Marine Sanctuaries Conservation Series ONMS-10-01 

U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Ocean Service

Office of Ocean and Coastal Resource Management

Office of National Marine Sanctuaries March 2010

The Application Of Observing System Data In 

California Current Ecosystem Assessments
About the Marine Sanctuaries Conservation Series

The National Oceanic and Atmospheric Administration’s National Ocean Service (NOS) administers the 

Office of National Marine Sanctuaries (ONMS). Its mission is to identify, designate, protect and manage 

the ecological, recreational, research, educational, historical, and aesthetic resources and qualities of nationally 

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of NOAA’s resource protection mandate.
The Application Of Observing System Data In California 

Current Ecosystem Assessments

Jennifer Brown, Robert Pavia (retired), Chad King, and Andrew DeVogelaere

NOAA Office of National Marine Sanctuaries, Monterey Bay National Marine Sanctuary

and Sanctuary Integrated Monitoring Network

Silver Spring, Maryland

March 2010

U.S. Department of Commerce

Gary Locke, Secretary

National Oceanic and Atmospheric Administration

Dr. Jane Lubchenco

Under Secretary of Commerce for Oceans and Atmosphere

National Ocean Service

David M. Kennedy, Acting Assistant Administrator

Office of National Marine Sanctuaries

Daniel J. Basta, Director
DISCLAIMER

Report content does not necessarily reflect the views and policies of the Office of 

National Marine Sanctuaries or the National Oceanic and Atmospheric Administration, 

nor does the mention of trade names or commercial products constitute endorsement or 

recommendation for use.

REPORT AVAILABILITY

Electronic copies of this report may be downloaded from the Office of National Marine 

Sanctuaries web site at www.sanctuaries.nos.noaa.gov. Hard copies may be available 

from the following address:

National Oceanic and Atmospheric Administration

Office of National Marine Sanctuaries

SSMC4, N/ORM62

1305 East-West Highway

Silver Spring, MD 20910

COVER 

Divers prepare to descend on a mooring to replace data loggers. This mooring is part of 

the NMSP West Coast Observatory project and collects data on ocean temperature and 

currents. For more information see:

http://www.mbnms-simon.org/sections/obs/nmsp_wco.php. Credit Josh Pederson, 

NOAA/MBNMS/SIMoN

SUGGESTED CITATION

Brown, J.A., R. Pavia, C. King, A. DeVogelaere. 2010. The Application Of Observing 

System Data In California Current Ecosystem Assessments. Marine Sanctuaries 

Conservation Series NMSP-ONMS-10-01. U.S. Department of Commerce, National 

Oceanic and Atmospheric Administration, Office of National Marine Sanctuaries, Silver 

Spring, MD. 112 pp. 

CONTACT

Jennifer Brown: jennifer.brown@noaa.gov

Robert Pavia: bob.pavia@gmail.com

Chad King: chad.king@noaa.gov

Andrew DeVogelaere: andrew.devogelaere@noaa.gov

ACKNOWLEDGEMENT

This work was conducted in partnership with the Pacific Coast Ocean Observing System 

with support from NOAA’s Integrated Ocean Observing System Program. The authors 

would like to thank Liam Antrim, Kathy Broughton, Lisa Etherington, Steve Katz, 

Danielle Lipski, and Jan Roletto for their review and comments on this report. Mitchell 

Tartt both reviewed this report and co-developed Figure 1.
i

ABSTRACT

Ecosystem-based management requires comprehensive assessments of the ecosystem to 

establish a feedback loop on the conditions in the systems under management. These 

assessments require observing data that reflect the pressures and ecosystem indicators of 

concern to managers. This report examines ongoing ecosystem assessment and modeling

efforts in the California Current Ecosystem (hereafter referred to as ‘ecosystem 

assessments’) in the context of NOAA’s model for Integrated Ecosystem Assessment 

(IEA) development. The goals of this effort are to 1) examine the ecosystem assessments 

in the context of a DPSIR (Driver, Pressure, State, Impact, Response) approach; and 2) 

identify ocean observing datasets in use by current assessments to identify gaps in the 

data and services available to support future assessments.

The purpose, scale, and drivers for 10 selected assessments were compared with the 

ocean observing data sources used in their development. These 10 assessments vary in 

the spatial scope of the assessment from the California Current Ecosystem scale to the 

local scale. A more detailed comparison of the California Current IEA, Module 1 and 

Northern California Current Ecosystem, Atlantis model was then undertaken to highlight 

their use of drivers, pressures, and indicators.

Five Sanctuary condition reports, assessments for individual sanctuaries, were examined 

in depth to understand the relationship between drivers, pressures and responses in the 

context of management requirements. The sources of data used to evaluate indicators of 

those responses were then identified. This provided a link between a pressure-stateresponse model of IEA development and ocean observing data sets. The final step was to 

examine observing datasets being used by one or more assessment efforts in the 

California Current Ecosystem. This work provides an assessment of how existing ocean 

observing efforts are informing assessments efforts in the California Current Ecosystem 

and where gaps exist.

We identified four datasets available through the Pacific Coast Ocean Observing System

that are being used by both large and small-scale assessment efforts. However, the 

overwhelming majority of the datasets identified in this analysis were used by either 

small or large-spatial scale assessment efforts but not both. A very large gap exists for 

data describing the level of human activities that impact the marine environment. In 

addition, the authors identify a need for more data collected at the sub-regional and local 

level. Currently, in no single sub-region are data available for all the physical, chemical, 

and especially biological indicators required for comprehensive analyses.

This review recognized four key barriers to fully exploiting ocean-observing data for 

ecosystem-based management: data discovery, data access, integrating disparate data, and 

closing the gap between data needs and data collection. One of the key challenges to IEA 

application in ecosystem-based management is the lack of available data. Even if there 
ii

were no barriers to discovering, accessing, and integrating existing data, effectively 

developing management alternatives and monitoring effectiveness requires investments 

in data collection and analysis. In many cases, the necessary data are not available, 

significantly hampering our ability for taking ecosystem-relevant management actions

and increasing uncertainty in outcomes. Resource managers must make the best decisions 

possible with available information. This requirement to move forward, even with data 

gaps highlights the importance of maximizing the use of what we do have through data 

management, improved accessibility, improved integration and compatibility, and more 

comprehensive analysis.

KEY WORDS

Pacific Coast Ocean Observing System, PaCOOS, Integrated Ocean Observing System, 

IOOS, Integrated Ecosystem Assessment, IEA, Ecosystem Based Management, EBM, 

National Marine Sanctuaries, Channel Islands, Monterey Bay, Gulf of The Farallones, 

Cordell Bank, Olympic Coast, DPSIR, California Current, Atlantis Model, Condition 

Report
iii

TABLE OF CONTENTS

Topic Page

Abstract and Key Words...................................................................................................... i

Table of Contents...............................................................................................................iii

List of Figures and Tables.................................................................................................. iv

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

Survey of Ecosystem Assessments in the California Current............................................. 5

Identifying Applicable Observing Data for Drivers and Pressures in the CCE.................. 8

Obstacles to Management Application of Observing Data............................................... 11

Conclusions....................................................................................................................... 15

References......................................................................................................................... 67

Appendix 1 – West Coast Sanctuary Data Inventory ....................................................... 70

Appendix 2 – Background Information on IEA Efforts in CCE .................................... 104

Appendix 3 – Acronyms and Abbreviations................................................................... 107
iv

LIST OF FIGURES AND TABLES

Figure/Table Number and Title Page

Figure 1 Correspondence between Sanctuary management process and Integrated 

Ecosystem Assessments........................................................................ 2

Figure 2 Selected Ecosystem Assessments in the California Current Ecosystem . 6

Figure 3 Integrated Ocean Observing System data used by small-scale or 

large-scale ecosystem assessments considering availability through the 

Pacific Coast Ocean Observing System data portal.............................. 12

Table 1 Resource characterization needs of the five west coast national marine 

sanctuaries as described in each site’s management plan..................... 18

Table 2 Management drivers of the five west coast national marine sanctuaries 

as described in each site’s management plan........................................ 22

Table 3 Description of ecosystem assessments in the California Current 

Ecosystem ............................................................................................. 26

Table 4 Comparing two ecosystem assessments for the California Current 

Ecosystem ............................................................................................. 27

Table 5 Human activities that are potential drivers and pressures in the 

California Current Ecosystem............................................................... 29

Table 6 Drivers and pressures identified in the condition reports for five 

National Marine Sanctuaries................................................................. 31

Table 7 Datasets used to assess the current conditions as identified in the 

condition report for the Olympic Coast National Marine Sanctuary.... 34

Table 8 Datasets used to assess the current conditions as identified in the

condition report for the Cordell Bank Sanctuary.................................. 38

Table 9 Datasets used to assess the current conditions as identified in the 

condition report for the Gulf of the Farallones Sanctuary .................... 41

Table 10 Datasets used to assess the current conditions as identified in the 

condition report for the Monterey Bay Sanctuary ................................ 45

Table 11 Datasets used to assess the current conditions as identified in the 

condition report for the Channel Islands Sanctuary.............................. 54

Table 12 Observing datasets that are being used by one or more of the on-going 

ecosystem assessment efforts in the California Current Ecosystem..... 58
1

INTRODUCTION

Incorporating ecosystem principles into resource management is a strategic goal of 

NOAA (NOAA 2009). This goal requires an ecosystem-based management (EBM) 

approach that moves beyond individual species or single-issue management to consider a 

range of relevant ecological, environmental, and human factors (Murawski and Matlock 

2006). Integrated Ecosystem Assessments (IEAs) are an EBM approach that helps to 

overcome barriers to implementation. NOAA defines an IEA as “a synthesis and 

quantitative analysis of information on relevant physical, chemical, ecological and human 

processes in relation to specified ecosystem management objectives (Levin et al. 2009).

IEAs can help improve our understanding of interactions among climate, water, habitat, 

living resources and human activities. Collaborative ecosystem-based management 

requires mobilizing contemporary and historical data from NOAA and other 

organizations to create a comprehensive picture of the ocean ecosystems and how they 

are changing. Creating this picture requires alliances among researchers and the 

professionals entrusted with managing marine resources and a deep understanding of the 

linkages between management needs and ecosystem observations. 

Achieving NOAA’s goal of moving to ecosystem-based management entails access to 

high quality data to develop IEAs that support resource manager’s requirements for 

adaptive management. Levin et al. (2009) have outlined a framework for the development 

of IEAs that consists of five key steps (Figure 1). This framework begins with a scoping 

process to identify key threats, management objectives and constraints, and appropriate 

indicators1 of ecosystem change. Risk assessments of individual indicators are combined 

into a determination of overall ecosystem status. The potential of different management 

strategies to alter ecosystem status is evaluated, and then management actions are 

implemented and their effectiveness monitored. The cycle is repeated in an adaptive 

manner. An assessment of stressors on the ecosystem identifies the “drivers” and 

“pressures”. Key relevant datasets are selected to assess the “state” of key indicators of 

ecosystem baseline conditions. An evaluation of the ecological and economic “impacts” 

of alternative management options help to identify the management “response” (Levin et 

al. 2008). The approaches Levin et al. describe provide a framework for understanding 

how to develop links that extend from observing data through adaptive management.

For IEAs to be useful they must relevant to the management priorities of organizations 

with ocean stewardship responsibilities (deReynier et al. 2009). Because management 

actions can only be implemented by those agencies with management authority, agency 

management processes must be synchronized with the IEA process. National marine 

sanctuaries bring together the scientific community, stakeholders, and the public to 

clearly define goals, protocols, and decision points for applying marine ecosystem-based 

management principles in order to manage ocean resources. Each sanctuary in the 

National Marine Sanctuary System has a management plan. In general, management 

 1 Following the definition in EPA (2000), “An ecological indicator is defined here as a measure, an index 

of measures, or a model that characterizes an ecosystem or one of its critical components. An indicator may 

reflect biological, chemical or physical attributes of ecological condition.”
2

plans are used to inform decision making and project planning, while articulating goals, 

objectives, and priorities. Management plans are organized into action plans that link to 

management issues. Actions plans have common themes among sanctuaries based on the 

general goals of the Office of National Marine Sanctuaries (ONMS). One of these goals

is to better characterize sanctuary resources, such as water quality, habitat, and living 

marine resources. Characterizing the condition of natural resources and ecosystem 

processes is the principal means by which the ONMS improves its understanding of the 

marine environment. A second major goal of the ONMS is to identify management 

actions needed to protect and conserve sanctuary resources. Examples of management 

actions include detecting the impacts of human activities or implementing new marine 

zones to protect vulnerable resources.

Figure 1 – Interaction between sanctuary management cycle and integrated ecosystem assessment process. 

