Linking Physical Monitoring to Coho and Chinook Salmon 

Populations in the Redwood Creek Watershed, California—

Summary of May 3–4, 2012 Workshop 

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2012-1245

Linking Physical Monitoring to Coho and Chinook Salmon 

Populations in the Redwood Creek Watershed, 

California—Summary of May 3–4, 2012 Workshop

By Mary Ann Madej, Alicia Torregrosa, and Andrea Woodward

Open-File Report 2012–1245

U.S. Department of the Interior

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

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2012 

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Suggested citation:

Madej, M.A., Torregrosa, Alicia, and Woodward, Andrea, 2012, Linking physical monitoring to coho and Chinook 

salmon populations in the Redwood Creek Watershed, California—Summary of May 3–4, 2012 Workshop: U.S. 

Geological Survey Open-File Report 2012-1245, 24 p.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 

endorsement by the U.S. Government. 

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

Introduction.................................................................................................................................................................... 1

Summary of Previous Fisheries Meetings...................................................................................................................... 3

April 15, 2008, Redwood National and State Parks, Orick, California ........................................................................ 3

August 30, 2011, Redwood National and State Parks, Arcata, California .................................................................. 4

Summary of Existing Data and Data Gaps .................................................................................................................... 4

Synthesis Approach Developed for Olema Creek (SFAN)............................................................................................. 7

Possible Data Syntheses and Modeling Efforts for RNSP ............................................................................................. 9

(1) Chinook Populations and Estuary Conditions Model ............................................................................................ 9

Background and Model Description........................................................................................................................ 9

Discussion of Model Merit .................................................................................................................................... 12

Potential Value of an Estuary Simulation Model................................................................................................... 13

Limitations to Model Construction and Usefulness............................................................................................... 13

Ideas for Future Work........................................................................................................................................... 14

(2) Comparison of Trends in Coho in Prairie Creek and Redwood Creek................................................................ 14

Background and Model Description...................................................................................................................... 14

Discussion of Model Merit .................................................................................................................................... 15

(3) Basin Characterization Model............................................................................................................................. 17

Field Visit to Monitoring Sites................................................................................................................................... 18

Questions to Answer and Next Steps .......................................................................................................................... 18

Concluding Remarks ................................................................................................................................................... 21

References Cited......................................................................................................................................................... 21

Appendix A. List of Participants ................................................................................................................................... 23

Figures

Figure 1. Schematic showing system-dynamics model built to describe the freshwater life cycle of coho salmon in 

Olema Creek, Point Reyes National Seashore, California............................................................................................. 8

Figure 2. Photographs showing changes in the configuration of the Redwood Creek estuary, California................... 10

Figure 3. Graph showing the timing of estuary closures ............................................................................................. 11

Figure 4. Graph showing estimates of Chinook populations in the Redwood Creek estuary, California, 

1997–2007................................................................................................................................................................... 11

Figure 5. Diagram showing proposed conceptual model showing linkages of estuarine conditions and Chinook 

populations in the Redwood Creek estuary, California. ............................................................................................... 12

Figure 6. Diagram showing conceptual model comparing good coho habitat (Prairie Creek, California) with an 

impaired watershed (Redwood Creek, California). ...................................................................................................... 16

Figure 7. Diagram showing the relationship of three Basin Characterization Model outputs, transpiration, runoff, 

and groundwater recharge........................................................................................................................................... 17

Tables

Table 1. Summary of relevant datasets for Redwood National and State Parks and Redwood Creek, California......... 5

Table 2. Questions identified by workshop participants, May 3–4, 2012. .................................................................... 19
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1

Linking Physical Monitoring to Coho and Chinook Salmon 

Populations in the Redwood Creek Watershed, 

California—Summary of May 3–4, 2012 Workshop 

By Mary Ann Madej, Alicia Torregrosa, and Andrea Woodward

Introduction 

On Thursday, May 3, 2012, a science workshop was held at the Redwood National and State 

Parks (RNSP) office in Arcata, California, with researchers and resource managers working in RNSP to 

share data and expert opinions concerning salmon populations and habitat in the Redwood Creek 

watershed. The focus of the workshop was to discuss how best to synthesize physical and biological 

data related to the freshwater and estuarine phases of salmon life cycles in order to increase the 

understanding of constraints on salmon populations. 

The workshop was hosted by the U.S. Geological Survey (USGS) Status and Trends (S&T) 

Program National Park Monitoring Project (http://www.fort.usgs.gov/brdscience/ParkMonitoring.htm), 

which supports USGS research on priority topics (themes) identified by the National Park Service 

(NPS) Inventory and Monitoring Program (I&M) and S&T. The NPS has organized more than 270 

parks with significant natural resources into 32 Inventory and Monitoring (I&M) Networks 

(http://science.nature.nps.gov/im/networks.cfm) that share funding and core professional staff to monitor 

the status and long-term trends of selected natural resources (http://science.nature.nps.gov/im/monitor). 

All 32 networks have completed vital signs monitoring plans (available at 

http://science.nature.nps.gov/im/monitor/MonitoringPlans.cfm), containing background information on 

the important resources of each park, conceptual models behind the selection of vital signs for 

monitoring the condition of natural resources, and the selection of high priority vital signs for 

monitoring. Vital signs are particular physical, chemical, and biological elements and processes of park 

ecosystems that represent the overall health or condition of the park, known or hypothesized effects of 

stressors, or elements that have important human values (Fancy and others, 2009). Beginning in 2009, 

the I&M program funded projects to analyze and synthesize the biotic and abiotic data generated by 

vital signs monitoring and previous in-park natural resource monitoring and inventories to provide 

useful information, models, and tools to park managers for addressing resource management issues. The 

workshop described in this report is an element of the project funded by USGS NPS-I&M program to 

conduct a synthesis of salmon-related datasets in the Klamath (KLMN) and San Francisco Bay Area 

(SFAN) networks of national parks. The synthesis focused on four park units: Redwood National Park 

(KLMN), Point Reyes National Seashore, Muir Woods National Monument, and Golden Gate National 

Recreation Area (SFAN). 

