially hazardous to field personnel (continued).Name Other Names Pathogen Carrier How transmitted 

Appearance on host Human symptoms 

Giardiasis Giardia intestinalis Infected soil and 

water; surfaces contaminated with animal or human feces 

Accidental 

ingestion 

Not visible Diarrhea and 

dehydration 

Red Plague Aeromonas 

salmonicida 

Wild and captive freshwater fish

Handling infected fish 

Diarrhea, skin infections

Source: Adapted from Olmsted 2008 
 

SOP 11.10 

Defensive and Safe Driving 

Before leaving, the driver should inspect the vehicle to make sure it is functioning properly and 

contains the necessary safety gear, including jumper cables, road reflectors, safety vests, a basic 

tool kit, a tire pressure gauge, and flashlight (Reicke, 2008). Drivers should also check that they 

know how to operate the vehicle, since all vehicles are slightly different. 

En route to field sites, drivers and passengers should always wear seat belts. Drivers should drive 

at a safe speed, which may be slower than the posted speed limit. On dirt or ranch roads, drivers 

should be aware of the road conditions and watch for other vehicles, even when behind locked 

gates. Drivers should leave gates locked as found. When turning on narrow roads, drivers should 

use a spotter and never back toward a hazard, such as a cliff edge (Fong et al, 2003). Extra 

caution should be used when driving in unfamiliar areas, remote areas, and places where large 

animals are likely to cross the road. Drivers should also pay extra attention when driving at night 

or in stormy conditions. Drivers should watch for signs of fatigue and take a nap or have a field 

partner drive if necessary. 
 

SOP 11.11 

CPR/AED and First Aid Training 

In case of emergency situations, all fisheries staff should be up-to-date in CPR/AED and First 

Aid Certification. This training is invaluable to personnel safety, particularly since fisheries staff 

often work in remote locations, outdoors for extended periods of time, and far from medical 

facilities. A variety of trainings are regularly offered by organizations such as the American Red 

Cross and American Heart Association. The nearest chapters of these organizations can be found 

on their websites. A combination course consisting of first aid, cardiopulmonary resuscitation 

(CPR), and automated external defibrillator (AED) training is often most valuable and 

economical. Up-to-date certification can usually be completed within one day and lasts 1-2 years 

for CPR/AED training and 3 years for first aid. Course options are described in table SOP 11.2, 

with wilderness training options in table SOP 11.3. table SOP 11.4 summarizes typical field 

and/or fisheries related injuries. 

Table SOP 11.2. First aid, CPR, and AED training options 

Source: Csoboth, 2008. 

The following information on training options for CPR/AED, first aid, and wilderness safety is 

referenced directly from Csoboth (2008) in the Fisheries Safety Handbook. 

“A few options exist for training employees/students. Each option includes instructor 

observations to ensure participants acquired the requisite knowledge and skills. 
 

SOP 11.12 

• An instructor can come to your facility and train your employees at a time that works 

for you—daytime, evenings or weekends. Typically, class sizes are 10 individuals, 

but can be larger if there are multiple instructors. 

• One of your employees can become an authorized instructor to provide first aid, CPR 

and AED training onsite. This cost-effective option allows you to schedule training at 

your convenience with instructors familiar with your specific emergency procedures 

and site-specific needs. This option tends to be feasible only for large programs or in 

those with a high interest level. 

• When only a few employees need training, classes are available at community 

locations. 

• The newest and most flexible option allows everyone to learn at their own pace. The 

Red Cross offers Blended Learning training, where the first part of the training is 

accessed online at the employee’s convenience, followed by an instructor-led skills 

practice and assessment. The American Heart Association offers CPR Anytime or 

AED Anytime training, where CPR skills and lessons are taught using a DVD and 

CD-ROM, followed by an instructor-led skills test.” 

Wilderness Safety Training Options

“For aquatic resource professionals that regularly work in remote wilderness settings, it may 

be beneficial to expand the scope of their first aid and rescue skills. 