The lower blue arrow shows the process of integrated ecosystem assessment (adapted from Levin et al. 

2009). The ovals illustrate how a management unit’s actions, in this case a sanctuary, both contribute to and 

depend on results from IEAs.

The connection between National Marine Sanctuary management and the IEA process is 

one that illustrates the interdependency of sound science and resource management. It is 

based in connecting science capabilities with management requirements and must 

consider science, analysis, policy, socioeconomics, and programmatic processes to allow 
3

effective implementation, beginning with public scoping sessions to inform managers on 

the range of issues that management should consider (Figure 1). A Sanctuary 

management plan provides the overarching connection between threats to managed 

resources, social and economic trends, and planned programmatic ecosystem-based 

management actions (see: http://sanctuaries.noaa.gov/jointplan/welcome.html). Sanctuary

management plans, including their associated public scoping process can inform IEA 

scoping, threat identification, and indicator development. Based on these inputs, 

managers develop annual operating plans to allocate resources and address the identified 

threats. IEA risk analysis supports this program planning and investment by identifying 

high risk and high priority resources, processes, and issues. Each of the elements on the 

blue arrows in Figure 1 is an integral component of the adaptive management cycle 

central to EBM.

Monitoring allows managers to assess the effectiveness of specific strategies and overall 

effectiveness. Sanctuary condition reports provide the assessment and analysis of 

conditions and trends of sanctuary resources in the context of management plan goals 

(see: http://sanctuaries.noaa.gov/science/condition). Research and assessment activities 

provide the information necessary to develop targeted, effective management options. In 

the sanctuary system, such options can include regulations, permits, non-regulatory 

actions, and other tools for implementing strategies to address the identified pressures 

and threats on sanctuary resources. IEA tools (like simulation models) support these 

options by helping managers evaluate alternative management actions.

Creating a more comprehensive understanding of ecosystem status or health is a goal of 

many research, modeling, and assessment efforts recently undertaken in the California 

Current Ecosystem2. In this report we compare a number of these efforts in the context of 

NOAA’s DPSIR (Driver, Pressure, State, Impact, Response) and IEA approaches. DPSIR 

is closely intertwined with IEAs (Koshel and Mcallister 2008; Levin et al. 2008; van 

Woerden et al. 2007) so it provides a useful comparison tool. The application of an IEA 

framework for EBM is a relatively new approach with few comprehensive examples. 

This report reviews assessments that while not meeting all requirements of a complete 

IEA, go beyond the individual species or single-issue assessment upon which mangers 

have often relied in the past. These assessments meet one or several of the key IEA 

components shown in Figure 1 and can provide insight into the kinds of ocean observing 

data that fully developed IEAs will require. This report refers to these efforts as 

ecosystem assessments to indicate that they do not necessarily meet all the characteristics 

of an IEA but do provide managers with insights into the conditions of ecological 

resources and functions beyond those possible with single sector assessments.

Tallis identifies data acquisition, quality, and utility as a key factor in manager’s ability to 

apply IEA approaches in EBM (Tallis et al. 2009). The goal of this report is to: 1)

examine ecosystem assessments in the context of a DPSIR approach; and 2) identify 

ocean observing datasets in use by current assessments in order to understand the data 

 2 The CCE extend from approximately La Paz Mexico to the U.S.-Canadian border (www.lme.noaa.gov/ 

(accessed 12/12/2009).
4

and services available to support future assessments. This report compares the purpose, 

scale, and drivers for 10 selected ecosystem assessments with the data sources used in 

their development. The CCE includes a wide range of spatial scales that are relevant to 

ecosystem-based management. Different geographies within the CCE can be described 

by physical processes (Hickey and Banas 2008), biogeography (Pacific Fisheries 

Management Council 2008), or by governance (Ekstrom 2009). The 10 assessments in 

this report represent different scales of investigation including the entire CCE, regions 

within the CCE, specific management units such as National Marine Sanctuaries, and 

local areas such as Monterey Bay.

A more detailed comparison of two ecosystem assessments efforts - the California 

Current IEA, Module I and Northern California Current Ecosystem Atlantis model - was 

undertaken to highlight their use of drivers, pressures, and indicators. Five Sanctuary 

condition reports, a component of IEAs for individual sanctuaries, were examined in 

depth to understand the relationship between drivers, pressures and indicators in the 

context of management requirements. The sources of data used to evaluate the state of 

sanctuary resources were then identified. This approach provided the link between the 

DPSIR model, the IEA framework, and data sources, some of which are IOOS data sets. 

The final step was to examine which of the observing datasets hosted by PaCOOS were 

being used by one or more ecosystem assessment efforts in the CCE. This work provides 

an assessment of how existing IOOS efforts are informing IEA efforts and where gaps 

exist in data availability.

This report identifies how the resource characterization (Table 1) and management action 

(Table 2) needs of the five west coast sanctuaries could be addressed, at least in part, by 

ocean observing data. The management plans for three sites in central California –

Monterey Bay NMS, Cordell Bank NMS, and Gulf of the Farallones NMS, were 

reviewed and updated in 2008 in a process called the Joint Management Plan Review 

(NOAA 2008a, 2008b, 2008c). Similarly, the management plan for the Channel Islands 

NMS was recently completed in 2009 (NOAA 2009). The management plan review 

process at the Olympic Coast NMS began in 2008 and information from issue 

identification workshops was used to identify site management needs.

The strategies and activities highlighted in action plans help define the specific research 

topics or questions that need to be answered at each site and the sites’ need for 

monitoring data. Many resource characterizations and management action needs are 

shared by most or all sanctuaries on the west coast (Tables 1, 2). For example, all five 

sites have a need for better subtidal benthic habitat characterization and a need to detect 

natural and human-induced changes to rocky intertidal habitat. However, some needs are 

more sanctuary specific. For example, the Monterey Bay NMS highlighted the need to 

monitor impacts to living resources from kelp harvest and desalination plants.

Using an existing inventory of monitoring programs in west coast sanctuaries (see 

Appendix I), we identified the programs that are collecting observing data applicable to 

each resource characterization or management action need. For resource characterization 

needs, we identified datasets that are: 1) being served by PaCOOS; 2) not being served by 
5

PaCOOS (Table 1). For example, the annual surveys of kelp canopy in California and 

Washington are two observing datasets hosted by PaCOOS that help characterize the 

status and trend in abundance of this subtidal biogenic habitat in the sanctuaries. In 

contrast, PaCOOS is not currently serving observing datasets that would help characterize 

the status and trends of intertidal habitats and the associated living resources. 

We also found that many management actions highlighted in management plans would 

benefit from better characterization of sanctuary resources. For example, assessing the 

effectiveness of areas within sanctuaries designed for additional levels of protection

requires characterizing both habitat and living marine resources. Multiple monitoring 

programs are collecting these types of data in the intertidal and shallow subtidal habitats 

in Monterey Bay and Channel Islands NMSs. However, these data are not served by 

PaCOOS. Thus, for each management action, we identified which resources needed 

characterization and which monitoring programs were directly addressing the 

management issue (Table 2).

CCE-specific ecosystem assessments incorporating the IEA development framework in use 

by NOAA should also examine requirements in the context of ecological scales. Reviewing 

ecosystem assessments at different scales for the CCE allows us to evaluate how existing 

data and analysis capabilities inform their development and where gaps exist. This report 

also examines the link between available datasets and management priorities of the five 

national marine sanctuaries in the California Current Ecosystem. Our goal is to identify the 

IOOS datasets, as well as other datasets, that could be used in developing IEAs that are 

relevant in managing resources in the CCE. 

Ecosystem Assessments in the California Current

Survey of Ecosystem Assessments at Multiple Spatial Scales

Organizations conduct assessments at scales representing different ecosystem 

components. These range from ecosystem (CCE scale) to ecosystem region (i e., 

Northern CCE), management-unit specific (e.g., a Sanctuary), and sub-management unit 

(e.g., Monterey Bay). A sanctuary condition report is an example of a management unitspecific ecosystem assessment. Undertaking ecosystem-based management requires 

knowledge and understanding of the larger ecosystem components of a managed area. 

There are many ecosystem assessment efforts underway in the CCE, from the local scale 

to the scale of the entire CCE that make use of observing data (Figure 2). These efforts 

are interlinked in a hierarchy of scales (Table 3) that allow comparison of drivers, 

pressures, indicators, and management needs. 

Examining ecosystem assessments at multiple scales enables us to frame the context for 

how observing data are being put to use across the CCE. It is necessary to look at specific 

examples to understand how existing data are being put to use in ecosystem assessments, 

where gaps exist, and why those gaps exist.
6

Figure 2 – Selected Ecosystem Assessments in the California Current Ecosystem. See Appendix 2 for 

background information on each of the ecosystem assessment efforts.

Three ecosystem assessments - the Atlantis model (Brand et al. 2007), Module I 

(Sydeman and Elliot 2008), and the NCEAS Human Impacts Assessment (Halpern et al 

2009) examine the entire California Current Ecosystem. Two of these efforts – the 

Atlantis model and the NCEAS Human Impact Assessment – also create ecosystem 

assessments at the ecosystem region and management unit level. Each site in the National 

Marine Sanctuary system is completing a condition report on the status and trends of 

managed resources at the site level. Finally, the Monterey Bay Crescent Ocean Research 

Consortium (MBCORC) has begun efforts to assess the status of the ecosystem at the 

sub-management unit level through both a report card approach and a ecosystem 

modeling approach. See Appendix B for a more detailed background of these efforts.

Because these ecosystem assessment efforts differ in both their purpose and geographic 

scale, there are differences in which drivers are examined, and which indicators are being 

used to determine ecosystem state (Table 3). We found that each ecosystem assessment 

effort is using IOOS-related datasets to determine the state of some indicators. However, 

each of the ecosystem assessments also include datasets that are not integrated into IOOS, 

which indicates that currently, IOOS datasets are not sufficient to fully meet the data 

needs of ecosystem assessment efforts in the California Current.
7

Comparing Two Large-scale Ecosystem Assessment

A more detailed comparison of two ecosystem scale assessments – California Current 

IEA, Module I (Sydeman and Elliott 2008) and the Northern California Current 

Ecosystem (NCCE), Atlantis Model (Brand et al. 2007) - illustrates how two ecosystem 

assessments with different approaches, result in substantial differences in their form and 

function. (Table 4). Although both the Atlantis model and Module I are focused on an 

assessment at the California Current Ecosystem scale, they have chosen to employ 

different approaches and, thus, indicators of ecosystem state.

The goal of California Current IEA Module I is to find a few good, robust indicator 

datasets that can be used to provide periodic reports on the status of the ecosystem. An 

additional goal is to identify important changes in ecosystem status and link those to 

changes in climate and human use drivers. This assessment includes oceanographic 

indexes and major components of the offshore, pelagic ecosystem such as forage species 

and top predators. They intend to use these datasets to understand the statistical 

relationships between the selected indicators and certain pressures to inform 

management. Based on the indicators that have been selected and the large geographic 

scale covered by those datasets, this assessment is best suited to drivers and pressures that 

operate at large spatial scales and those that impact foodweb dynamics, especially toplevel vertebrate predators. 

In contrast, the NCCE Atlantis is a simulation modeling approach that is spatially explicit 

and attempts to include as many ecosystem components as possible. Datasets include 

hydrographic processes, biogeochemical processes, foodweb relationships between 

multiple functional groups, and human-use patterns, such as harvest. Based on the 

structure of this model, the Atlantis NCCE can provide more spatial resolution than 

Module I, though the resolution is limited by how model compartments are established 

when the model is initialized. Depending on the model structure and datasets used, 

Atlantis works best for understanding the influence of pressures that impact high 

biomass, resident, and/or exploited species, such as those found in the middle of the 

foodweb.

Both Module I and Atlantis have the potential to inform resource management needs, 

such as those of the Office National Marine Sanctuaries or National Marine Fisheries 

service. Both assessment approaches can help address characterization and management 

action needs at large scales. However, the spatial scale of these two models will not be 

fine enough to address many management needs, such as those of a specific sanctuary 

site.

Some of the efforts in the CCE have both LME and ecosystem region components. For 

example, an Atlantis model for the central California ecosystem region is under 

development. The Atlantis model, which incorporates finer scale data when available, can 

be useful in addressing more management unit specific or broader regional management 

needs. 
8

Comparison of the spatial scale of the ecosystem assessments underdevelopment in the 

CCE helps to illustrate the need to match assessment scale, type, and scope to 

management need. There needs to be a proper match between the spatial scale of the 

drivers and pressures that an assessment sets out to address, the data that are used, and the 

approach for reporting the assessment. Though data may be collected in the CCE on the 

status and trends of indicators of interest, it may not be collected at a spatial resolution 

that matches the scale at which the management decision must be made. Identifying the 

primary indicators for different drivers and pressures and the spatial scale of those 

management needs is a key step in identifying the observing datasets that are most 

valuable to the IEA process. 