KLMN and SFAN span the Pacific coast of northern California and inland Oregon. In this 

region, daily, seasonal, and decadal variation in abiotic drivers (for example, precipitation, fog, 

streamflow, and temperatures of air, ocean, and streams) regulate many ecological processes, including 

the distribution of vegetation and wildlife and the frequency of disturbances from fires, floods, 
2

landslides, and biotic pests. However, the exact nature of the linkages between abiotic drivers and the 

direct and indirect effects of these drivers on species of concern and their habitat are not well 

understood. Specifically, abiotic drivers commonly are analyzed as individual elements (that is, 

calculating mean annual precipitation) and the linkages between drivers (such as the influence of 

changes in streamflow on stream temperature) are poorly defined.

In addition to an understanding of the basic linkages between abiotic and biotic ecosystem 

elements, the question of climate change is of increasing concern to land managers in the national parks. 

Land managers need to understand how climate change already has affected natural resources and 

whether other changes may be looming. Without this understanding, it is increasingly difficult to judge 

the effects of management efforts (for example, stream restoration), to evaluate the resilience of existing 

habitats, or to plan future management actions. For example, climate change has been linked to more 

rain and less snow in the Sierras (Cayan and others, 2008), identifying the need for land managers to 

address long-term water storage. In contrast, there has been a scarcity of information depicting the 

effects of natural climatic cycles and anthropogenic climate change, aside from sea-level rise, in coastal 

California and Oregon including KLMN and SFAN (Suffling and Scott, 2002; Hayhoe and others, 

2006). 

Complicating a manager’s ability to respond to climate change effects is the common 

assumption of stationarity—the idea that natural systems fluctuate within an unchanging envelope of 

variability (Milly and others, 2008). The stationarity assumption is being compromised by major shifts 

in background environmental conditions. As a result, the timing, magnitude, and intensity of critical 

abiotic elements in national park units may be changing. Additionally, the common assumption that 

restoration planning can use historical reference conditions as a goal may not be valid if extrinsic drivers 

in national parks show non-stationarity. Consequently, the understanding of trends, variability, and 

interactions among abiotic drivers is needed to inform and prioritize restoration sites or activities and to 

implement scenario planning to foster strategic thinking about future conditions and management 

alternatives.

In central and northern California, several salmon populations have been in decline for years. In 

1997, coho salmon (Oncorhynchus kisutch) were federally listed as threatened in the Southern OregonNorthern California Coast (SONCC) Evolutionary Significant Unit, including Redwood National and 

State Parks, and as endangered in the Central California Coast Evolutionary Significant Unit, including 

SFAN parks. In 2012, the National Oceanic and Atmospheric Administration (NOAA) Fisheries Service

is finalizing a recovery plan for the SONCC coho, and they identify Redwood Creek coho as a core 

population. Redwood Creek drains an area of 738 km2

 and enters an estuary at Orick, California. In the 

uppermost 72 km of Redwood Creek, the river flows through privately owned land primarily under 

timber management, and in the lower 36 km, it flows through RNSP. Prairie Creek, the largest tributary 

of Redwood Creek (100 km2 in area), supports much of the coho population. Millions of dollars are 

being spent in coastal parks on watershed and stream restoration projects. As the NPS plans salmon 

restoration activities in coastal watersheds, it is critical to understand the abiotic factors and interactions 

that affect salmonid populations (MacCall and Wainwright, 2003; Battin and others, 2007). 

Many long-term datasets are being collected by SFAN and KLMN as part of the vital signs 

monitoring program, and additional datasets are available from park units and other agencies. The 

USGS-NPS program funded the authors to conduct a synthesis of salmon-related datasets in Redwood 

National Park, Point Reyes National Seashore, Muir Woods National Monument, and Golden Gate 

National Recreation Area. The overall goals of the synthesis are to better understand (1) the linkages 

among abiotic drivers, (2) the direct and indirect effect of these drivers on salmon and salmon habitat; 

and (3) to make predictions about the effects of potential management actions on salmon habitat and 
3

populations. A step in reaching these goals was to convene a workshop for researchers and resource 

managers working in RNSP to share data and expert opinions concerning salmon populations and 

habitat in the Redwood Creek watershed. 

Workshop objectives were to: 

• Provide natural resource managers of RNSP with initial data compilations, analyses, and 

syntheses in forms relevant for decisions on issues of park concern, such as restoration of 

native habitats; 

• Solicit expert opinions on conceptual models representing various synthesis approaches; 

• Show an example of synthesis of salmonid population and habitat data developed for SFAN; 

• Examine datasets from Prairie Creek, Redwood Creek, and the Redwood Creek estuary to 

develop conceptual models that synthesize the vital signs of Redwood National Park for park 

management use; 

• Solicit input from the group to identify the synthesis approach that best fits the available data 

and the needs of park resource managers and specialists; 

• Identify data gaps and action items to advance analyses; and

• Engage workshop participants in the effort to fill data gaps by contributing existing but 

unincorporated data or by deriving proxies for data gaps. 

Summary of Previous Fisheries Meetings

Following introductions (for a list of participants, see appendix A) and a presentation of 

workshop objectives, we summarized results from previous Redwood Creek fisheries meetings.

April 15, 2008, Redwood National and State Parks, Orick, California

On April 15, 2008, Redwood National and State Parks (RNSP) hosted a workshop to share 

information on fisheries research being conducted in the Redwood Creek watershed. More than 70 

people participated in the workshop. 

Presentations included: 

• Monitoring of the Redwood Creek estuary and mainstem summer steelhead (David

Anderson, RNSP); 

• Growth of Chinook salmon in the Redwood Creek estuary (Brian Wells, NOAA); 

• Research in Prairie Creek (Walter Duffy, USGS); 

• Redwood Creek juvenile salmonid abundance (Michael Sparkman, California Department of 

Fish and Game [CDFG]); 

• Fish distribution in the Redwood Creek basin (Baker Holden, RNSP); 

• Freshwater mussels in Redwood Creek (Keith Bensen, RNSP); 

• Long-term monitoring of channel morphology, hydrology, and stream temperature (Mary 

Ann Madej, USGS); and

• Summary of the Redwood Creek basin assessment (North Coast Watershed Assessment 

Program; Steve Cannata, CDFG). 