Remote settings are identified based upon both the miles-from-care, as well as the 

accessibility of the site. Generally, areas beyond two hours from definitive care are 

considered remote. Wilderness safety training may also be beneficial for individuals working 

alone or in small groups that would require administering emergency care for an extended 

period before professional medical assistance could arrive. The primary hazards associated 

with working in remote locations are: 

• Isolation from public rescue services; 

• Limited means of communication; 

• Exposure to adverse/severe weather 

If extended period of time outside of normal cell coverage areas is expected, it may be 

prudent to consider purchasing a satellite phone. Wilderness first aid courses can be found 

throughout the country (and world), and are typically rigorous, fast-paced, with many handson training components. Certifications are typically three years. If you choose to go this 

route, it is imperative that you go with an industry-recognized training organization. The top 

three such organizations in the U.S. are: Wilderness Medical Associates, SOLO, and the 

Wilderness Medicine Institute”. 
 

SOP 11.13 

Table SOP 11.3. Wilderness First Aid training options. 

Source: Csoboth, 2008. 

Table SOP 11.4. Typical field and/or fisheries related injuries. 

Table SOP 11.4. Typical field and/or fisheries related injuries (continued). 

Type of Injury Injury Characteristics 

Flesh Wounds Scrapes and 

Abrasions 

Usually does not penetrate skin, slow bleeding 

Cuts Blood is dark red, flows at a steady pace, can be life-threatening 

Puncture Wounds Blood is bright red, flows very rapidly. If major artery is punctured, 

treat immediately 

Skeletal Sprained Joints 

and Dislocations 

Range from aching to severe pain. Dislocations show signs of 

deformity, swelling, discoloration, pain, inability to move injured 

area, and can emit a grating sound. 

Broken Bones Deformity, swelling, discoloration, grating sound, pain, inability to 

move area, exposed bone in the case of compound fracture 

Head and Neck Change in consciousness, breathing difficulty, impaired vision, 

inability to move body part, headache, vomiting, loss of balance, 

tingling in hands, fingers, feet, and/or toes 

Toxins, Bites, 

Stings 

Spider Bite (Brown 

Recluse) 

Swollen, painful, and itchy in area of bite. Wound blisters. Wound 

may develop in a large ulcerated area within hours or days. Severe 

symptoms include fever, chills, nausea/vomiting, and body rash. 

Spider Bite (Black 

Widow) 

Minimal to sharp pain, followed by redness and swelling at site. 

Bite may not be painful initially. Severe symptoms include 

abdominal pain, dizziness, headache, fever, severe cramps, 

weakness and difficulty breathing. 

Scorpion Bite Immediate pain, itching, swelling, skin changing color, anxiety, 

fainting, numbness of tongue, vision problems, diarrhea. 

Tick Bite Possible rash, tick usually visible. Risk of Lyme's disease. 

Snake Bite Swelling around bite usually. 

Insect Sting Never pull out stinger. Use edge of credit card or something similar 

to snag venom sack about skin level. 
 

SOP 11.14 

Table SOP 11.4. Typical field and/or fisheries related injuries (continued). 

Type of Injury Injury Characteristics 

Contact 

Allergies 

Jellyfish Sting Typically painful, red rashes limited to area of direct contact. 

Lesions can last days/weeks. Severe stings can cause weakness, 

headaches, vomiting, fever, chills, muscle spasm, difficulty 

breathing, possibly shock. 

Stingray Sting Immediate, excruciating pain, bleeding, wounded area may turn red 

or blue, nausea, vomiting, fever, chills, muscle cramps, paralysis, 

fainting. 

Catfish Sting Severe pain, inflammation at site of sting 

 Poison Ivy, Oak, & 

Sumac 

Redness, itchy skin; red bumps or large oozing blisters; often in 

streaks or patches 

Medical 

Emergencies 

Allergic Reactions Skin (redness, itching, blistering, hives), lungs (wheezing, 

tightness, cough, shortness of breath), head (swelling of face, 

eyelids, lips, tongue, throat), nose (stuffy, runny, sneezing), eyes 

(red, itchy, swollen, watery), stomach (pain, nausea, vomiting, 

diarrhea) 