Identifying Applicable Observing Data for Drivers and Pressures in the CCE

To identify the observing datasets that are most useful for IEAs in the CCE, it is 

important to understand the Drivers and Pressures operating in the ecosystem. A recent 

study lead by researchers at the National Center for Ecological Analysis and Synthesis 

(NCEAS) identified and mapped human threats to marine ecosystems in the California 

Current (Halpern et al. 2009). This study identified the human activities that are potential 

drivers and pressures on coastal and marine habitats in the CCE and determined the 

availability of data sets to model the impacts of those drivers. Of the 57 land-based or 

ocean-based human activities identified in Table 5,CCE-scale observing data were not 

available for 19 of them. For an additional eight pressures, the authors decided against 

using the available data because either a comprehensive dataset was not available and the 

impacts were likely small, or the direction of impacts was not clear (i.e., some positive 

impacts and some negative impacts) and would be difficult to model.

This study provides a good assessment of the human pressures in the CCE for which data 

is available for incorporation into an IEA. The available observing data are being 

combined with information on associated impacts to develop a spatially explicit model of 

the distribution and magnitude of human threats to marine resources in the CCE. The 

next step in the DPSIR approach would be to combine this information on the human

pressures with observing data on the state of key indicators that will be influence by the 

pressures threatening the resource. This would allow managers to explore the impact of 

the pressures and the potential responses of those indicators to management actions that 

modify human activities. However, because this study is attempting to model pressures 

for the entire CCE some datasets that only cover a smaller spatial scale were not 

included. Current and future studies at the sub-regional level (Figure 2) should allow 

incorporation of those smaller scale datasets and allow further assessment of the 

variability in the intensity of human pressures at the sub-regional scale.

The drivers and pressures that are important at even smaller spatial scales, such as the 

ecoregion and local levels, can be examined by looking at ecosystem assessment efforts 

occurring at these smaller spatial scales (Figure 2). For example, each National Marine 

Sanctuary is developing, reviewing, and issuing their condition reports. The reports are 
9

part of the ONMS System-Wide Monitoring framework (ONMS 2004). They were

developed based on a Pressure-State-Response framework (PSR) that correlates to the 

(D)PSIR approach. Each report provides a summary of natural and anthropogenic 

pressures on resources in the focal sanctuary, the current conditions and trends in 

resources, and management responses to the anthropogenic pressures affecting resources. 

The PSR framework allows managers to both prioritize management actions and evaluate 

their effectiveness in meeting conservation or restoration goals.

To identify the current and emerging drivers and pressures at the sanctuary (management 

unit) scale, we reviewed the pressures section of condition reports from the five 

sanctuaries in the CCE – Olympic Coast (ONMS 2008), Cordell Bank (ONMS 2009b), 

Gulf of the Farallones (ONMS draft), Monterey Bay (ONMS 2009c), and Channel 

Islands (ONMS 2009a) (Table 6). Of the 26 current or emerging pressures identified by 

one or more sites, nine pressures were common to all sites. These pressures included such 

activities as harvesting, vessel traffic, oil spills, introduced species, and marine debris. 

Seven of the pressures were identified by only one or two sites. For example Monterey 

Bay and Gulf of the Farallones were the only sites to identify dredging/dredge disposal, 

road construction/landslide disposal, and coastal armoring as human activities that put 

pressure on sanctuary resources. One or more sites identified six human activities as an 

emerging pressure. These pressures included aquaculture (both coastal and open ocean 

based), global climate change, ocean-based energy generation, and bioprospecting. 

Although three of the sanctuary sites – Cordell Bank, Gulf of the Farallones, and 

Monterey Bay – occur in the central California region, there is substantial variability in 

the pressures identified as important in the site’s condition reports (Table 6). There are a 

number of potential reasons for this variability. One of the sites, Cordell Bank, is an 

offshore site so land-based and nearshore human activities will not exert as strong of an 

influence on the resources in this sanctuary. Also, some inconsistencies may be due to 

each report being separately authored. For example, the sites differed in the extent to 

which emerging pressures were discussed in the reports.

Understanding the existing and emerging pressures allows us to frame the need for data 

to support the analysis of conditions and trends. Condition reports also identify the 

indicators and observing datasets used by each site to assess the current state of sanctuary 

resources (Table 7-11). Each site determined the status and trends of resources by 

responding to a standardized set of questions that covered the resource areas of water 

quality (4 questions), habitat (4 questions), and living resources (6 questions). Each site 

used readily available information, including observing datasets, to assess the state of 

multiple indicators and ultimately identify a status rating (e.g., Good, Fair, Poor) and 

trend (improving, declining, unchanging) for each question. The summaries provided in 

Tables 7-11 show a comparison of both the indicators identified by each site to address 

the fourteen standardized question as well as the information used to determine the state 

of those indicators.

Some of the datasets used in one or more condition reports are currently part of IOOS. 

Seafloor mapping data, collected by a variety of programs (e.g., CSUMB, OCNMS, 
10

MBARI, USGS) and available on the PaCOOS West Coast Habitat Portal, were used by 

each site in the assessment of the abundance of benthic physical habitat. In addition, 

Monterey Bay and Olympic Coast used kelp canopy monitoring data available through 

the habitat portal to assess the status of this biogenic habitat. Datasets available on the 

PaCOOS Data Integration Demonstration website were used by one or more sites to 

assess the status of various living resource indicators. For example, Monterey Bay used 

data collected by CIMT on phytoplankton and harmful algal blooms. The Olympic Coast 

used data collected by COASST on beachcast seabirds. Multiple sites used data from 

NMFS monitoring programs, such as NWFSC groundfish surveys, NOAA Fisheries coldwater corals, and SWFSC marine mammal surveys. In some cases the PaCOOS Data

Integration Demonstration website provides access to subsets of these data.

However, many of the datasets available through IOOS, such as those focused on 

physical oceanography, were not used in the condition reports. One reason that some 

IOOS datasets were not used is that most of the standardized questions in the condition 

reports are focused on subjects for which few data are available through IOOS. Of the 

four questions focused on water quality, at least two cannot be addressed by 

oceanographic data alone. For example, indicators of human health risks and indicators of 

human activity levels were needed to answer questions 3 and 4, respectively. The 

remaining 10 questions were focused on the conditions of habitats and living resources, 

subjects for which limited data is currently available through IOOS.

There are a variety of other potential reasons that some IOOS datasets, which were 

applicable to the standardized questions, were not used in the sanctuary condition reports. 

Sanctuary sites may not have been aware of the availability of some of the IOOS datasets. 

The PaCOOS data portals were being developed during the same time the condition 

reports were being drafted so the authors may not have been aware of the types of data 

available. Also, even if a site was familiar with the datasets available, that site may not 

have the time or expertise to access, analyze, or interpret the data. Alternatively, a site 

may have chosen to use other datasets. For example, a site may have used data collected 

at the site or local level instead of at the regional level. 

Comparison of the indicators and datasets used in the five condition reports reveals that, 

although the questions were standardized, there was considerable variability in the 

indicators selected by each site to assess each question. Some of this variability was due 

to the lack of available observing data at larger spatial scales. For example, site-specific 

monitoring programs, such as the OCNMS intertidal monitoring program, Center for 

Integrated Marine Technology (CIMT), and Channel Islands National Park (CINP), 

collected much of the observing data used to assess the state of living resources.

Additional variability was due to the fact that on-going monitoring programs do not 

target some of the indicators of interest. For example, there are very few programs 

monitoring the abundance of contaminants in habitats and little monitoring data available 

to determine the health of the key species identified in the reports. Due to the lack of 

monitoring data, sites had to rely on one-time studies, which are often limited in spatial 

and/or temporal coverage, as a basis for their status assessment. For example, Olympic 
11

Coast and Cordell Bank used one-time studies to assess the abundance of persistent 

organic contaminants in subtidal habitats. Lastly, when monitoring data and published 

studies were not available to the sites to evaluate the condition of indicators of interest, 

the sites had to rely on the professional opinion of local science experts. 

Obstacles to Management Application of Observing Data

Developing CCE IEA frameworks requires identifying gaps in existing observing 

capabilities so as to inform IOOS data and product development. While IOOS product 

development can initially focus on the five core variables, it will need to include other 

relevant data sets not yet incorporated into the IOOS system. Table 12 lists the datasets 

that were used by one or more of the CCE IEA frameworks and identifies the datasets 

that are currently available through PaCOOS data portals. Figure 3 illustrates which 

datasets were used by small-scale or large-scale ecosystem assessment efforts and 

highlights the datasets that were used at both scales. In addition, Figure 3 highlights the 

datasets available through IOOS, and identifies those that are not currently being used by 

any ecosystem assessment efforts in the CCE.

We identified six datasets available through PaCOOS that are being used by both large 

and small-scale ecosystem assessment efforts. The Essential Fish Habitat, NWFSC 

groundfish survey, SWFSC Upwelling Index, and the California Fish Landing database 

were used by IEAs at multiple spatial scales. Surprisingly, the CIMT and Monterey Bay 

Time Series datasets, though limited in spatial scale to the Monterey Bay, was used in 

ecosystem, management unit and, local ecosystem assessments. An additional eight 

datasets were used in assessments at both spatial scales, but were not available through 

IOOS. However, the overwhelming majority of the datasets identified in this analysis 

were used by either small or large-spatial scale ecosystem assessment efforts. 

The limited overlap in the use of datasets at both the large and small-scale is likely due to 

multiple factors. Probably the most influential factor is the spatial scale over which the 

data are collected. Many of the datasets used in the LME and ecosystem region levels are 

collected over a fairly large geographic scale. These datasets provide the wide spatial 

coverage needed by large-scale IEAs, but may be very limited in the amount of data 

available for an IEA at the local or management unit level. Therefore, the small-scale 

IEAs must target datasets with higher density of data points at the small scale, but those 

studies may have limited utility for large-scale IEAs unless similar data are collected at 

other sites in the region. 
12

Figure 3. IOOS data as used by small-scale or large-scale ecosystem assessments considering availability 

through the PaCOOS data portal. At the time of the review, PaCOOS was only hosting oceanographic data 

and the ecosystem assessments were only using biological data so there was no overlap in the data hosted 

vs. data used.

There are some examples of datasets being used at both spatial scales (intersection of the 

pink and yellow circles in Figure 3). Most of these datasets can be used at both large and 

small scales because they are surveys with wide regional coverage, but fairly high data 

density at the local level. In addition, these surveys provide the basis for assessments of 

the status of either fished stocks (e.g., SWFSC rockfish recruitment surveys, CA 

Recreational Fish Surveys) or sensitive populations (e.g., SWFSC shipboard and aerial 

surveys) and thus can be a main source of data in any IEA incorporating those assessed 

species. 

In some cases, similar data are collected by two or more studies at the ecosystem region, 

management unit or, local scale and have the potential to be combined to expand spatial 

coverage and utility for large-scale IEAs. The Module I large-scale IEA uses data from 

separate small scale studies occurring over the larger region of interest. For example, it 

uses hydrographic data collected by Line P in British Columbia, the Newport 

Hydrographic Line in Oregon, and the CalCOFI surveys in California. Seabird data 

collected by five different survey efforts are also incorporated into the Module I IEA. 

Many other datasets currently in use by small scale IEAs appear to have similar potential 
13

for incorporation into larger-scale IEAs. These include annual kelp surveys, sea otter 

census data, beachcast seabird data (e.g., BeachCOMBERS, Beach Watch, COASST), 

and rocky intertidal surveys (OCNMS, PISCO, MARINe). Each monitoring effort is 

likely to have different data collection methods; therefore combining the datasets across 

larger areas will require a thorough understanding of how the data were collected and 

what types of intercomparisons are valid.

In some cases data are being collected on indicators of interest at multiple sites, but those 

datasets have not been integrated into a larger scale monitoring dataset because the 

monitoring programs at each site are using different methods. For example, beachcast 

seabirds are monitored in Olympic Coast, Gulf of the Farallones, and Monterey Bay 

sanctuaries by three separate monitoring efforts, COASST, Beach Watch, and 

BeachCOMBERS, respectively. Similarly the abundance of sea otters and of kelp canopy 

is being monitored in both the Monterey Bay and the Olympic Coast sanctuaries, but by 

separate programs with different methods.

Many of the datasets that are being used by ecosystem assessment efforts are not being 

hosted by IOOS. Data from many of the NMFS monitoring programs, such as the 

Newport Hydrographic Line time series, SWFSC Aerial and Shipboard Surveys, and 

Rockfish Recruitment Surveys, were used by multiple assessment efforts (see Figure 3). 