Recommendations from the 2008 workshop were to: 

1. Facilitate communication among researchers, fishery biologists, and interested people; 

2. Develop a comprehensive list of relevant publications and datasets for Redwood Creek; 

3. Ensure researchers send copies of field notes, data, and reports to Redwood National Park 

Curator, James O’Barr; and 

4. Create annual synthesis reports of fisheries research in Redwood Creek. 
4

A complete copy of the meeting notes from 2008 is available from RNSP upon request. 

Since the April 15, 2008 workshop, several new observations and events have occurred: 

• Four additional years of biological and streamflow monitoring data are available to add to 

trend analysis; 

• Invasive New Zealand mudsnails have been found in the Redwood Creek estuary; 

• A conference was held on environmental degradation owing to marijuana plantations, and 

the use of rodenticides on marijuana plots has been implicated in poisoning carnivores 

(Gabriel and others, 2012), leading to water-quality concerns; and

• Water-quality and algal-growth observations in upper Redwood Creek suggest possible 

nitrogen and phosphorus inputs from private lands. 

August 30, 2011, Redwood National and State Parks, Arcata, California

On August 30, 2011, USGS scientists met with RNSP resource managers to discuss datasets 

available from the vital signs monitoring program and from in-park and other sources. We summarized 

the types of datasets used to assess time series trends, bivariate relationships, and multivariate 

relationships, and we discussed preliminary results from these analyses. We discussed park management 

concerns, especially regarding the restoration of Chinook and coho salmon populations. The 

management questions raised were: (1) Given current watershed characteristics, what could we be doing 

to improve fish survival?, (2) What is the rate of natural restoration?, (3) How do the freshwater and 

estuarine systems of the Redwood Creek watershed function?, and (4) How can we more effectively 

combine physical and biological monitoring? High-priority topics identified at the August 30, 2011 

meeting included fish distribution in the Redwood Creek basin and Redwood Creek estuary dynamics. 

As a follow-up to the meeting, David Anderson provided data to USGS staff on fish numbers, 

distribution, and size, and on the dates of closing and opening of the Redwood Creek estuary berm. The 

USGS posted data summaries and temporal trends of abiotic and outmigrant smolt data on a website: 

http://www.werc.usgs.gov/project.aspx?projectID=229. 

Summary of Existing Data and Data Gaps 

In the introductory phase of the workshop, participants were encouraged to identify any data 

they possessed that were not previously compiled and that would be relevant to the workshop goals. As 

the workshop progressed, additional potential datasets were revealed, as were data and knowledge gaps. 

Table 1 summarizes datasets available from the National Park Service and other agencies, followed by a 

summary list of data needs and data challenges.
5

Table 1. Summary of relevant datasets for Redwood National and State Parks and Redwood Creek, California.

[RAWS, Remote Automatic Weather Stations; RNSP, Redwood National and State Parks; PRISM, Parameter-elevation

Regressions on Independent Slopes Model, Oregon State University; CDFG, California Department of Fish and Game; HSU, 

Humboldt State University; USFWS, U.S. Fish and Wildlife Service; NOAA, National Oceanic and Atmospheric 

Administration]

Variable Location Time scale Organization/Agency

Air temperature Westside Access Road Daily (2004-2012) RAWS (Mesowest)

Schoolhouse Peak Daily (2001-2012) RAWS (Mesowest)

Orick/Prairie Creek State 

Park

Daily (1938-2012) National Weather Service, 

RNSP 

Crescent City, CA Daily (1897-2012, intermittent) National Weather Service

Park average Monthly (extrapolated from 1895 

to 2010)

PRISM (Oregon State 

University)

Precipitation Westside Access Road Daily (2004-2012) RAWS (Mesowest)

Schoolhouse Peak Daily (2001-2012) RAWS (Mesowest)

Crescent City, CA Daily (1897-2012, intermittent) National Weather Service

Orick/Prairie Creek State 

Park

Daily (1938-2012) National Weather Service, 

RNSP 

Little Lost Man Creek Daily RNSP

Park average Monthly (extrapolated from 1895 

to 2010)

PRISM (Oregon State 

University)

Streamflow Redwood Creek at Orick Daily (1954-2012) USGS

Redwood Creek near Blue 

Lake

Daily (1973-2012) USGS

Prairie Creek above Boyes

Creek

Daily (2004-2012) RNSP

Prairie Creek at Wolf Creek 

Bridge

Daily (1991-2012) RNSP

Upper Prairie Creek Daily (1990-2012) RNSP

Little Lost Man Creek Daily (1975-2012) RNSP, USGS

Turbidity Prairie Creek stations Daily (2003-2012) RNSP

Water temperature, 

in-situ

Redwood Creek –several 

sites

Hourly during summers, 1997-

2012

RNSP, CDFG

Prairie Creek stations Hourly during summers RNSP

Little Lost Man Creek Hourly during summers RNSP

Redwood Creek estuary Hourly during summers RNSP

Water temperature, 

thermal infrared

Redwood Creek-entire length Single day, July 29, 2003 RNSP

Channel 

morphology

Redwood Creek and 

tributaries –many sites

1975-present, intermittent RNSP, USGS

Outmigrant smolts Redwood Creek –

River mile 4 

Weekly, Spring and summer,

2004-2012

CDFG

Redwood Creek –

River mile 33

Weekly, Spring and summer, 

2000-2012

CDFG

Prairie Creek Weekly, 1999-2008, 

2011-12

CDFG, USGS, HSU

Adult escapement Prairie Creek 1994-2012 CDFG, USGS, HSU

Water levels Redwood Creek Estuary Daily, 1997-2012, partial RNSP

Bathymetric surveys Redwood Creek Estuary Summers, intermittent RNSP

Dissolved oxygen Redwood Creek Estuary Summers, intermittent RNSP, USFWS

Juvenile population 

and growth 

estimates (Seining)