Diabetes Fatigue, excessive thirst, excessive urination, irritability, blurry 

vision 

Stroke Weakness, numbness of face, arm, leg, blurred vision, severe 

headache/dizziness/confusion 

Cardiac Arrest No heart beat, unresponsive, not breathing 

Seizures Person makes a sound followed by abnormal stiffening and jerking 

of arms and legs 

Environmental 

Emergencies 

Hypothermia Shivering, numbness, apathy, weakness, loss of consciousness 

Hyperthermia Heat Exhaustion: cool, moist skin, headache, nausea, weakness, 

heavy sweating 

Heat Stroke: red, hot, dry skin, vomiting, loss of consciousness 

Frostbite Lack of feeling, waxy, cold, discolored skin 

Sunburn Red, dry skin; blisters form when more severe 

Drowning/NearDrowning Coughing, choking, vomiting, shortness of breath/gasping, blue 

lips/tongue, clenched teeth, frothy sputum, weak pulse, slow 

absent breath, and coma 

Source: Csoboth 2008. 

Literature Cited 

Berry, Jr., C. R. 1996. Safety in fisheries work. Page 71 in B. R. Murphy and D. W. Willis, 

editors. Fisheries techniques. Second edition. American Fisheries Society, Bethesda, 

Maryland. 

Brands-Maloney, C. 2001. Working in poison oak. Point Reyes National Seashore Safety 

Briefing. U.S. Department of Interior, National Park Service, Point Reyes Station, 

California. 
 

SOP 11.15 

Cooprider, M. A., and Carson, R. G. 2006. Personnel Training and Safety, Version 1.02, 

Standard Operating Procedure 2. In San Francisco Area Network Freshwater Quality 

Monitoring Protocol Version 2.11. NPS/SFAN/NRR—2006/016. Appendix H-SOPs, 

National Park Service, San Francisco Bay Area Network, California. 

Csoboth, L. 2008. CPR/AED and first aid training. Pages 22-27 in Fisheries safety handbook. 

Professional Safety Committee of the American Fisheries Society, Bethesda, Maryland. 

Kolz, A. L., J. Reynolds, A. Temple, J. Boardman, and D. Lam. 1998. Principles and techniques 

of electrofishing. Course Manual. U.S. Fish & Wildlife Service National Conservation 

Training Center, Branch of Aquatic Resources Training, Shepherdstown, West Virginia. 

Lane, S. L., and Fay, R. G., October 1997. Safety in field activities: U.S. Geological Survey 

Techniques of Water-Resources Investigations, book 9, chap. A9. Online. 

(http://pubs.water.usgs.gov/twri9A9/) accessed 23 November 2009. 

Olmsted, L. 2008. Fish handling safety. Pages 28-34 in Fisheries safety handbook. Professional 

Safety Committee of the American Fisheries Society, Bethesda, Maryland. 

Reicke, D. 2008. Defensive and safe driving. Pages 8-10 in Fisheries safety handbook. 

Professional Safety Committee of the American Fisheries Society, Bethesda, Maryland. 
SOP 11.16 
SOP 11.17 

Appendix SOP 11A. Fisheries Job Hazard Analysis 

Job Hazard Analysis 

PORE 

U.S. Department of Interior WORK PROJECT/ACTIVITY LOCATION 

National Park Service

Aquatic surveys and projects Point Reyes National Seashore 

JOB HAZARD ANALYSIS (JHA) DEVELOPED BY JOB TITLE 

Michael Reichmuth Fishery Biologist 

APPROVED BY: DRequired and/or Recommended Personal Protective Equipment: Sturdy work boots Personal Flotation Device Warm clothing / hat Lug sole waders (chest, hip, neoprene) Sun hat Lug sole wading boots Polarized Sun glasses Cotton gloves / wool gloves Sunscreen Linesman gloves Personal water bottles Latex gloves First Aid Kit Survivor kit Park radio Wetsuit/Dry Suit Technu (poison oak cleanser) Maps Forceps / vial Mask and snorkel / neoprene gloves Safety glasses Throw Bag

TASKS/PROCEDURES HAZARDS ABATEMENT A

Engineering Controls*Substitution

Personal Protection 

All Tasks and Procedures Unfamiliarity All people (permanent, seasonal, VIPs

should receive a general orientation aspecific to the task prior to beginning 

1. Driving to and from remote field sites. 1a. Narrow, single-lane 

roads with bumpy or “washboard” surfaces; 