However, very few of the data collected by these efforts are currently available through 

PaCOOS data portals. In two cases (Newport Hydrographic Line and rockfish 

recruitment surveys) PaCOOS is hosting some oceanographic data, but the biological 

data, which are the primary data being used by the assessment efforts, are not hosted by 

PaCOOS data portals. 

One very large gap in the data available from IOOS is the level of human activities that 

impact the marine environment. Although some data on fishing effort (e.g., California 

Fish Landing database) and impacts on sensitive species (e.g., West Coast Groundfish 

Observer Program) are available through PaCOOS, not enough data are available to 

create comprehensive catch reconstructions. This information is crucial for any type of 

model incorporating fishing activity (I. Kaplan, NMFS-NWFSC, pers. comm.). In 

addition, no data on the levels of other human activities are hosted. However, data on 

human activities that are pressures on marine resources in the CCE are available and 

could be targeted by IOOS. For example, the NCEAS regional ecosystem assessment

identified 30 human activity datasets (Table 5). Additional data on the levels of human 

activities impacting water quality, habitat and living resources is a need identified in all 

the condition reports from the west coast region. Sydeman and Elliot (2008) also 

highlighted the need for socio-economic data and other long-term data on human 

activities in the CCE.

Conversely, many of the datasets available through IOOS were not used by any of the 

ecosystem assessments identified here (see blue shaded region of Figure 3). For example, 

much of the data hosted by IOOS could not help answer many of the standardized 

questions in the ONMS condition reports. Data on contaminants levels in habitats and 

organisms, such as the data collected by the mussel watch program and by harmful algal 
14

bloom monitoring programs (e.g., ORHAB) are not currently hosted by PaCOOS. Very 

few data on the state of intertidal and nearshore living resources are available through 

PaCOOS, although this is a key data need for many management questions and there are 

a number of monitoring programs collecting the data at the local level and ecosystem 

region (e.g., PISCO, CRANE, MARINe, CINP, OCNMS intertidal monitoring). In 

general, biological data for a wide variety of indicator species were needed for the 

condition reports and very few biological data sets are available through IOOS.

Sydeman and Elliot (2008) discuss a number of gaps in the long-term datasets available 

for use in regional IEAs. For example the structure of the phytoplankton community 

(especially the ratio of diatoms to dinoflagellates) appears to be an important index for 

foodweb development. These data are available in the Monterey Bay region and data 

collection is commencing in Oregon, but having this type of information available for 

other locations in the CCE would be extremely valuable. In addition, the authors identify 

a need for more data collected at the sub-regional and local level. Currently, no single 

sub-region has the data available for all the physical, chemical, and especially biological 

indicators required for comprehensive analyses. For a full analysis the ecosystem data has 

to be combined between regions. However, because there are regional differences within 

the CCE in climate forcing and ecosystem response, it may prove most useful to evaluate 

each sub-region separately.

Data on the distribution and abundance of subtidal invertebrates and biogenic habitat was 

identified as a data gap by the Atlantis NCCE model team (I. Kaplan, NMFS-NWFSC, 

pers. comm.). Though some data are available through PaCOOS on biogenic habitat (e.g., 

corals, sponges), the existing data quality is poor relative to the high priority this 

indicator has for both ONMS and NMFS management needs. The existing Essential Fish 

Habitat (EFH) data primarily provide kelp and seagrass coverage and sediment type. The 

best sources of information on the distribution and abundance of structure-forming 

invertebrates (and the abundance of invertebrates in general) at depths deeper than about 

25 meters, are a few scattered studies with limited sample sizes. The Atlantis ecosystem 

model is focused on groundfish, and one can expect these stocks to be influenced by 

abundance of invertebrate prey species. Data on the distribution and abundance of 

benthic invertebrates is a need highlighted in the ONMS condition reports (Table 7-11) 

and the resources characterization needs outlined in sanctuary management plans (Table 

1).

Many other data gaps were identified based on west coast NMS management plans. 

Though some monitoring data are being collected related to most of the resource 

characterization (Table 1) and management action needs (Table 2) summarized in the 

management plans of the five west coast sanctuaries, a very limited amount of that data is 

currently available through IOOS. Notable gaps include water quality data (e.g., 

sediment, pathogens, chemical contaminants) and information on most living resources.
15

Conclusions

Ecosystem-based management requires closely coupled Integrated Ecosystem 

Assessments to establish a feedback loop on the conditions in the systems under 

management. These IEAs require observing data that reflect the pressures and ecosystem 

indicators of concern to managers. The National Marine Protected Area Federal Advisory 

Committee (2008) identified this need to build strong links between IOOS capabilities 

and MPAs to provide the data necessary to support adaptive management. Marine 

protected areas such as national marine sanctuaries reinforce IOOS ocean observation 

efforts by serving as reference sites to monitor impacts from human activities. The 

information reported here provides comprehensive assessment of the relationship 

between IOOS and ocean management requirements. This report brings together 

information on multiple ecosystem assessment efforts allowing us to identify how 

existing IOOS capabilities inform IEAs in CCE, where key gaps exist in data necessary 

to support IEAs, and priorities for closing the gaps. This review recognized four key 

barriers to fully exploiting ocean-observing data for ecosystem-based management.

Data Discovery

Data have been collected from decades of research and monitoring but managers or 

scientists cannot easily access them. The most common problems are inconsistency in 

nomenclature over the history of a data set, incomplete data documentation and quality 

control, and fragmented data access over the life of the data collection. It is also often 

difficult to identify data collections relevant to a specific management issue, such as 

ocean acidification or harmful algal blooms, across data holders. These issues are ones 

where the IOOS program and others such as NOAA’s National Coastal Data 

Development Center (NCDDC) are making rapid progress by creating standards for data 

documentation, formatting, and exchange.

Data Access

Bringing existing data into the IOOS system is the primary barrier to access. While in 

some cases the barrier is primarily one of available resources, there are other factors. 

There is often a significant lag between data collection and when a principle investigator 

is willing to make those data available either because of the potential for inappropriate 

data use or to allow time for their own analysis and publication. The cost and effort of 

data quality control and assurance is another common barrier. However, cost is not 

always the problem, access to expertise and computer tools often stymie potential data 

providers. The data gap is largest in the areas of biological data and data on human 

activities, the data often most critical to IEAs. There also needs to be a focus on including 

local data sets that can be highly relevant to specific management actions. For example, it 

would be useful for data on regional-scale pressures to be collected using the same 

methods at all locations. Because national programs often prioritize large data sets, 

multiple data sets at local scales are often overlooked. These are a few of the many crossorganizational issues that are hurdles to incorporating more datasets into IOOS. Solving 
16

data access problems will take a large commitment of funds at the national, regional, and 

local levels.

Integrating Disparate Data

Ecosystem analysis is fundamentally impeded by disparities among data sets. Those 

disparities range from incompatible methods, differences in spatial and temporal scale, 

and inconsistencies in documentation. Tools that help to match management needs with 

available data, for example bridging the spatial scale of data and the spatial scale of an 

ecosystem assessment, can help overcome these disparities. The Southwest Fisheries 

Science Center Environmental Research Division is developing tools that can have a 

large impact on how managers access and use data. Joint efforts between model 

developers and managers, such as the Northwest Fisheries Science Center working with 

Monterey Bay National Marine Sanctuary to implement the Atlantis model, are also key 

to useful application of observing data. The Atlantis model being implemented in Central 

California will allow managers to evaluate alternatives by using predictive scenarios to 

understand the consequences of actions on ecosystem components and humans. This fills 

a gap in the IEA process for Sanctuaries identified in Figure 1.

Closing the Gap Between Data Needs and Data Collection

One of the key challenges to IEA application to ecosystem-based management is the 

increase in uncertainty the lack of available data creates for managers. Even if there were 

no barriers to discovering, accessing, and integrating existing data, effectively developing 

management alternatives and monitoring outcomes requires investments in data 

collection. In determining the types of data needed to meet the resource characterization 

and management actions, we found that while some data are hosted by PaCOOS or 

regional associations, in most cases, the necessary data are not available for all areas. 

This makes management unit and ecosystem scale analysis difficult.

Analysis of the indicators and datasets used by sanctuaries in the western region provides 

an opportunity to identify priority datasets for management at the management unit or 

larger spatial scale. A priority dataset should meet one or more of the following criteria:

a. Provide the status and trend for one or more indicators related to the questions in 

the condition report

b. Help accomplish one or more strategies in management plan action plans

c. Observing data collected in more than one west coast sanctuary

While it is important to connect ecosystem assessment and observing data to management 

requirements, not all management challenges are known in advance. Management areas, 

like sanctuaries, can serve as sentential sites for detecting, tracking and responding to 

human-caused and natural changes affecting ocean health. Sentinel sites are places that 

attract and support collaboration by researchers seeking to understand processes that 

control ecosystems. This understanding improves our ability to manage the human 

activities known to affect natural systems, respond to emerging threats, and adapt to 

changes that are beyond our control. For example, ocean acidification measurements 
17

across all 5 west coast sanctuaries could provide a key indication of changes in ocean 

chemistry due to atmospheric CO2 inputs.

IEAs and tools for evaluating management strategies depend upon useful, responsive 

indictors to address management issues and assess management effectiveness. Those 

indicators require data with temporal and spatial relevance that allows analyses rich 

enough to support adaptive management and monitoring of the impacts of management 

actions and progress towards ecosystem goals. While managers’ ability to discover, 

access, and integrate California Current Ecosystem data is rapidly advancing, significant 

challenges remain in closing the gap between information needs and data availability and 

analysis capabilities. Resource managers must make the best decisions possible with 

available information. This requirement to move forward, even with insufficient data 

highlights the importance of maximizing the use of what we do have through data 

management, improved accessibility, improved integration and compatibility, and more 

comprehensive analysis.
Table 1

18

Table 1: Resource characterization needs of the five west coast national marine sanctuaries as described in each site’s management plan or in 

the case of Olympic Coast, management plan review documents. (NOAA 2008a, 2008b, 2008c, 2009). 

ID 

# Sanctuary

Resource 

Characterization 

Need

Specific 

Topics/Questions Data Needs

Ocean Observing Data 

Available though 

PaCOOS (Appendix I ID 

#)

Ocean Observing Data Not Available 

through PaCOOS (Appendix I ID #)

Geographic 

Scale

Physical Habitat

1 OC, CB, 

GF, CI

Oceanographic 

Habitat and 

Processes

Improved 

characterization of 

oceanographic and 

atmospheric conditions 

including spatial and 

temporal patterns

wind speed and direction, 

current direction and speed, air 

and water temperature, density, 

salinity, upwelling, nutrients, 

dissolved oxygen, PAR

WCObs (1); CIMT (3); 

MOOS (6); NPS HF 

Radar (8); SEAMAP (55); 

SWFSC Shipboard 

Cetacean Surveys (60); 

CoastWatch (64); 

CalCOFI (65); MBTS 

Program (66); NOAA 

NDBC (68); COCMP (79);

R/V Fulmar and R/V Shearwater data 

logger (4); MBARI cruise data (11); 

CDIP/ Wave Rider buoys (14); NEOCO 

(16); CBOMP (19); TOPP (22); 

SCCWRP (26); SEAS (28); PnB Project 

(38); ASOS (52); BML-COS (58); 

Humboldt Line (69); PRBO At-Sea 

Surveys (81); Pt. Lobos time series (84)

Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit, Local

2 OC, GF, 

MB

Coastal Habitat 

and Processes

Improved understanding 

of nearshore circulation 

patterns. Monitor coastal 

and estuarine erosion 

and sediment transport

nearshore current meters, 

satellite images; current meters 

in coastal streams and 

estuaries; erosion rates; 

turbidity; currents; sediment 

transport; salinity

WCObs (1); CIMT (3); 

NPS HF Radar (8); 

COCMP (79)

USGS Stream Gauge Network (5); 

LOBO (12); CDIP/ Wave Rider buoys 

(14); NEOCO (16); CCLEAN (31); 

NERR system monitoring (32); SC Co 

SWQMP (33); CCoWS (34); PORTS 

(36); PnB Project (38); coastal LiDAR 

collection (45); MISO (57); PISCO (59); 

CI-CORE (75)

Management 

Unit, Local

3 MB Wetlands Wetlands: inventory and 

assessment

map of existing coastal 

wetlands

coastal LiDAR collection (45) Ecosystem 

Region, 

Management 

Unit, Local

4 OC, CB, 

GF, MB, 

CI

Subtidal Benthic 

Habitat

Improved 

characterization of 

benthic habitat. Improved 

understanding of spatial 

distribution of habitats.

high resolution maps of 

benthos delineating depth, 

substrate type, relief, rugosity, 

etc.