Redwood Creek Estuary Summers, 1980-2012, intermittent RNSP
6

Adult summer 

steelhead abundance

Redwood Creek Annual, 1981-2012 RNSP

Chinook life history 

(scale analysis) 

Redwood Creek Estuary 1980-1995, intermittent RNSP, NOAA-Fisheries

Riparian vegetation 

mapping

Redwood Creek levees Single survey Humboldt County

Little or no data are available for: 

• Genetics analysis to differentiate Chinook stocks (Sparkman, CDFG, has data that still need

to be analyzed), 

• Analysis of circuli on fish scales collected in estuary post-1995 (NOAA) to determine 

growth rates of Chinook and coho salmon, 

• Fish-scale collection and analysis from lower Redwood Creek smolt trap, 

• Freshwater and estuarine food sources (Salamunovich, 1987), 

• Large wood surveys (but assumption is that wood loading has not changed significantly 

during last decade), 

• Vegetation change (but assumption is that vegetative cover has not changed significantly 

during last decade), 

• Effects of commercial and sport ocean fishing on adult returns, 

• Winter rearing habitat inventory in Redwood and Prairie Creeks, 

• Redds in Redwood Creek (turbid conditions preclude frequent observations), 

• DIDSON (dual frequency identification sonar imaging system) fish counter (pilot studies are 

being conducted, initial results are promising, but additional funding is needed to develop a 

robust data collection strategy,) 

• Disease (blackspot infestation, caudal fin rot, subcutaneous nematode bumps), 

• New Zealand mudsnail infestation, 

• Fish use in South Slough of estuary, 

• Uncertainty analysis for population estimates from estuary seining, 

• Predation in Redwood Creek and estuary, 

• Mortality in Redwood Creek and estuary, 

• Basin-wide distribution of salmon egg-eating oligochaetes in redds, 

• The relation of flow magnitude to channel bed scour depth and redd scour, and

• The relation of flow timing to spawning success. 
7

Data challenges include: 

• Different periods of record for various metrics; 

• Short periods of record for several metrics; 

• Different sampling frequencies (hourly to annually); 

• Different sampling locations throughout the drainage basin; 

• Different types of equipment for same metric (for example, tipping bucket versus storage 

rain gages); 

• Data gaps and equipment failure; 

• Changes in technology over sampling period; 

• Lack of consistency or changes in sampling protocol over time; 

• High observer variability with different sampling crews; 

• High spatial variability of habitat units within rivers; 

• Uneven distribution of fish in estuary during seining operations; 

• Some older data are in uncorrected, non-electronic format; and

• Sample design does not enable inference. 

Synthesis Approach Developed for Olema Creek (SFAN) 

Andrea Woodward, USGS, Michael Reichmuth, NPS, and Alicia Torregrosa, USGS, presented 

the results of the coho-freshwater vital signs synthesis for the SFAN I&M network (Olema Creek). The 

synthesis tool, a dynamic systems simulation model, was developed to investigate salmon survival 

during the freshwater life-stages (fig. 1). Salmon survival is an important management concern and can 

only be explained by integrating data from many sources to describe relationships among explanatory 

variables and salmon outcomes. Although data describing relevant relationships may exist from vital 

signs monitoring and other sources, they are difficult to synthesize because they were not collected at 

the same time, in the same place, or over a long time series. Moreover, it may be necessary to

incorporate expert opinion and hypotheses when data are not available. Finally, it is necessary to make 

predictions about the effects of potential management actions. To meet these needs, Woodward and 

Torregrosa used Stella® software to create the system-dynamics model to simulate salmon populations. 

System-dynamics models consist of stocks of state variables (that is, things that can be counted) at a 

point in time, and flows, which describe the change in stocks over time. Flows can be determined by 

external factors (for example, environmental conditions), or feedbacks from other stocks or flows ( for 

example, density dependent effects). The stocks (fish) are assessed at each modeled time step depending 

on how flows (mortality) respond to external and internal conditions during that time step. With this 

modeling approach, multiple disparate data sources could be integrated to describe relationships of 

environmental variables with salmon mortality, including literature-based or hypothetical relationships 

to assess their potential influence. The Stella® software also enabled the creation of a user-friendly 

interface to allow park staff and others to change model parameters and to conduct sensitivity analyses, 

to incorporate future knowledge, or to implement future climate scenarios.
8

Figure 1. Schematic showing system-dynamics model built to describe the freshwater life cycle of coho salmon 

in Olema Creek, Point Reyes National Seashore, California. Fish cohorts progress through stocks of eggs, 

juveniles at the beginning of summer (Juv BoS), juveniles at the end of summer (Juv EoS), and smolts. Mortality 

factors and input values determine the survival of fish between each pair of stocks.

Michael Reichmuth, fisheries biologist, Point Reyes National Seashore, described the success of the 

tool, his experience contributing expert knowledge during the tool development, and its advantages. The 

system-dynamics model helps the NPS understand the relationship between monitoring and restoration 

activities. The model can accept more data as they are generated; incorporate other data in addition to 

the I&M network protocol-derived data, including expert opinion and knowledge; and be transferred to 

other systems. Available data also can be used to create testable predictions based on professional 

judgment. 

Reichmuth described a grant proposal he had submitted to conduct sensitivity analyses to

explore which monitoring data are the most important to collect. The proposal would address an insight 

inferred from the model results suggesting that higher frequency of data collected at specific locations 

for a long time period is important, yet the regional monitoring plan proposed by CDFG for interagency 

adoption suggests a more randomized, spatially distributed approach. 
9

Possible Data Syntheses and Modeling Efforts for RNSP

A major objective of the workshop was to use the participants’ collective knowledge to refine 

the conceptual model of the salmonid system at RNSP and to define the synthesis approach that best fit 

the model, available data, and the needs of resource managers and specialists. The presentation of the 

Olema coho-freshwater systems dynamic model gave participants insight into the data requirements of 

that synthesis approach, enabling a more informed discussion of possible options. 

Three models were proposed by USGS scientists and discussed by workshop participants. 