WEAR SEATBELTS AT ALL TIMES WH1a. Maintain a safe speed (this if often be

road conditions; 
SOP 11.18 

1b. Driving with limited visibility; 1c. Sharp rocks on edge or in middle of road; 1d. Large animals crossing or standing in roads (including park bypass); 1f. Fatigue at night and after a long shift in the field; 1g. Storm conditions –wind, lightning, muddy/ slippery roads; 1h. Fallen trees on 

stay clear to the right, especially on curvetimes; when turning around on mountain roads (versus backing toward the cliff edge, e.gand spot for driver when backing up; 1b. Maintain windshield cleaner fluid levewindows regularly (remember back windoslow down; if blinded by sun or dust, proceed slowly to pass; keep to the right hand side of the on; 1c. Get out and move sharp rocks out of substantially in places with large amounts make sure tires are properly inflated and for damage; make sure tire jack fits the vehicle and al1d. Slow down where animals might be pdo not swerve abruptly to avoid hitting an to ride out the impact; 1f. Be aware of signs of fatigue- pull over or eat a snack or have a partner drive; do to drive; communicate with your field part1g. Keep informed on the current weathe

www.wrh.noaa.gov;

if winds exceed 15 mph, or the excessive scale (tree tops swaying, twigs and leavethe field; avoid going to the field if lightning is presdrive slowly when roads are muddy and swith geologists if you are uncertain of bacavoid wet clay roads as much as possiblestorms, especially in spring, maintain a sthese roads!; if you damage waterbars make sure you 1h. For small trees, try and remove tree o
SOP 11.19 

road; 1i. Others driving on the road; 

remove portion of tree; for large trees, notree; 1i. Do not assume you are the only one o(day or night), people from other agenciebe alert to the idea that others may be coearly a.m. - drive slow and keep right!; 

if you encounter an unusual situation, conand notify the supervisor or park ranger- situations with visitors- let the rangers ha

2. Communication 2a. Unable to reach a 

radio repeater in a remote location. 

2a. Make sure radio is charged- try to raisinform them of your predicament; if you are unable to reach a repeater from toward a ridgetop or knoll and try again; try at regular intervals, just meandering asignal; use cell phone in vehicle (if available), as communication in remote locations. 

3. Hiking 3a. Steep, rugged, 

and slippery terrain 3b. Undergrowth 

3a. Assess terrain conditions to find safe plans to avoid unsafe areas; Proper footwboots with Vibram or other slip-resistant sankle, broken in before the field season, socks, NO TENNIS SHOES; if wearing wthey are slippery on grass and mud, carry 

sure pack is comfortable and secure, waitake care when walking on hardwood leamaintain an erect posture when contourinavoid walking below another person due dislodge from above; use caution when c3b. Wear safety glasses (or other glassesto protect eyes from protruding objects. 

4. Encountering noxious plants, animals, disease, and people 

4a. Poison oak 4a. Make sure you can identify poison oa

bare twigs, and berries (the plant is toxic absent!); apply barrier cream to prevent ewear long sleeves or Tyvex suit (or compavoid sitting with arms resting on knees; similar) lotion to prevent exposure; wash after returning from the field; bring an ext
SOP 11.20 

4b. Bees/Wasps/ Hornets 4c. Ticks 4d. Scorpions 4e. Rattlesnakes 4g. Mountain lions 4h. Disease (bubonic plague and Hanta Virus) 4i. Encounters with strangers 

change into after coming out of field; wasother laundry. 4b. Determine if any field crew are allergcrew members and the supervisor if you stings. Ensure that individual carries presanaphylactic shock; Carry a bee sting kit or Benadryl or other Be aware of the ground where you step- ground at the base of trees or shrubs, or buzzing in and out of holes or around groif possible, flag a nest so future surveyors 4c. Know how to identify and distinguish Lyme disease, from the “wood tick” that dif bitten by a tick, remove it (grasp tick wstraight out), and follow instructions for pcounty health department so they can defill out a CA-1 (accident report) in the evedisease appear eventually; 4d. Inspect items left lying on the groundprior to putting them on; 4e. Avoid rattlesnakes by inspecting the gstepping over them; avoid placing hands hoists without visually inspecting them firbitten by a rattlesnake, stay calm, sit still, 4g. Avoid mountain lions; if you encounteyou- leave the area; if attacked- fight bac4h. Stay away from dead rodents and robuildings. 4i. Report uncomfortable encounters witsupervisor as soon as possible; report ap
SOP 11.21 