OCNMS Habitat Mapping 

(18); EFH (21); USGS 

Habitat Mapping (47)

CSUMB-SFML (17); MBARI Monterey 

Bay Multibeam Survey (20); El Nino 

coastal erosion study (27); Central CA 

Habitat Characterization (37); Cordell 

Bank Habitat Characterization (77)

Ecosystem 

Region, 

Management 

Unit, Local

Water Quality
Table 1

19

ID 

# Sanctuary

Resource 

Characterization 

Need

Specific 

Topics/Questions Data Needs

Ocean Observing Data 

Available though 

PaCOOS (Appendix I ID 

#)

Ocean Observing Data Not Available 

through PaCOOS (Appendix I ID #)

Geographic 

Scale

5 GF, MB, 

CI

Sediment and 

Nutrients Loads

Develop integrated water 

quality monitoring for 

estuarine and nearshore 

waters. Assess levels of 

land-based discharges 

and impacts on 

Sanctuary resources.

total suspended sediment/ 

turbidity, nutrients, chlorophyll/ 

phytoplankton; fresh water flow 

rates and inputs

USGS Stream Gauge Network (5); 

LOBO (12); NEOCO (16); SCCWRP 

(26); CCAMP (30); CCLEAN (31); 

NERR system monitoring (32); SC Co 

SWQMP (33); CCoWS(34); PnB Project 

(38); SWAMP (41); USGS WQ 

monitoring (49); First Flush (56); USGS 

SFBay/Delta (63); SFEI RMP (86); 

Santa Barbara Channelkeeper Stream 

Team (93); Snapshot Day(100)

Ecosystem 

Region, 

Management 

Unit, Local

6 OC, GF, 

MB, CI

Pathogens/ 

Biological 

Contaminants

Monitoring of pathogens 

and biological 

contaminant loads.

bacteria, viruses, HABs San Diego Ocean Monitoring (24); 

SCCWRP (26); CCAMP (30); CCLEAN 

(31); SC Co SWQMP (33); SWAMP 

(41); SFEI RMP (86); Mussel Watch 

(88); Santa Barbara Channelkeeper 

Stream Team (93); Snapshot Day (100)

Ecosystem 

Region, 

Management 

Unit, Local

7 OC, GF, 

MB, CI

Chemical 

Contaminants

Monitoring of chemical 

contaminant loads.

heavy metals, organic 

pollutants

SCCWRP (26); CCAMP (30); CCLEAN 

(31); EPA CA coastal Project (39); 

SWAMP (41); SFEI RMP (86); Mussel 

Watch (88)

Ecosystem 

Region, 

Management 

Unit, Local

8 OC, CB, 

GF

Harmful Algal 

Blooms (HABs)

Track phytoplankton 

populations to detect 

HABs. Detect presence 

of biotoxins in Sanctuary 

waters or organisms.

bioaccumulation monitoring 

(mussels, sand crabs, 

sardine/anchovy); 

phytoplankton 

abundance/species 

composition; bird and mammals 

stranding

CIMT (3); COASST (15) BeachCOMBERS (2); LOBO (12); 

NEOCO (16); CBOMP (19); SEAS (28); 

CCLEAN (31); PnB Project (38); 

BeachWatch (54); Mussel Watch (88); 

MBARI ESP (89); ORHAB (97)

Ecosystem 

Region, 

Management 

Unit, Local

Living Marine Resources

9 CB, GF, 

MB, CI

Biogenic Habitat Improved 

characterization, 

distribution, and 

abundance of biogenic 

habitat including deepsea corals, kelp beds, 

seagrass beds

Non-destructive sampling 

methods: video surveys of 

submerged habitats (reef and 

soft bottom); aerial surveys of 

kelp/seagrass to monitor bed 

location and size

WA Annual Kelp Surveys 

(9); NWFSC Groundfish 

Surveys (67)

CA Annual Kelp Surveys (10); CenCA 

habitat characterization (37); deep-sea 

corals (43); SBC LTER (51); PISCO 

(59); CRANE (76); Habitat 

Characterization/ Biological Monitoring 

Cordell Bank (77); Love Lab Surveys 

(78); MARINe (91)

Management 

Unit, Local

10 OC, GF, 

MB, CI

Intertidal Habitat 

(hard bottom); 

Tidepools

Improved 

characterization of 

distribution and 

abundance of intertial 

algae, fish, invertebrates; 

improved understanding 

of temporal and spatial 

patterns

repeated surveys of intertidal 

sites; monitoring of recruitment

OCNMS intertidal monitoring (35); 

LiMPETS (48); PISCO (59); MARINe 

(91); PRNS Intertidal Monitoring (95)

Ecosystem 

Region, 

Management 

Unit, Local
Table 1

20

ID 

# Sanctuary

Resource 

Characterization 

Need

Specific 

Topics/Questions Data Needs

Ocean Observing Data 

Available though 

PaCOOS (Appendix I ID 

#)

Ocean Observing Data Not Available 

through PaCOOS (Appendix I ID #)

Geographic 

Scale

11 MB, CI Intertidal Habitat 

(soft bottom); 

Beaches and 

estuaries

Improved 

characterization of 

distribution and 

abundance of dune 

plants, invertebrates, 

shorebirds; improved 

understanding of 

temporal and spatial 

patterns

repeated surveys of dunes and 

surf zone; shorebird surveys; 

surveys of mudflats and 

marshes

LiMPETS (48); BeachWatch (54); 

ESNERR bird monitoring (90); ESNERR 

elasmobranch monitoring (92); PRBO 

Snowy Plover monitoring (96); ESNERR 

invertebrate monitoring (99)

Ecosystem 

Region, 

Management 

Unit, Local

12 OC, GF, 

CB, MB, 

CI

Subtidal Habitat 

(hard bottom); 

Kelp Forests and 

deep reef

Improved 

characterization of 

distribution and 

abundance of demersal, 

subtidal fish and 

invertebrates (hard 

substrate); improved 

understanding of 

temporal and spatial 

patterns

repeated surveys of subtidal 

reefs; monitoring of recruitment; 

movement patterns

WA annual kelp surveys 

(9)

sea otter surveys (7,25); CA annual kelp 

surveys (10); CDFG/CINP White 

abalone surveys (40); Deep Sea Corals 

(43); SBC LTER (51); PISCO (59); 

REEF Volunteer Surveys (72); CRANE 

(76); Habitat Characterization/ Biological 

Monitoring Cordell Bank (77); Love Lab 

subtidal surveys (78)

Ecosystem 

Region, 

Management 

Unit, Local

13 OC, GF, 

CB, MB, 

CI

Subtidal Habitat 

(soft bottom)

Improved 

characterization of 

distribution and 

abundance of demersal, 

subtidal fish and 

invertebrates (soft 

substrate); improved 

understanding of 

temporal and spatial 

patterns

repeated surveys of subtidal 

soft bottom habitats including 

epifauna and infauna; 

monitoring of recruitment

NWFSC Groundfish 

Surveys (67)

San Diego Ocean Monitoring (24); 

SCCWRP (26); CenCA habitat 

characterization (37); MB Cable Survey 

(62); CCSF Beach and Ocean 

Monitoring (74); MLML class trawls (98)

Ecosystem 

Region, 

Management 

Unit, Local

14 OC, GF, 

CB, MB, 

CI

Pelagic Habitat 

(Invertebrates 

and Fish)

Improved 

characterization of 

distribution and 

abundance of pelagic 

fishes and invertebrates; 

improved understanding 

of temporal and spatial 

patterns

focus on fisheries independent 

data: net surveys of 

phytoplankton, larval fish and 

inverts, nekton (fish and 

invertebrates); acoustic 

backscatter surveys of 

zooplankton and nekton; 

satellite tagging

CIMT (3); CalCOFI (65); 

MBTS Program (66)

CBOMP (19); TOPP (22); SCCWRP 

(26); SEAS (28); PISCO (59); Humboldt 

Line (69); PWCC Surveys (80); PRBO 

At-Sea Surveys (81); MLML class trawls 

(98)

Ecosystem 

Region, 

Management 

Unit, Local
Table 1

21

ID 

# Sanctuary

Resource 

Characterization 

Need

Specific 

Topics/Questions Data Needs

Ocean Observing Data 

Available though 

PaCOOS (Appendix I ID 

#)

Ocean Observing Data Not Available 

through PaCOOS (Appendix I ID #)

Geographic 

Scale

15 OC, GF, 

CB, MB, 

CI

Pelagic Habitat 

(Seabirds, 

Turtles, 

Mammals)

Improved 

characterization of 

distribution and 

abundance of seabirds, 

turtles, mammals; 

improved understanding 

of temporal and spatial 

patterns

seabird, mammal, marine turtle 

surveys (aerial, shipboard, 

land-based, acoustic); satellite 

tracking; rookery/haulout 

census

CIMT (3); COASST (15); 

SEAMAP (55)

BeachCOMBERS (2); sea otter surveys 

(7,25); SPLASH (13); CBOMP (19); 

TOPP (22); Tracking Black-footed 

Albatross (23); SEAS (28); OCNMS 

offshore surveys (42); SAMSAP (44); 

USFW seabird colony surveys (46); 

BeachWatch (54); SWFSC Shipboard 

Cetacean Surveys (60); SWFSC Central 

CA Aerial surveys (71); PRBO At-Sea 

Surveys (81); PRNS pinniped monitoring 

(94); SBC Aerial Surveys (101)

Ecosystem 

Region, 

Management 

Unit, Local
Table 2

22

Table 2: Management drivers of the five west coast national marine sanctuaries as described in each site’s management plan or in the case of 

Olympic Coast, a management plan under review. (NOAA 2008a, 2008b, 2008c, 2009). 

Sanctuary Management Topic Specific Topics/Questions Data Needs

General Resource 

Characterization 

Needs (Table 1 ID#)

Monitoring Programs Directly 

Addressing Management 

Topic (Appendix I ID#)

Geographic 

Scale

Marine Protected Areas

CB, MB, 

CI

Impacts to Physical 

Habitat

Detecting impacts of spatial 

protection to health of the 

physical habitat inside and 

outside of MPAs

habitat mapping, 

monitoring biogenic habitat 

(corals, kelp, etc.), 

structure of sediments; 

compare changes overtime 

inside and outside MPAs

Subtidal benthic habitat 

mapping (4); Biogenic 

habitat surveys (9)

Management 

Unit, Local

OC, CB, 

GF, MB, 

CI

Impacts to Biological 

Resources

Detecting impacts of spatial 

protection to health of the 

biological community inside 

and outside of MPAs. 

Evaluate spillover effect for 

harvested populations. 

Distinguish between natural 

and anthropogenic changes.

species composition, 

richness, diversity of 

intertidal and subtidal 

communities; size/age 

structure, abundance, 

distribution of populations 

(including harvested 

species)

Intertidal habitats 

(10,11); subtidal 

benthic habitats 

(12,13); pelagic 

habitats (14,15)

CRANE (76); CINMS marine 

reserve monitoring program 

[PISCO (59), REEF Volunteer 

Survey Project (72), Love Lab 

surveys (78), PIER Acoustic 

Telemetry Monitoring (82), 

CINP] 

Management 

Unit, Local

Detecting Human Impacts

OC, CB, 

GF, MB

Fishing Identifying impacts of fishing 

on Sanctuary resources. 

Differentiate between fishing 

impacts and other humaninduced or environmental 

changes.

size/age structure, 

biodiversity, density of 

benthic and pelagic 

communities (including 

biogenic habitat); 

decreased reproductive 

output (larval abundance 

or juvenile recruitment); 

changes in physical 

structure of habitat; 

physical oceanography

Intertidal habitats 

(10,11); subtidal 

benthic habitats 

(12,13); pelagic 

habitats (14,15); 

biogenic habitat (9); 

seafloor mapping (4); 

oceanographic 

processes (1)

Olympic Coast cable recovery 

study

Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit

MB Kelp Harvest Monitor impacts to living 

resources from kelp harvest

abundance of kelp canopy 

and associated fish, 

invertebrates, sea otters; 

compare areas with 

harvesting and without 

harvesting

kelp canopy surveys 

(9); kelp forest habitat 

(12); sea otters (15)

Management 

Unit, Local

OC, GF, 

MB, CI

Tidepools Detecting natural and humaninduced changes to rocky 

intertidal habitat. Evaluating 

impacts of human activities 

(e.g., trampling, collecting) to 

tidepool communities

Distribution and 

abundance of sessile and 

mobile species at 

accessible vs. nonaccessible sites

rocky intertidal habitat 

(10)

Tenera Environmental study (Pt. 