(1) Chinook Populations and Estuary Conditions Model

Background and Model Description 

The Redwood Creek estuary is a bar-built system where fish, both returning adult spawners and 

smolts going to the ocean, can migrate between the ocean and the estuary only when streamflow and 

nearshore conditions are sufficient to create an opening through a coastal sand berm (fig. 2). In most 

years, the berm is closed from July through October (fig. 3), capturing some portion of the smolt 

Chinook population, which usually migrates downstream to the estuary and ocean from April through 

August (fig. 4). Benefits to fish from extended estuary residence include increased growth prior to 

entering the challenging ocean environment; costs include increased mortality because of declining 

water quality and increased risk of predation. Costs of estuary residence are thought to have increased 

since 1945, when estuary conditions changed drastically owing to agricultural development, and 

especially after construction of flood control levees in 1968 impaired and degraded the physical habitat 

and biological functioning of the Redwood Creek estuary and lower river, and their aquatic resources 

(fig. 2). Estuary volume decreased, circulation patterns shifted, areas of stagnant water increased, and 

connectivity with low velocity refugia diminished (Ricks, 1995). 

USGS scientists provided a conceptual model to summarize the discussion of estuarine 

dynamics among USGS and RNSP staff members at the August 30, 2011 meeting (fig. 5). The model 

illustrates that estuary lagoon existence and size, and, therefore, habitat quality and availability, depend 

on weather, effects of ocean waves and human actions on berm integrity, and sediment movement from 

upstream and by the ocean during winter. This model was presented as the potential basis for a systemdynamics simulation model of the estuary.
10

 A 

B 

Figure 2. Photographs showing changes in the configuration of the Redwood Creek estuary, California. A, 

Redwood Creek Estuary in 1948; B, Redwood Creek estuary in 1988. The area of estuary has decreased and the 

deep scour pool at the north end of the estuary (bottom left side of photograph) no longer exists. 
11

19-Jul 23-Jul 14-Jul 12-Jul

1-Jun

23-Jun

24-Jul

27-Jun

7-Sep

8-Jul

4-Aug

9-Jul

4-Aug 25-Jul

21-Sep

29-Oct 28-Oct 29-Oct

16-Nov 6-Nov 14-Nov 28-Nov

3-Nov 4-Nov

11-Oct

3-Nov 7-Nov

24-Oct

26-Feb

17-Apr

6-Jun

26-Jul

14-Sep

3-Nov

23-Dec

Redwood Creek Estuary Closures 1997-2010

Closed

Open

Figure 3. Graph showing the timing of estuary closures. The Redwood Creek, California, estuary is a 

bar-built system. Fish can only migrate into and out of the estuary when the sand berm is open.

Figure 4. Graph showing estimates of Chinook populations in the Redwood Creek estuary, 

California, 1997–2007 (from David Anderson, Redwood National and State Parks). 
12

*NDVI: Normalized Difference Vegetation Index

Figure 5. Diagram showing proposed conceptual model showing linkages of estuarine conditions and Chinook 

populations in the Redwood Creek estuary, California. 

Discussion of Model Merit

Feedback from workshop participants was that the model generally reflected estuary dynamics 

but that a few elements were missing. Future restoration activities, including planned work in 2013 for 

Strawberry Creek (a tributary of the estuary), could feasibly improve off-channel habitat, provide refuge 

from high-velocity flows, and improve canopy cover for the estuary. If restoration elements were 

included in the model, they could be manipulated to predict effects of restoration. Additionally, the 

model does not express the connection between the amphipod Corophium, which is a high-oil food 

source for fish, and the requirement of berm closure for Corophium growth. Although the population 

dynamics of Corophium are not well known, it seems that the tube-dwelling organism cannot colonize a 

moving sand substrate. The model may be more accurate if a connection between food resources and 

berm integrity were added. The model also should be able to accommodate temperature-related stress, 

not just a threshold. Additionally, the relationship between the diurnal fluctuations in dissolved oxygen 

and algae growing on the bottom of the estuary when the berm closes could be a water quality-factor 

affecting fish.
13

Finally, the model does not include New Zealand mudsnails (Potamopyrgus antipodarum) 

(NZms), which have recently been observed in the lower estuary. The NZms were first found in the U.S. 

in the Snake River drainage in 1987, and have been detected in lagoons and estuaries in the western 

United States since 2008 and in the Redwood Creek estuary beginning in 2010 (Benson, 2011). 

Although the potential impacts largely are unknown, in some places NZms have reordered food webs 

completely and harmed water quality (http://www.dfg.ca.gov/invasives/mudsnail/). Adam Sepulveda 

(USGS) is addressing these issues for Redwood Creek. The potential for NZms spreading throughout 

lower Redwood Creek and the estuary, with their highly mobile channel bed and saltwater intrusion, is 

still unknown, however. 

Potential Value of an Estuary Simulation Model 

The estuary is of critical importance to the salmon populations in Redwood and Prairie Creeks. 

Quiñones and Mulligan (2005), Bond and others (2008), and Hayes and others (2008) show that 

juvenile fish residing longer in the estuarine setting have increased survival in the marine setting, 

resulting in increased potential to return as spawning adults. Moreover, the estuary is important to 

Chinook and steelhead, and with improvement in off-channel habitat, would benefit coho as well. 

Unlike the upper watershed where regulations regarding timber harvest, road decommissioning, and 

other restoration activities have been implemented, there are no immediate plans to improve the estuary, 

which was affected severely 40 years ago. The complex situation involving public and private lands and 

a mix of objectives (flood control, agricultural use, and aquatic habitat improvement) have hampered 

efforts to modify levee configuration. Nevertheless, poor estuary habitat is one of the greatest 

impediments to salmon production, and there are many potential restoration activities that would benefit 

the estuary and that would likely result in a measurable response in salmon populations. A simulation 

model could be a useful tool for prioritizing potential restoration efforts. Finally, a simulation model 

could describe baseline estuarine dynamics for comparison with the potential effects of NZms.