ranger, do not get into a confrontation wit

5. Exposure to environmental variables 5a. Treatment of 

general injuries 5b. Hypothermia 5c. Hyperthermia 5d. Giardia 5e. Sunburn 

5a. All NPS field staff and contractors wiFirst Aid certification. 5b. Always anticipate bad weather and dclothes with you. Always travel in pairs adry as possible. Eat high energy nutritionCover the head and neck to prevent heat the body’s metabolism. Drink plenty of liq

although an individual does not “feel” thirUnderstand the effects of cold and wind: develop between 30°F and 50°F. 5c. Hyperthermia may occur during high dehydration, heat exhaustion, heat crampsymptoms include nausea, headache, andrink plenty of water (even when you are as heat increases, take frequent breaks ishirt. 5d. Giardia is caused by drinking contamwater on outings. Consider all streams c5e. Much of the work takes place in full ssnorkeling, etc.) so prevent sunburn, use sunscreen and lip balm; and wear a hat, 

6. General work in or near streams 6a. Working near 

unstable, steep, deep channels, swift flows. 6b. Giardia 6c. Sunburn 6d. Undergrowth 

6a. Reconnoiter to familiarize yourself witto project. Know the current and projecteweather forecasts and stream gauge infowork area prior to fieldwork. Review mapdetermine access points, reference pointpoints. Develop evacuation plans for rem

sure you sign out (including location) on tleaving for the field. 6b. Refer to 5d. 6c. Refer to 5e. 6d. Refer to 3b. 
SOP 11.22 

7. Aquatic surveys, Culvert Surveys, Spawning/Carcass Counts, Habitat Monitoring, Downstream Migrant Trapping, Frog Surveys, Fish Distribution Study, Habitat Improvement Design and Layout, and Project Monitoring 

7a. Wading/walking in and across streams 7b. Wading/walking in and across aquatic sites 7c. Crossing Debris Jams 7b. Hypothermia 7c. Giardia 7d. Sunburn 

7a. Wear proper waders, lug-soled, chesWhen using waders, wear wading belt or use waders with lug soles or retrofitted wweather, wear neoprene waders or wear garments with standard waders. Use wa

in current. Walk slowly and carefully. Woand within sight of one another. Cross-stravoid deep, swift areas. Consult weather local observer to determine stream and fland slippery rocks. Sign out/in at board ipeople must be CPR and First Aid Certificommunication (e.g., cell phone or radio)7b. Refer to 7a. When wading in aquatic sediments, test fine sediment depths with Do not enter when fine sediment depths 7c. Determine the safest route along the on either side of the banks, or by going uWhen crossing you should be in sight of yanything should occur. Free both hands crossing under and/or on top of the jam, integrity. Walk or crawl on the larger key smaller woody pieces are more prone to way. Usually, the larger pieces are the msound. The same is true for any handholdthe jam. If unsure, do not put all your weislow and maintain your handholds if posswithout bark and if cold, be aware of ice tDO NOT JUMP onto log pieces. 7b. Refer to 5b. 7c. Refer to 5d. 7d. Refer to 5e. 

8. Boats (non-motorized) 9a. Drowning 9a. Wear proper boating protective/floata

repellent clothing) at all times. Use boats knowledgeable in boat use. Work in pairgauge to determine stream safety level. 
SOP 11.23 

9b. Capsizing 9c. Hypothermia 

9b. Watch out for large organic debris (swScout unfamiliar obstacles before paddlinweight in the boat. Be cognizant that a bshifting your weight. 9c. See 5a. 