Pinos)

Management 

Unit, Local
Table 2

23

Sanctuary Management Topic Specific Topics/Questions Data Needs

General Resource 

Characterization 

Needs (Table 1 ID#)

Monitoring Programs Directly 

Addressing Management 

Topic (Appendix I ID#)

Geographic 

Scale

OC, MB Submerged Cables; 

Benthic Disturbance

Identifying impacts of 

submerged cables and other 

seafloor disturbance to benthic 

habitats. Identify location of 

sensitive habitats and species.

Distribution of seafloor 

habitats, distribution and 

abundance of sensitive 

benthic fish and 

invertebrate species

seafloor mapping (4); 

subtidal benthic habitat 

(12,13)

Monterey Bay Cable Survey 

(62); Olympic Coast cable 

recovery study

Management 

Unit, Local

MB Desalination Monitor long-term impacts of 

discharge of desalination 

facilities.

species composition 

around discharge; water 

circulation patterns; salinity

subtidal soft-bottom 

community (13); 

coastal processes (2)

Management 

Unit, Local

MB Coastal Armoring Monitor long-term impacts of 

coastal armoring structures.

monitor size and slope of 

beaches; develop sand 

budgets; nearshore 

currents, sediment 

transport, wave refraction 

patterns; map of existing 

coastal armoring sites; 

monitor biological 

community structure

coastal habitat and 

processes (2); intertidal 

habitat - beaches (11)

El Nino coastal erosion study 

(27)

Management 

Unit, Local

OC, GF, 

MB, CI

Introduced Species Detection of new 

introductions, monitoring 

populations of existing 

introduced species.

distribution and 

abundances of aquatic 

plants, algae, benthic fish 

and invertebrates; surveys 

to detect and monitor 

introduced species; maps 

of current distribution of 

introduces species; 

plankton surveys to detect 

larvae of introduced 

species

intertidal habitats, 

especially estuaries 

(10,11); subtidal 

habitats (12,13); 

pelagic habitats (14)

MBNMS Undaria monitoring, 

ESNERR "least wanted" 

monitoring program;

Management 

Unit, Local
Table 2

24

Sanctuary Management Topic Specific Topics/Questions Data Needs

General Resource 

Characterization 

Needs (Table 1 ID#)

Monitoring Programs Directly 

Addressing Management 

Topic (Appendix I ID#)

Geographic 

Scale

OC, GF, 

MB

Special Status Species Improved understanding of 

population size and trends for 

special status species 

(species listed under the 

federal or state ESA or those 

designated as overharvested 

by NMFS) or other sensitive 

species identified by 

Sanctuary program. 

Identification of critical habitats 

for these species. 

Identification of causes of 

mortality.

distribution, abundance 

and population trends of 

special status and 

sensitive species; 

monitoring of sick, 

stranded, and dead 

organisms animals

intertidal habitats 

(10,11); subtidal 

habitats (12,13); 

pelagic habitats (14,15)

Black Abalone monitoring; 

BeachCOMBERS (2), 

BeachWatch (54), COASST(15); 

most studies listed under 

"Pelagic habitat characterization 

- seabirds, turtles, mammals; 

PRNS pinniped monitoring (94); 

Xantus's Murrelet, Brown 

Pelican & Ashy Storm-Petrel 

nest monitoring (CINMS); 

Cascadia cetacean monitoring; 

USFWS Marbled Murrelet 

surveys; USFWS Common 

Murre restoration; PRBO Snowy 

Plover monitoring (96); sea otter 

necropsies

Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit

OC, GF, 

MB, CI

Wildlife Disturbance Disturbance to wildlife from 

human activities (e.g., marine 

vessels, low flying aircraft, 

acoustics): detecting 

disturbance and identifying 

sensitive areas, seasons, and 

migration routes

bird, mammal, and turtle 

distributions, movement 

patterns over time, location 

and magnitude of 

disturbance; GIS database 

of mammal sightings

pelagic habitats -

seabirds, turtles, 

mammals (15)

SEALS program; CIMT passive 

acoustic monitoring (3); 

TeamOCEAN; 

BeachCOMBERS (2), 

BeachWatch (54), COASST (15)

Ecosystem 

Region, 

Management 

Unit, Local

CB, GF, 

MB

Entanglement/ Marine 

Debris

Identify impacts to wildlife from 

entanglement in active and 

abandoned fishing gear, 

aquaculture pens. Identify 

impacts of other marine debris 

(e.g., plastic debris). Monitor 

and inventory marine debris in 

the Sanctuary.

location and abundance of 

beach cast birds, 

mammals; observer data of 

entanglement in active 

fishing gear; GIS database 

to track type, location, and 

amounts of debris; bird and 

mammals surveys

pelagic habitats -

seabirds, turtles, 

mammals (15)

BeachCOMBERS (2), 

BeachWatch (54), COASST 

(15); Fishery bycatch and 

mortality (SWFSC); CBOMP 

(19)

Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit, Local

OC, GF, 

CI

Oil or Chemical Spill Improve spill and drift models. surface currents, fine-scale 

bathymetry, biological 

productivity

Oceanographic Habitat 

and Processes(1); 

Coastal habitat and 

Processes(2); 

Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit
Table 2

25

Sanctuary Management Topic Specific Topics/Questions Data Needs

General Resource 

Characterization 

Needs (Table 1 ID#)

Monitoring Programs Directly 

Addressing Management 

Topic (Appendix I ID#)

Geographic 

Scale

OC, GF, 

MB

Oil or Chemical Spill; 

Landslide

Predicting impacts to and 

tracking recovery of Sanctuary 

resources.

intertidal community 

structure; subtidal 

community structure; 

biogenic habitat (e.g., kelp, 

seagrass); seabird colony 

size; mammals 

rookery/haul-out size; 

seabird, turtle, mammal 

foraging hotspots

Biogenic habitat (9); 

intertidal habitat 

(10,11); subtidal habitat 

(12,13); pelagic 

habitats - seabirds, 

turtles, mammals (15)

BeachCOMBERS (2), 

BeachWatch (54), COASST(15)

Ecosystem 

Region, 

Management 

Unit, Local

Ecosystem Monitoring and Assessment

OC, CB, 

GF, MB

Integrated analysis and 

synthesis to determine 

the health of the 

ecosystem and track 

changes over time (e.g., 

SWiM condition reports)

How are the physical and 

biological resources changing 

in the ecosystem? How do 

changes in physical processes 

affect the distribution and 

abundance of organisms? 

How are changing 

oceanographic conditions 

affecting productivity and 

trophic dynamics?

extensive characterization 

of the physical process and 

biological resources

All characterization 

data sources (1-15)

CIMT (3); CBOMP (19) Large 

Marine 

Ecosystem, 

Ecosystem 

Region, 

Management 

Unit, Local

MB Integrated Monitoring of 

Big Sur Coast

Integrated GIS database for 

Big Sur coastal and marine 

resource management

maps of physical and 

biological resources along 

Big Sur coast (updated 

through "live" portals)

All characterization 

data sources (but only 

data collected along 

Big Sur Coast)

WCObs (1); PISCO (59); 

CRANE (76)

Management 

Unit, Local
Table 3 

26

Table 3: Description of Ecosystem Assessments in the California Current Ecosystem

Name Purpose Geographic 

Scale Output Type Drivers/ Pressures Datasets used that are available 

through PaCOOS

Atlantis 

Ecosystem Model

Spatially explicit 

ecosystem modeling and 

management strategy 

evaluation

California Current 

Ecosystem; 

Central California 

ecosystem region

Dynamic

Natural and 

anthropogenic, with 

emphasis on fisheriesrelated drivers.

GLOBEC, EFH, CalCOFI, NWFSC 

Groundfish Surveys, West coast 

groundfish observer program, 

California Fish Landings 

California Current 

IEA, Module I

Identifying biological 

indicators of ecosystem 

state and ocean climate 

California Current 

Ecosystem; (3 

ecosystem 

regions 

proposed)

Static

Natural and 

anthropogenic, with 

emphasis on drivers 

impacting top vertebrate 

predators

CIMT, CalCOFI, NWFSC 

Groundfish Surveys, MBTS?

NCEAS California 

Current Marine 

Ecosystem 

Human Impacts 

Assessment

Mapping how human 

activities are affecting 

marine ecosystems

California Current 

Ecosystem; and 

6 ecosystem 

regions

Static Anthropogenic

Annual Kelp Surveys, EFH, AVHRR 

Pathfinder Satellite data, California 

Fish Landings

ONMS SWiM 

Condition Reports

Assessing the status and 

trends of water, habitat, 

and living resources and 

the human activities that 

affect them

5 management 

units Static Natural and 

anthropogenic

CIMT, NWFSC Groundfish 

Surveys, COASST, MBTS, Annual 

kelp surveys, CSUMB-SFML, 

USGS Pacific Coast Habitat 

Mapping Program, MBARI 

multibeam survey, OCNMS Habitat 

Mapping

MBCORC Report 

Card

Assessing ecosystem 

health using a series of 

indicators

1 local site 

(Monterey Bay) Static

Natural and 

anthropogenic, with 

emphasis on 

anthropogenic 

CIMT, NWFSC Groundfish 

Surveys, MBTS, California Fish 

Landings 

MBCORC Virtual 

Monterey Bay

Coastal oceanographic 

observing and modeling 

system

1 local site 

(Monterey Bay) Dynamic Primarily natural Not yet available
Table 4

27

Table 4: Comparing two Ecosystem Assessments for the California Current Ecosystem.

California Current IEA, Module I (Sydeman and Elliott 

2008) 

Northern California Current Ecosystem, Atlantis 

model (Brand et al. 2007)

Geographic Range:

• Entire California Current Ecosystem (Vancouver 

Island, British Columbia, Canada to Punta 

Eugenia, Baja California Mexico)

• Considering creating separate IEAs for the 

three sub-ecosystems

o Northern: southern B.C. to Cape 

Blanco, southern Oregon

o Central: Cape Blanco to Pt. 

Conception

o Southern: Pt. Conception to Punta 

Eugenia, Baja Mexico

Geographic Range:

• Atlantis model has been created for the 

Northern California Current Ecosystem (Cape 

Flattery, Washington to Point Conception, 

California).

• In the process of creating separate models for 

Puget Sound and central California

Drivers/Pressures: The Module I IEA will probably work 

better for drivers that operate at large spatial scales 

and/or impact foodweb dynamics, especially top 

vertebrate predators: 

• Environmental change

o Climate change / climate warming

o ENSO events

o PDO phases

o Ocean acidification (maybe)

• Wildlife disturbance

o Bycatch/ entanglement/ marine debris

o Oil spill

o Harmful Algal Blooms

Drivers/Pressures: The Atlantis model will work for 

drivers that operate at the scale of the boxes in the 

model and impact large biomass population in the middle 

of the foodweb. May be able to detect changes in 

abundance of habitat type (at a large scale) and/or living 

resources with strong habitat associations: 

• Environmental change

• Fishing-related removal of biomass

o Gear-types

o Spatial patterns

o Temporal patterns

• Gear-related impacts to benthic habitat

• Bycatch/entanglement (of species with medium 

to high biomass)

• Species introductions (e.g., jumbo squid)

Indicators: This model is currently based on the 

following indicators:

• Environmental indices

o Basin-scale PDO index

o Basin-scale ENSO index

o Sub-ecoregion Wind, Upwelling, SST

• Zooplankton

o Copepod species richness and 

biomass indices (Newport 

Hydrographic Line)

o Small plankton volume index (CalCOFI 

data)

o Krill abundance (Thysanoessa 

spinifera) in diet of fish (Vancourver 

Island Zooplankton study)

o Krill abundance in diet of Cassin’s 

Auklet (Southeast Farallon Island 

Seabird Ecology Surveys)

Indicators: this model is based on the following 

indicators:

• Benthic Habitat (from EFH data set)

o Sediment type (hard or soft)

o Kelp and seagrass 

• Hydrographic submodel

o Nutrients

o Salinity

o Dissolved oxygen 

• Ecology submodel contains 54 biomass pools 

(species or functional groups)

o Abundance and distribution information

o Growth and consumption rates

o Reproduction rates

o Migration rates

o Predator-prey dynamics
Table 4

28

California Current IEA, Module I (Sydeman and Elliott 

2008) 

Northern California Current Ecosystem, Atlantis 

model (Brand et al. 2007)

• Squid abundance from fishery landings and diet 

of CA sea lions

• Forage fish

o Anchovy egg abundance (CalCOFI 

data)

o Sardine egg abundance (CalCOFI 

data)

o Juvenile rockfish abundance in surveys 

(Rockfish Recruitment Surveys) and 

diet of Common Murre (Southeast 

Farallon Island Seabird Ecology 

Surveys)