Limitations to Model Construction and Usefulness 

A major limitation to building a system-dynamics model is the lack of basic understanding of 

what is driving the observations. For example, although early-season estuary Chinook population 

numbers vary greatly, by the time the estuary berm breaks in autumn, there are never more than 5,000 

juvenile Chinook remaining and experiencing an extended estuary rearing (fig. 4), suggesting a carrying 

capacity for the estuary. Participants raised several questions regarding this observation: (1) Is the high 

variance earlier in the season driven by sampling or environmental factors?, (2) How much feeding and 

rearing occur between the CDFG smolt trap on lower Redwood Creek and the estuary?, and (3) Could 

we crosswalk between the lower trap and the estuary population numbers? The fundamental problem 

with formulating a system-dynamics model based on stocks of fish at different traps is that presently 

(2012) there is no way to resolve the temporal movement of fish. After fish migrate past the smolt trap, 

we do not know when they enter the estuary or how long they stay in the estuary. One possibility is that 

they are changing their life history to respond to poor estuary conditions by leaving the estuary before 

the berm closes at the mouth of Redwood Creek. It seems that answering some of these basic questions 

is a precursor to building a model. A limitation to the usefulness of the model is the need to understand 

the estuary in the context of the entire system, including the upper watershed, the channelized levee 

reach, the north and south sloughs, and access to tributary habitat. 
14

Ideas for Future Work

The group made several suggestions for future work. One idea was to use the data from periods 

when the berm is closed to compare numbers of fish passing the lower smolt trap with numbers 

estimated in the estuary. This would indicate something about how fish use the lower river and 

residence time in the estuary. However, the limitation of narrowing the focus to a short time period is 

the loss of the population context. For example, if the fish that remain when the berm closes do not 

contribute significantly to the whole population, are they important? Moreover, if only a small 

percentage of the population is experiencing the high mortality rates in the closed lagoon, it does not 

mean that more fish would choose to stay if conditions were more favorable. We also do not have a 

historic perspective on berm behavior. Because of the deep (10–15–meter) scour hole that historically 

was present at the north end of the estuary, Redwood Creek, with a larger tidal prism, may not have had 

a closed summer berm as frequently in the past as it does now. Another suggestion was to use the 

available data, such as the opening and closing of the estuary (fig. 3), and bathymetric surveys and water 

levels throughout the summer, to compute changes in the volume of the estuary. These data then could 

be used to determine what percentage of the population had migrated prior to berm closure and how the 

growth rate of fish in the estuary relates to water temperature, estuary volume, dissolved oxygen, fish 

density, and other factors. 

A key need is to determine whether there is differential smolt-to-adult survival between fish that 

reside for some time and grow in the estuary versus fish that move directly to the ocean from the river at 

a small size. In other words, which life history is more successful—fewer, bigger fish or many small 

ones? Residence time of the fish in the estuary is currently (2012) unknown, but eventually may be a 

good metric to measure the success of estuary restoration actions. We need a dataset containing the full 

expression of fish number and habitat diversity to evaluate the r-to-K ecological selection relationship, 

where “r” is the maximum growth rate of the population and “K” is the carrying capacity of its local 

environmental setting (MacArthur and Wilson, 1967). Fish scale samples have been collected from 

returning adults to begin addressing this question. However, the samples have not been processed 

completely by the NOAA laboratory where they are being analyzed. Several participants have made a 

commitment to investigate the status of the sample analysis.

Finally, planned monitoring with a DIDSON (dual frequency identification sonar imaging 

system) fish counter in lower Redwood Creek and Prairie Creek will help put adult fish migration 

patterns into perspective. From November 2009 to March 2010, a pilot study by Dr. Walter Duffy 

(USGS) and Matthew Metheny (Humboldt State University) using a DIDSON monitored escapement of 

adult salmon and steelhead in Redwood Creek. Initial results are promising, and such monitoring also 

can be used to validate redd counts in the creeks. 

(2) Comparison of Trends in Coho in Prairie Creek and Redwood Creek 

Background and Model Description

Coho salmon spawn and rear in Redwood Creek and its tributary, Prairie Creek. The Redwood 

Creek basin was logged heavily until the national park was established in 1968 and expanded in 1978, 

and logging continues on private lands in the drainage basin. Consequences of logging include high 

water temperatures because of lack of riparian shade, high sediment loads owing to slope erosion, and 

generally harsh summer conditions. In contrast, Prairie Creek has been protected since the 1920s, is 

relatively intact, and hosts most of the coho population. 
15

The contrast between these basins is the basis for a second approach to integrative modeling 

proposed by USGS scientists and illustrated in another conceptual model (fig. 6). The conceptual model 

describes different levels of impairment that are expected to result in contrasting responses to climatic 

drivers. These responses are expected to produce different survival rates of coho eggs to smolts. 

Because we do not have long-term, detailed climatic data throughout the basins, the distribution of 

precipitation from any given storm will have to be inferred from storm characteristics such as 

precipitation at a given station, air temperature, and topography to determine snow line, storm direction, 

and other factors. These relationships must be developed from the existing time series of data. 

Discussion of Model Merit

The most fundamental problem with the model is that the differences between the basins extend 

to many dimensions besides level of impairment. Prairie Creek is a low-gradient system with different 

bedrock types than most of the Redwood Creek basin, whereas other Redwood Creek tributaries 

generally are steep and the Redwood Creek basin is about six times larger than the Prairie Creek basin. 

Habitat complexity generally is much greater in Prairie Creek than Redwood Creek. One approach to 

address these contrasts would be to normalize fish use by habitat abundance (that is, spawning, overwintering, and summer rearing). However, the driver for juvenile-to-smolt survival in Prairie Creek 

probably is overwinter survival rather than summer conditions, as it is in Redwood Creek. 

The potential for developing the model is limited by data availability. Although the proposed 

model has most of the important parameters, data have not been collected for all the parameters (for 

example, large wood as a habitat element). Turbidity has been measured at the “Wolf Creek” gaging 

station in Prairie Creek, but those turbidity levels may be lower than the turbidity levels at the Prairie 

Creek trap site located downstream on private lands. Turbidity probably is more of an issue in Redwood 

Creek, where suspended sediment concentrations are higher, but no turbidity measurements are 

available there. When turbidity is high, the fish may wait out the high flows before migrating. Wright 

(2011) showed a low probability of movement of coho salmon in Prairie Creek on days with higher 

turbidity. 