10. Electrofishing 10a. Electrocution 10a. Wear proper chest waders, lug-sole

and polarized glasses. Wear linesmen gDo not put hands in water when shocker Crew should discuss field methods, safetcommunication prior to beginning electrocondition (e.g., pacemaker) or pregnant speople must be CPR and First Aid Certifi

11. Snorkel dive fish counts 11a. Snorkeling, 

swimming, negotiating rapids (Drowning and blunt force injuries) 11b. Hyperthermia 11c. Giardia 11d. Sunburn 

11a. Divers must be able to swim well in work in pairs or teams. Wear wetsuits, inmask and snorkel. Fins or wading boots depth and length of reach. Do not attempcascades; or under logs, ledges, or bould

around these hazards. On extended mulfirst aid, warm clothing, camping gear, raKnow and respond quickly to hypothermipeople must be CPR and First Aid Certifiphotos to determine access points, refereevacuation points. All crewmembers shopoints. When diving, crews should be coto giardia. Do not dive in areas known to 11b. Refer to 5b. 11c. Refer to 5d. 11d. Refer to 5e. 
SOP 11.24 

12. Downstream Migrant Trapping 12a. Trap 

construction and maintenance 12b. Hyperthermia 12c. Giardia 12d. Sunburn 

12a. Consult weather forecast each mordetermine stream and flow conditions. Adebris or other objects floating downstreamaintaining traps. Wear Neoprene or leaconstruction and maintenance. When reaware of both the weight of the object an

downstream. Survey the area downstrepotential dangers or pullouts to be aware member is swept downstream. Have safhand. 12b. Refer to 5b. 12c. Refer to 5d. 12d. Refer to 5e. 

 JHA Instructions 

The JHA shall identify the location of the work project or activity, the name of 

Emergency Evacuation In

Work supervisors and crewmembers are responsibfield emergency evacuation procedures (EEP) and 
SOP 11.25 

employee(s) involved in the process, the date(s) of acknowledgment, and the name of the appropriate supervisor approving the JHA. The supervisor acknowledges that employees have read and understand the contents, have received the required training, and are qualified to perform the work project or activity.  Identify all tasks and procedures associated with the work project or activity that have potential to cause injury or illness to personnel and damage to property or material. Include emergency evacuation procedures (EEP). Identify all known or suspect hazards associated with each respective 

task/procedure listed. For example:

a. Research past accidents/incidents.b. Research the Health and Safety Code, or other appropriate literature.c. Discuss the work project/activity with participants.d. Observe the work project/activity.e. A combination of the above.

person(s) becomes seriously ill or injured at the w Be prepared to provide the following information:

a. Nature of the accident or injury (avoid using vi

b. Type of assistance needed, if any (ground, air, c. Location of accident or injury, best access rou

name/number),

 Identifiable ground/air landmarks. d. Radio frequencies.e. Contact person. f. Local hazards to ground vehicles or aviation.

g. Weather conditions (wind speed & direction, vh. Topography. i. Number of individuals to be transported.

j. Estimated weight of individuals for air/water ev

The items listed above serve only as guidelines foevacuation procedures. 

JHA and Emergency Evacuation Proce

 Identify appropriate actions to reduce or eliminate the hazards identified. 

Abatement measures listed below are in the order of the preferred abatement method:

We, the undersigned work leader and crewmembedevelopment of this JHA (as applicable) and accomprocedures. We have thoroughly discussed and uthese documents:

a. Engineering Controls (the most desirable method of abatement). 

 For example, ergonomically designed tools, equipment, and SIGNATURE DATE  Furniture.

b. Substitution. For example, switching to high flash point, non-toxic solvents.c. Administrative Controls. For example, limiting exposure by reducing the work schedule; establishing appropriate procedures and practices.

d. PPE (least desirable method of abatement). For example, using hearing 

 protection when working with or close to portable machines 

(chain saws, rock drills, and portable water pumps).

e. A combination of the above.

Copy of the JHA as justification for purchase orders when procuring PPE.
 