• Vertebrate predators

o Coho salmon survival and juvenile 

coho growth

o Pacific hake biomass (NWFSC 

Groundfish Surveys)

o Seabird breeding success (Southeast 

Farallon Island Seabird Ecology 

Surveys)

o CA sealion pup abundance (Pinniped 

Aerial Surveys Project)

This model works best for indicators that have:

• Medium to high biomass

o especially good for species with good 

information / high volume in fisheries 

(as bycatch or target species)

o not good for species with small 

biomass levels

• Good information on feeding habits

o model works well for main predators in 

the study system

• Good information on spatial distribution; 

o model works well for species with 

widespread distribution in the study 

area

o model works well for species that 

spend most of their time in the study 

area

o Not good for highly migratory species 

and/or seasonal visitors

ONMS or NMFS management needs

• Characterization of primarily pelagic habitat, 

species, and foodweb

• Special status species management

• Wildlife disturbance issues

• Offshore Spatial Management (identification of 

hotspots / pelagic MPAs / areas to avoid for 

offshore energy production or aquaculture)

ONMS or NMFS management needs

• Characterization

o pelagic habitat and foodweb especially 

middle levels of foodweb

o benthic habitat and demersal fishes

• Fisheries management

o Gear changes

o Size limits

o Take restrictions

• Spatial management

o Time-area closures

o Marine protected areas (fewer larger 

MPAs will be easier to model than 

many smaller MPAs)

• Special Status Species (those with medium 

biomass and/or fairly resident in area)
Table 5

29

Table 5. Human activities that are potential drivers and pressures in the California Current 

Ecosystem as identified by the National Center for Ecological Analysis and Synthesis (NCEAS) 

working group (Carrie Kappel, NCEAS, pers. comm.). The availability of ecosystem-wide 

observing data used to assess the impact of the pressures on ecosystem resources are 

identified. Authors decided against inclusion of data for some human activities for various 

reasons, such as too difficult to model with available data and comprehensive dataset not 

available.

Human Activities Data Source Data Not 

Available

Decided 

Against

Land-based

Agriculture National Atlas of Canada

Industrial farms EPA Toxics Release Inventory

Small farms X

Urbanization National Atmospheric Deposition Program

Land infill X

Forestry X

Road building X

Shoreline hardening NOAA’s Environmental Sensitivity Index (ESI)

Estuarine mouth alterations X

Salt ponds/mines X

Human access to beaches, 

intertidal

California Coastal Access Guide; Oregon Geospatial 

Enterprise Office; Washington State Department of 

Ecology BEACH Program

Atmospheric deposition National Atmospheric Deposition Program

Dams National Inventory of Dams (Army Corps of Engineers)

Sewage outfall/ Septic EPA Toxics Release Inventory

Factories EPA Toxics Release Inventory

Paper/ Pulp mills EPA Toxics Release Inventory

Mines EPA Toxics Release Inventory

Ocean-based

Aquaculture

Marine plant X

Shellfish X

Finfish (herbivores) X

Finfish (predators) visually located using Google Earth

Fishing

Demersal destructive California Fish Landings; FAO & Sea Around Us Project 

Demersal non-destructive 

low bycatch California Fish Landings; FAO & Sea Around Us Project 

Demersal non-destructive 

high bycatch California Fish Landings; FAO & Sea Around Us Project 

Pelagic low bycatch California Fish Landings; FAO & Sea Around Us Project 

Pelagic high bycatch California Fish Landings; FAO & Sea Around Us Project 

Aquarium fishing X

Recreational fishing California Recreational Fisheries Survey 

Artisanal fishing FAO & Sea Around Us Project 

Forestry operations

Log booms, dumps, sorts X

Scientific research

Collecting X

Experiments X

Surveys X

Ocean mining X
Table 5

30

Human Activities Data Source Data Not 

Available

Decided 

Against

Dredging X

Shipping

Commercial shipping traffic World Meteorological Organization Voluntary Observing 

Ships Scheme

Cruise ship traffic X

Ferry traffic Department of Transportation (California and 

Washington)

Invasive species (Ports) US Army Corps of Engineers Navigation Data Center

Oil rigs Pacific States Marine Fisheries Commission

Ocean dumping

Marine debris on beaches California Coastal Commission Public Education 

Program

Toxic materials X

Lost fishing gear X

Ship wrecks X

Tourism

SCUBA diving X

Recreational boating X

Kayaking X

Power or Desalination plants Platts database (part of McGraw-Hill Companies)

Military Activity X

Harmful Algal Blooms X

Hypoxic zones X

Ocean pollution (oil, chemicals) California Coastal Commission Public Education 

Program

Climate change

Sea surface temperature AVHRR Pathfinder Version 5.0 SST data 

UV radiance GSFC TOMS EP/TOMS satellite program at NASA

Ocean acidification aragonite saturation state (Guinotte et al. 2003)

Sea level rise X
Table 6

31

Table 6. Drivers and pressures identified in the condition reports for Olympic Coast (OC; ONMS 2008), Cordell Bank (CB; ONMS 2009b), Gulf of 

the Farallones (GF; ONMS DRAFT), Monterey Bay (MB; ONMS 2009c), and Channel Islands (CI; ONMS 2009a) National Marine 

Sanctuaries. Grey shading is used to identify the three sanctuaries that occur in the central California sub-region. X = current pressure; E = 

emerging pressure

Drivers Pressures OC CB GF MB CI Potential impacts

Seafood consumption; Commerce; 

Recreational activities Harvesting - targeted species X X X X X

Population, community, and ecosystem-level impacts 

from biomass reduction and removal of forage species or 

predators

Seafood consumption; Commerce; 

Recreational activities Harvesting - bycatch X X X Entanglement in active fishing gear by mammals, birds, 

turtles; Harvest of non-target fishes and invertebrates

Seafood consumption; Commerce; 

Recreational activities Harvesting - habitat impacts X X X X X

Disturbance to seafloor habitat and biogenic habitat from 

bottom-contact gear; Disturbance of seabirds and 

mammals from lights

Seafood consumption Land-based/Nearshore 

Aquaculture E X X E

introduction of pathogens, chemicals, non-native species; 

eutrophication and/or harmful algae blooms near 

enclosures or discharges; disturbance of kelp-associated 

species from kelp harvest to feed cultured abalone; 

disturbance to seabed

Seafood consumption; Recreational 

activities; Land-based commerce and 

development; Maritime trade 

Marine debris (lost fishing 

gear, plastics, etc.) X X X X X

Entanglement of habitat, organisms, humans, and 

vessels; Diminished aesthetic qualities of sanctuary; 

Ingestion; Transfer of disease, harmful chemicals, nonindigenous species

Maritime trade (vessel traffic, cruise 

ships, marinas, sunken vessels); 

Petroleum exploration, production, and 

refining

Oil and hazardous material 

spill X X X X X

wildlife injury and mortality (seabirds, marine mammals, 

intertidal communities); habitat degradation (physical and 

biogenic); fishing closures; water quality; reductions in 

tourism and local economy

Maritime trade; National security (military 

operations) Vessel traffic X X X X X

noise pollution (see below); oil or hazardous material 

spill; lost containers and other large debris; Disturbance 

to wildlife (e.g., mammals, sharks); Collisions with 

mammals, turtles

Commerce and development Global climate change E X E E X

sea level rise, temperature increase, acidification, etc.; 

changes in species distribution, primary productivity, 

community composition, etc.

Oceanographic conditions

Natural shifts in climate: 

seasonal, annual, and longerterm (ENSO/PDO) X X X X

shifts in prey availability and distribution; altered body 

condition, survivorship and reproductive success; shifts in 

migratory patterns and timing

Maritime trade; Seafood consumption 

(aquaculture. harvesting); Aquarium 

trade; Research; Restoration

Non-indigenous species X X X X E

competing with or preying on native and harvested 

species; altering species composition; altering ecosystem 

function; habitat degradation; disrupting commercial and 

recreational activities; introduction and spread of 

infectious disease
Table 6

32

Drivers Pressures OC CB GF MB CI Potential impacts

Maritime trade (marinas); Seafood 

consumption, Recreational activities

Dredging and dredge material 

disposal X X

physical disturbance to seafloor and benthic organisms; 

burial of benthic organisms; chemical contamination;

turbidity; alteration of water flow and sedimentation and 

erosion rates

Commerce and development Coastal armoring X X habitat conversion or loss; alteration of erosion and 

sediment transport and deposition patterns; 

Commerce and development Road construction and 

landslide disposal X X burial of intertidal and subtidal habitat and organisms; increased sand scour

Livestock and agriculture; Forestry; 

Maritime commerce (marinas and cruise 

ships); Coastal development

Sediment and nutrient pollution X X X X elevated nutrient levels, sedimentation, turbidity; harmful 

algal blooms; 

Livestock and agriculture; Maritime 

commerce (marinas and cruise ships); 

Coastal development

Chemical pollution (pesticides, 

oil and grease, heavy metals, 

detergents, industrial 

chemicals, radioactive waste)

X X X X contamination of water, habitat and food chain; health 

impacts to animals and humans

Livestock and agriculture; Maritime 

commerce (marinas and cruise ships); 

Coastal development

Biological contamination

(biotoxins/harmful algal 

blooms, bacteria, protozoa, 

viruses)

X X X X X contamination of water, habitat and food chain; health 

impacts to animals and humans; beach closures

Ecotourism; Research; Seafood 

consumption; Recreational Activities

Wildlife disturbance - shorebased (tidepoolers, hikers) X X X X trampling; collecting; flushing breeding, foraging, and 

resting seabirds and mammals;

Ecotourism; Research; Seafood 

consumption; Recreational Activities

Wildlife disturbance - waterbased (whale, bird and shark 

watching, kayaking, surfing, 

SCUBA)

X X X X flushing breeding, foraging, and resting seabirds and 

mammals; 

Ecotourism; Research; Coastal 

commerce; National security (military 

operations)

Wildlife disturbance - aircraft X X X flushing breeding, foraging, and resting seabirds and 

mammals; collisions with whales, sea otters

National security (military operations); 

Petroleum exploration; Maritime trade; 

Research

Wildlife disturbance: noise 

pollution/sonar X X X X X altered behavior, injury, or death in marine mammals and 

fish; 

Commerce and development; National 

security (military operations); Research Submerged cables X X seafloor habitat disturbance; entanglement of anchors, fishing gear and organisms

Commerce and development Ocean-based energy 

generation E E damage to seafloor habitat, disturbance of marine mammals and seabirds

Commerce and development Open-Ocean Aquaculture E E E pathogen and nutrient loading, seafloor disturbance, 

entanglement or other disturbance to wildlife

Commerce and development Desalination X brine waste effluent, disturbance to the seafloor; 

entrainment and impingement of fish and invertebrates

Maritime trade; National Security 

(military operations); Fishing; 

Recreational Activities

Sunken vessels X X X release of hazardous materials (e.g., fuel), entanglement 

of fishing gear, anchors, etc.
Table 6

33

Drivers Pressures OC CB GF MB CI Potential impacts

Commerce; Research Bioprospecting E

excessive removal of marine life or plants; habitat 

disturbance; alteration to structure or function of the 

community or local ecosystem
Table 7

34

Table 7. Datasets used to assess the current condition of water, habitat, and living resources as 

identified in the condition report for the Olympic Coast National Marine Sanctuary (ONMS 

2008). References listed in this table can be found in the “Cited Resources” section of the 

OCNMS condition report. Blue Text = lack of information noted in report. Green Text = 

Project ID # from Appendix 1.

Questions Indicators Source

Water

1) Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water 

quality?

dissolved oxygen oceanography monitoring stations (OCNMS monitoring 

data); long-term dataset in sanctuary waters lacking

dead crabs, fish kills reported observations (Quinault Natural Resources 

Department)

seawater acidity (pH), water temperature, 

current direction and velocity, fluorometry, 

conductivity

Wootton unpublished data, Grantham et al. 2004, Barth 

et al. 2007, Chan et al. 2008; oceanography monitoring 

stations (OCNMS monitoring data)

HABs/domoic acid levels in razor clams monitoring since early 1990s (Washington Department of 

Fish and Wildlife); long-term dataset not available

chemicals in water, sediment and biota at 30 

stations in OCNMS

30 stations sampled as part of EMAP in 2003 (Partridge 

2007); long-term monitoring of some chemicals (NOAA’s 

Status and Trends, Mussel Watch Program (ID 88))

2) What is the eutrophic condition of sanctuary waters and how is it changing?

nutrient concentrations in coastal waters EMAP 2003/Partridge 2007; long-term datasets and 

sufficient instrumentation are lacking - trend unknown

water circulation/nutrients/primary 

production/HABs

satellite imagery (temperature, color), buoy data in and 

near OCNMS; Foreman et al. 2007, MacFadyen et al. 