In other cases, some of the parameters that had to be estimated for the Olema Creek model are 

collected in RNSP, enabling empirically based values. Specifically, for the Prairie Creek–Redwood 

Creek model, the fecundity of the female salmonids is known, redd counts index the adults, summer 

field work estimates juvenile abundance, and the smolt trap catches some juvenile coho. Currently 

(2012), there is a proposal for funding to look at juvenile overwinter survival. 

There also are many important influences on and questions regarding fish populations that were 

not addressed in the Olema model. In Prairie Creek, years with poor sport fishery catches had higher 

numbers of returning Chinook. How do exploitation rates affect wild stocks of salmon? We also need to 

learn more about distribution of coho in the tributaries of Redwood Creek, and we may see more coho 

in Redwood Creek as streams recover. Based on fish scale work, the ratio of 1-year to 2-year steelhead 

smolts in upper Redwood Creek is 14 to 1, and 8 to 1 in lower Redwood Creek, which may reflect the 

harsh conditions in Redwood Creek (in contrast, the nearby Mad River, which also has a long history of 

timber harvest and grazing, has a ratio of about 1 to 5). As conditions in Redwood Creek improve, will 

we see a shift in the smolt age ratios? A new (2013) study that is starting will look at the distribution of 

juveniles in the drainage basin (basin-wide randomized approach). In terms of model structure, the 

model needs to account for a continuum of effects, such as stress levels, in addition to specific 

thresholds. 
16

Finally, the relevance of the model to management decisions was questioned. It was observed that, of all

the parameters in the model, the only one that is amenable to management activities is habitat. But even 

if habitat were to improve (for example, by adding wood to the upper watershed), we would not know 

whether fish merely were redistributed or whether production actually increased. This concern is 

supported by the observation that, to date (2012), the road restoration work in the Redwood Creek basin 

has not resulted in higher fish population numbers. Additionally, some factors (for example, stream 

temperature mortality threshold), are not amenable to management action. On the other hand, a 

Redwood Creek watershed model might be useful, especially in the context of management activities, 

current and planned, such as addressing Sudden Oak Death and the effect of lost shading on increasing 

water temperature.

Figure 6. Diagram showing conceptual model comparing good coho habitat (Prairie Creek, California) with an 

impaired watershed (Redwood Creek, California). 
17

(3) Basin Characterization Model 

Water-balance modeling can be used to determine the flow of water into and out of a watershed. 

A Basin Characterization Model (BCM) calculates water-balance components by using spatially 

distributed climatic data (precipitation and air temperature) and information on soil, geology, and 

topography (fig. 7). Flint and Flint (2012) developed a BCM to reconstruct historical conditions and to 

simulate future conditions for climatic scenarios in the San Francisco Bay area (Russian River Valley 

and Santa Cruz Mountains). The model considers potential evapotranspiration, snow accumulation, and 

snowmelt across a watershed, and combines that information with soil and bedrock properties. The 

potential water available for recharge and runoff is calculated using monthly time steps using a grid 

scale of 866 ft (270 m). The data necessary to run the model for the Redwood Creek basin are available, 

so the model could be applied to this area in the future if park staff thinks it might be useful.

Figure 7. Diagram showing the relationship of three Basin Characterization Model outputs, transpiration, runoff, 

and groundwater recharge. Of the many inputs required to run the model—such as precipitation, solar radiation, air 

temperature, potential evapotranspiration—only transpiration is shown in the diagram. [Diagram from Surface 

Water Cycle from Wikimedia Commons, accessed April 10, 2012, at

http://en.wikipedia.org/wiki/File:Surface_water_cycle.svg].
18

Field Visit to Monitoring Sites

The May 3, 2012, science workshop concluded on May 4, 2012, with field visits to (1) examine 

estuary configuration and monitoring sites, and (2) observe outmigrant smolt trapping in lower 

Redwood Creek upstream of Prairie Creek. Discussion continued on the topics raised the previous day , 

with an emphasis on filling in the details of the analyses identified through the group process. 

Questions to Answer and Next Steps

The discussion of models and options for synthesizing data raised many science questions, some 

that could be answered with existing data. There were many opinions about the relative advantage and 

disadvantage of empirical analytic approaches versus simulation modeling approaches. One advantage 

of empirical analytic approaches is the defensibility of an analysis that can define unambiguously the 

confidence level of a reported statistical relationship. In contrast, an advantage of the system dynamics 

simulation modeling approach includes the capacity to include expert opinion and hypothesized 

relationships to gain insight into the system. Many science questions discussed by the group were 

fundamental questions about the functioning of the system best investigated with traditional statistical 

analysis.

Table 2 groups the questions by ecosystem component and lists the datasets needed to address 

the question. The relative importance value assigned to each question in table 2 reflects the authors’ 

sense of the group consensus and is not a result of a structured priority process. Previous experience 

with vital signs data compilation highlighted for the group the value of knowing how much work still 

might be required for data to be ready to be used in a statistical analysis; hence, the discussion also 

focused on data readiness. The following codes describe levels of data completeness for questions in 

table 2.

1 – Data have been collected, quality assured, and are available digitally.

2 – Data are available, but need additional level of review, calibration, or manipulation. 

3 – Data are not known to be available. 
19

Table 2. Questions identified by workshop participants, May 3–4, 2012. 

Ecosystem 

Component

Resource Question Relative 

Importance

Datasets

Estuary Is Chinook abundance correlated with 

water volume?

1 Summer fish seine data (1)

Water levels 1997-2011 (2)

Bathymetric surveys 1998-2011 (1)

Pre-1997 calibrated water levels (2) 

Estuary Is Chinook growth correlated with water 

volume?

1 Fork length-weight data 2001-2011 (1)

Water levels 1997-2011 (2)

Pre-1997 calibrated water levels (2)

Bathymetric surveys 1998-2011 (1)

Scale analysis 1980-1995 (1)

Updated scale analysis, including adult scales (NOAA) (3)

Estuary Is dissolved oxygen correlated with water 

volume?