SOP 11.26 

Appendix SOP 11B. Volunteer Agreement Form
 

SOP 11.27 
 

SOP 11.28 

Volunteer Position Description for

Coho and Steelhead Monitoring Program Volunteer, FY 2010

Supervisor: Michael Reichmuth 

Location: Lagunitas Creek, Olema Creek, Pine Gulch Creek, Easkoot Creek, and 

Redwood Creek in Point Reyes National Seashore and Golden Gate National 

Recreation Area 

Project Duration: ongoing 

Time commitment: 6 hours per workday, from 9:00am to 3:00pm 

Minimum age: 16 

Goals/Outcome of Position: 

1) To assist park staff in determining long-term trends in: a) distribution, 

abundance, and size of spawning coho salmon; b) abundance of smolt coho 

salmon and steelhead trout; and c) species diversity, distribution, abundance and 

size and age composition of juvenile coho salmon and steelhead trout 

2) To assist park staff in identifing gross changes in stream habitat 

Description of Duties

• Collect data relating to stream habitat, water quality, fish and 

invertebrate populations, salmon spawning, riparian area condition and 

stream channel substrate composition 

• Count numbers of spawning salmon, carcasses, and redds (nests) along 

Olema, Pine Gulch, Redwood, and Cheda Creeks during winter surveys 

• Help erect, repair and check smolt trapps near creek mouths of Olema, 

Pine Gulch, and Redwood Creeks during spring surveys 

• Assist project staff during electrofishing operations by netting, measuring 

and recording data on juvenile fish during summer and fall surveys 

• Identify and record gross changes in habitat in Olema, Pine Gulch, 

Redwood, and Easkoot Creeks during summer and fall surveys 

Tools and Equipment to be Used in the Performance of Duties

• Wading staff and wading boots 

• Measuring tape, stadia rod, measuring board, and weighing scale 

• Five gallon buckets, dip nets, block nets, and seines 

• Clip board, data sheets, and writing utensil 

• For downstream migrant trap installation only: shovels, sandbags, scissors, 

wire cutters, fencing tool, hardware cloth, erosion cloth, PVC pipe, fyke net, 

live box, wire, and T-posts 

National Park Service 

U.S. Department of the Interior 

Point Reyes National Seashore

Point Reyes 
 

SOP 11.29 

Training Provided and/or Required

Must receive proper training by crew leader before performing each survey 

technique 

Knowledge/Skills/Experience Desired

• Must be able to follow verbal and written instructions 

Special Requirements of the Position

• Must be able to walk long distances over rough, uneven terrain in streams 

subject to high flows while carrying 20 to 40 lbs of equipment 

• May be exposed to ticks, poison oak, rain and extreme temperatures 

Benefits to the Volunteer

• Volunteer will gain knowledge on stream and fish sampling techniques. 

• Volunteer will enjoy the satisfaction of helping to preserve salmon for 

current and future generations. 

Please note: Your email address will be passed on to Melanie Gunn, the park-wide Volunteer Program 

Manager, to keep you updated on volunteer news. If you would prefer not to have your email address on a 

park-wide volunteer list, please notify your supervisor, Mike Reichmuth. 
 

SOP 11.30 

Appendix SOP 11C. Checklists for Standard Safety Equipment

Checklists are helpful for ensuring that personnel have the appropriate safety equipment 

available during field trips. Each study team needs to consider the specific needs for their work 

and should customize these checklists as necessary (Cooprider & Carson, 2006). 

√ Climatic and UV protection, etc. 

 Boots, rubber soled or felt soled depending on substrate. 

 Waders + wading belt 

 Fluids (for example, water and sports drinks) 

 Hat, wide-brimmed 

 Insect repellent (unscented) 

 Rain gear 

 Sunglasses 

 Sunscreen 

 Antibacterial soap or hand lotion 

 Temperature-modifying clothing 

Items for Vehicles 

√ Flotation and reflective protection 

 Personal Flotation Devices 

 Safety harness 

√ Communications and instructions 

 Field folder (including maps, emergency phone numbers for medical facilities, office 

contacts, family contacts) 

 Cellular phone/communication equipment (check that the service is operational for the 

area to be traveled) 

√ First aid and protective equipment 

 Complete change of clothes (stored in dry area) 

 Fire extinguisher (safely secured) 

 First aid kit and manual (check for missing or old, expired items and replace if necessary)

 Orange reflective vest 

√ Miscellaneous equipment 

 Bungee cords (to secure loose articles) 

 District flood plan (most current version) 

 Flagging 

 Flares 

 Flashlight (including fresh batteries) 

 Safety cones 

 Tool kit 

 U.S. Geological Survey TWRI Book 9 Chapter A9. 
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 963/102571, 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 

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