2 Dissolved oxygen data (2)

Water levels 1997-2011 (1)

Bathymetric surveys 1998-2011 (1)

Estuary Is water temperature correlated with 

water volume and algal growth in the 

estuary? 

2 Water temperature data (1)

Water levels 1997-2011 (2) 

Bathymetric surveys 1998-2011 (1)

Distribution and abundance of algae (3)

Estuary Is the distribution of New Zealand mud 

snails expanding and affecting the food 

web? 

1 Visual inventories of snail aggregations in lower estuary 2010-2011

(1)

Quantitative surveys in full estuary (3)

Effects on food web (3)

Freshwaterestuary transitionHow do ratios of smolts at RM4 to 

estuary seine catches relate to the closing 

of the berm?

1 Estuary berm closure dates 1997-2011 (1)

CDFG smolt data-Lower Redwood Creek 2004-2012 (1)

Summer estuary seine data (1) 

Freshwaterestuary transitionDoes smolt-to-adult survival differ 

between riverine and estuarine-rearing

fish?

1 CDFG smolt data-Lower Redwood Creek 2004-2012 (1)

Summer estuary seine data (1)

Updated scale analysis, ,including adult scales (NOAA) (3)

Freshwater How do Chinook and coho populations 

and migration patterns relate to flow 

regimes?

2 Daily stream discharge 1953-2012 (1)

CDFG smolt data-Lower Redwood Creek 2004-2012 (1)

Updated fry/smolt ratio data for Redwood Creek (2)

Freshwater How do Prairie Creek populations relate 

to those in Redwood Creek

2 Escapement- Prairie Creek 1999-2011 (1)

Smolt data-Prairie Creek, 1999-2008, 2011 (2)

Smolt data-lower Redwood Creek 2004-2012 (1) 

Freshwater How does turbidity in Prairie Creek affect 

coho growth?

3 Daily turbidity in Prairie Creek (1) 

Fork lengths and weights of smolts 2009-2011 (1) 
20

Freshwater Does fish condition in Redwood Creek 

relate to flow or temperature?

2 Fork lengths and weights of smolts, (1)

Daily flow and water temperature, 2004-2011 (1) 

Freshwater What is the effect of water temperature on 

fish disease?

2 Daily water temperature (1)

Disease recorded in field notes, but not in database (2)

Freshwater What is the effect of Sudden Oak Death 

on water temperature?

3 Coarse scale vegetation surveys (2)

Hourly water temperature (1) 

Detailed mapping of dead trees in riparian zone of Redwood Creek 

(3)

All How will climate change affect flow and 

temperature regimes?

1 Daily air temperature, precipitation, stream flow, water temperature

(1)

More accurate summer low flow measurements, winter water 

temperatures (2) 

All What biotic and abiotic variables are

valuable to continue monitoring?

1 All datasets 
21

Concluding Remarks

This meeting was one step in the process of synthesizing vital signs data and, as a byproduct, 

may help coordinate salmonid habitat research among various disciplines and agencies. Draft copies of 

the meeting notes were sent to all workshop participants, requesting comments and feedback. Many 

actions identified during the meeting will require follow up, such as completing the datasets listed in 

table 2.

The workshop reinforced the opinion of the authors that a collaborative process can help guide 

analyses of complex systems, such as physical and biological interactions of the coastal ecosystems of 

northern California. Although developing simulation models to relate science to resource management 

decisions eventually may be desirable, this workshop's collaborative process determined that developing 

fundamental relationships among ecosystem components in RNSP is needed first. Once the system is 

better understood, data synthesis can progress to include multiple connections among the interacting 

system elements, possibly to the stage of a simulation model. Meanwhile, this workshop provided a 

starting point for future research and analysis, which can lead to a better understanding of how the 

freshwater and estuarine life phases of salmon are influenced by interacting abiotic factors in the 

watershed. 

References Cited

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6,725. 

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poisoning of a rare forest carnivore: PLoS ONE, v. 7, no. 7, e40163, 

doi:10.1371/journal.pone.0040163. 

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MacFarland, R.B., 2008, Steelhead growth in a small central California watershed—Upstream and 

estuarine rearing patterns: Transactions of the American Fisheries Society, v. 137, p. 114–128, doi: 

10.1577/T07-043.1. 
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Hayhoe, H., Frumhoff, P., Schneider, S., Luers, A. and Field, C., 2006, Regional assessment of climate 

impacts on California under alternative emissions pathways—key findings and implications for 

stabilization in Schellnhuber, H.-J., Cramer, W., Nakiccnovic, N., Wigley, T., and Yohe, G.W. (eds.), 

Avoiding dangerous climate change: Cambridge, UK: Cambridge University Press, p. 227–234. 

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N.J., Princeton University Press, ISBN 0-691-08836-5M. 

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doi:10.1577/T04-092.1. 

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23

Appendix A. List of Participants

Last Name First Name Affiliation

Anderson Cynthia National Oceanic and Atmospheric Administration Fisheries Service

Anderson David Redwood National and State Parks

Bensen Keith Redwood National and State Parks

Bowman Scott Consultant

Bueno Monica Redwood National and State Parks

Harvey Bret U. S. Forest Service Redwood Sciences Laboratory

Lavery Koa Redwood National and State Parks

Madej Mary Ann U.S. Geological Survey 

O'Barr James Redwood National and State Parks

Ozaki Vicki Redwood National and State Parks

Parkinson Aida Redwood National and State Parks

Parkinson Doug Consultant

Reichmuth Michael Point Reyes National Seashore

Roemer David Redwood National and State Parks

Seney Joe Redwood National and State Parks

Short Darci Redwood National and State Parks

Sparkman Michael California Department of Fish and Game

Torregrosa Alicia U.S. Geological Survey 

Vaughan Patrick California State Parks

Wolff Leslie National Oceanic and Atmospheric Administration Fisheries Service

Woodward Andrea U.S. Geological Survey
24

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Madej and others— Linking Physical Monitoring to Coho and Chinook Salmon Populations, Redwood Creek Watershed, Calif.—Open-File Report 2012-1245