2008

3) Do sanctuary waters pose risks to human health?

biotoxins (PSP and ASP) in shellfish routine monitoring since 1991 (coastal tribes and 

Washington Department of Health)

Harmful Algal Blooms

monitoring began in the 1990s (Juan de Fuca Eddy 

Steering Committee 2004; Trainer 2005; Trainer & 

Suddeson 2005)

bacteria (e.g, fecal coliform, E. coli, 

Enterococcus) in marine waters

Washington Department of Health 2008; Surfrider's Blue 

water task force 2003-05; limited monitoring

4) What are the levels of human activities that may influence water quality and how are they changing?

frequency and tracks of vessel traffic

Canadian vessel traffic system at mouth of Strait of Juan 

de Fuca; Marine Exchange of Seattle vessel tracking 

throughout sanctuary

timber harvest levels general public information; data not researched

annual number of cruise ship passengers 

through the Port of Seattle (2000-2007) WDOE 2008

coastal population size and rate of coastal 

development Chamber of Commerce and US Census

Habitats

5) What is the abundance and distribution of major habitat types and how is it changing?

relative abundance of species and number of 

trampled organisms in rocky intertidal

infrequent monitoring of high and low traffic sites 

(Erickson and Wullschleger 1998; Erickson 2005)

high resolution imaging of seafloor Intelmann 2006; Bowlby et al. 2008, unpublished 

OCNMS data (ID 18)

low resolution mapping surveys Intelmann 2006; Bowlby et al. 2008, unpublished 

OCNMS data (ID 18)
Table 7

35

Questions Indicators Source

seafloor habitat (impacts of submarine cable 

installation and bottom contact fishing gear); 

ROV and video used

periodic monitoring on submarine cable route and 

benthic surveys (OCNMS data)

location and intensity of bottom trawling effort Shoji 1999, National Marine Fisheries Service and 

Washington Department of Fish and Wildlife data

groundfish landings Shoji 1999; National Marine Fisheries Service data

number of vessels in the trawl fishery Shoji 1999

6) What is the condition of biologically-structured habitats and how is it changing?

abundance and distribution of rocky intertidal 

macroalgae and invertebrates

monitored since 1989 (Olympic National Park and 

OCNMS data (ID 35)

spatial extent of kelp canopy

monitored since 1989 (Washington Department of 

Natural Resources, in collaboration with OCNMS since 

1995) (ID 9)

distribution and abundance of subtidal 

structure-forming invertebrates

NWFSC Groundfish Surveys (ID 67) data since 1980 

(Whitmore and Clarke 2007); occasional observations 

(Etnoyer and Morgan 2003); OCNMS video surveys in 

limited areas (Brancato et al. 2007 (ID 43)); aerial extent 

of monitoring data is very limited

Location of hard substrate with potential to 

host biologically-structured habitat Essential Fish Habitat (ID 21)

7) What are the contaminant concentrations in sanctuary habitats and how are they changing? 

limited data available to determine trends

PCBs, DDT, and other chlorinated pesticides 30 stations sampled as part of EMAP in 2003 (Partridge 

2007)

PAHs and metals in the sediment Washington State Department of Ecology 1995

Silver and chromium in sediments Long et al. 1995, O'Connor 2004

Chemical concentrations of contaminants in 

tissues in a variety of invertebrates and sea 

otters

NOAA’s Status and Trends, Mussel Watch Program (ID 

88); EMAP 2003 study; Brancato et al. 2006

tar balls on beaches and oil sheens noted during monthly beach surveys for dead seabirds 

(COASST monitoring data (ID 15))

deposition of atmospheric contaminants some air contaminant monitoring conducted in adjacent 

freshwater systems

8) What are the levels of human activities that may influence habitat quality and how are they changing?

bottom trawl effort WDFW and NMFS data

area subject to commercial trawling Shoji 1999; National Marine Fisheries Service data

visitation rates and locations in Olympic 

National Park on-going monitoring (Olympic National Park data)

other intertidal recreational harvesting 

activities haphazard and infrequently monitored

trampling and intertidal exploration Erickson 2005; not currently monitored

razor clam digs (harvesting activity) on-going monitoring (Erickson and Wullschleger 1998)

amount and location of marine debris on 

beaches annual beach cleanup event since 2000 (OCNMS data)

location and type of subtidal derelict fishing 

gear

one-time subtidal survey around Cape Flattery (OCNMS 

data); limited area of survey

rates of coastal development, road building, 

timber harvest anecdotal information

location and frequency of military operations broad area information only; no details on types of 

operations

location and frequency of underwater noise 

generation monitoring data not available
Table 7

36

Questions Indicators Source

location and intensity of vessel traffic vessel traffic monitoring (Canadian vessel traffic system; 

Marine Exchange of Seattle)

Living Resources

9) What is the status of biodiversity and how is it changing?

No monitoring of biodiversity except in the intertidal 

portion of the OCNMS

biodiversity in the rocky intertidal monitored at sites in ONP since 1989 (Olympic National 

Park data and OCNMS data (ID 35)); Dethier 1995

abundance of harbor seals On-going monitoring by WDFW (Jeffries et al. 2003)

abundance of sea otters on-going collaborative monitoring program (WDFW, 

USFWS, and OCNMS data (ID 25)); Lance et al. 2004

seabird abundance (especially Common 

Murre, Tufted Puffin, Marbled Murrelet, 

Cassin's Auklet, Brandt's Cormorant)

monitored during periodic flights and cruises (US Fish 

and Wildlife Service (ID 46) and OCNMS data (ID 42))

abundance of assessed fished stocks NMFS /PFMC stock assessments

fish species of concern no monitoring studies focused on population changes in 

sanctuary waters

abundance and distribution of listed marine 

bird and mammal species

some species monitored during periodic flights and 

cruises (US Fish and Wildlife Service (ID 46) and 

OCNMS data (ID 42))

biodiversity of deep water fish assemblages Rogers and Pikitch 1992, Jagielo et al. 2003; very limited 

monitoring

biodiversity in deep water invertebrate 

communities

Etnoyer and Morgan 2003, Morgan et al. 2006, Lumsden 

et al. 2007, Brancato et al. 2007 (ID 43); very limited 

monitoring

10) What is the status of environmentally sustainable fishing and how is it changing?

abundance of 22 groundfish species 

managed at the species level NMFS/PFMC stock assessments (PFMC 2008a)

other groundfish grouping or stock complexes assessed and managed in groupings or stock 

assessments not available or insufficient data available

abundance of groundfish species in OCNMS 

and/or off Washington state 

data collected and available (NWFSC Groundfish 

Surveys (ID 67)), but not analyzed at this spatial scale

Dungeness crab landings and number of 

license holders Washington Department of Fish and Wildlife data

pink shrimp landings and number of vessels 

in fishery Washington Department of Fish and Wildlife data

Pacific halibut spawning biomass off WA, OR, 

CA combined NMFS 2004

landings from ocean troll fishery for salmon 

off WA PFMC 2008b

11) What is the status of non-indigenous species and how is it changing?

abundance of Sargassum muticum ONP and OCNMS observations

range expansion of green crab collaborative monitoring program (OCNMS and other 

partners including Canada)

intertidal surveys OCNMS Rapid Assessment 2001-2002

monitoring for invasives one-time snapshot in 2005 using settlement plates 

(deRivera et al. 2005); OCNMS monitoring

12) What is the status of key species and how is it changing?

abundance of 5 seabird species of concern

monitoring along Washington coast (WDFW data; Wahl 

and Tweit 2000, Manuwal et al. 2001, Warheit and 

Thompson 2003, Wahl et al. 2005, Raphael 2006; Lance 

et al. 2008)
Table 7

37

Questions Indicators Source

abundance of sea otters annual census since 1989 (ID 25) (Jameson and Jeffries 

2008)

abundance of deep sea coral and sponge 

communities

OCNMS data primary source (ID 43); aerial extent of 

monitoring is limited

regional abundance of groundfish stocks few stock assessments are completed at the regional 

level

13) What is the condition or health of key species and how is it changing?

pathogens and chemical contaminants in sea 

otters Brancato et al. 2006

contaminant loads in killer whales Ross et al. 2000, Ross 2006

genetic variability in sea otters Larson et al. 2002

age structure in rockfish PFMC 2008a; data not available for all species

mortality and reproductive rates of Common 

Murres Parrish et al. 2001, Warheit and Thompson 2003

beach-cast seabirds COASST monitoring data since 1999 (ID 15), Hass and 

Parrish 2000

nesting success in Marbled Murrelets Raphael and Bloxton 2008

14) What are the levels of human activities that may influence living resource quality and how are they changing?

shipping traffic frequency and location/risk of 

oil spill

vessel traffic monitoring (Canadian vessel traffic system; 

Marine Exchange of Seattle); Washington Dept. of 

Ecology data

location and intensity of fishing activity National Marine Fisheries Service and Washington 

Department of Fish and Wildlife data
Table 8

38

Table 8. Datasets used to assess the current condition of water, habitat, and living resources as 

identified in the condition report for the Cordell Bank National Marine Sanctuary (ONMS 

2009b). References listed in this table can be found in the “Cited Resources” section of the 

CBNMS condition report. Blue Text = lack of information noted in report. Green Text = 

Project ID # from Appendix 1

Questions Indicators Source

Water

1) Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water 

quality?

salinity, water temperature, fluorescence 

chlorophyll-a levels, stratification

Cordell Bank Ocean Monitoring Program (CBOMP) 

monthly cruises (ID 19) unpubl. data

satellite-based SST (AVHRR), chlorophyll-a 

levels (SeaWiFS) and turbidity (SeaWiFS) 

assessed for 1997-2004

Stumpf et al. 2005

upwelling index, regional buoy data (not 

specific to CBNMS) Peterson et al. 2006

terrestrial-based floating debris and trash CBOMP monthly cruises (ID 19) unpubl. data

compounds in treated wastewater (e.g., 

pharmaceuticals, personal care products, 

household chemicals) 

concern, but no data available

2) What is the eutrophic condition of sanctuary waters and how is it changing?

monthly chlorophyll-a levels 1997-2008 1997-2004 in Stumpf et al. 2005; 2004-present 

CBOMP monthly cruises (ID 19) unpubl. data

chlorophyll-a and presence of HABs

CBOMP monthly cruises (ID 19) collects samples; 

samples analyzed by and data available from 

California Department of Health Services

3) Do sanctuary waters pose risks to human health?

HABs [dinoflagellate Alexandrium catenella, 

diatom Pseudonitzschia spp] 

CBOMP monthly cruises (ID 19) collects samples; 

samples analyzed by and data available from 

California Department of Health Services

discharges from cruise ships concern, but no data available

4) What are the levels of human activities that may influence water quality and how are they changing?

Large vessel traffic (1999-2005) USCG Automatic Identification System unpubl. data

discharges from large vessels and cruise ships no data available

Habitats

5) What is the abundance and distribution of major habitat types and how is it changing?

High resolution backscatter and bathymetry 

data

California State University Monterey Bay - Seafloor 

Mapping Lab (CSUMB-SFML) (ID 17); not enough 

data to determine trend

benthic communities, habitats, derelict fishing 

gear

Habitat Characterization and Biological Monitoring of 

Cordell Bank submersible surveys 2001-2005 (ID 77); 

CBNMS continental shelf soft bottom community 

characterization camera sled surveys 2004, 2007 (ID 

37)

6) What is the condition of biologically-structured habitats and how is it changing?

benthic communities, habitats; derelict fishing 

gear

Habitat Characterization and Biological Monitoring of 

Cordell Bank submersible surveys 2001-2005 (ID 77); 

CBNMS continental shelf soft bottom community 

characterization camera sled surveys 2004, 2007 (ID 

37); not enough data to determine a trend

7) What are the contaminant concentrations in sanctuary habitats and how are they changing?

contaminants (e.g., DDT, PCB, PAH) in 

sediments (limited samples from shelf and I. Hartwell, unpublished data
Table 8

39

Questions Indicators Source

slope in CBNMS and Bodega Canyon)

contaminants in benthic habitats

Very limited data; further work is needed to 

understand contaminant levels, transport pathways, 

and changes in contaminant concentrations over time

8) What are the levels of human activities that may influence habitat quality and how are they changing?

Fishing with bottom-tending fishing gear no monitoring data available

Living Resources 

9) What is the status of biodiversity and how is it changing?

seabird population size, migratory species 

population size, local breeding colony size, 

mortality rates and reproductive success rates 

shipboard monitoring of seabirds during NMFS 

rockfish recruitment cruises (data published in Ainley 

and Hyrenbach 2007), Sydeman et al. 2006

marine mammals stock assessments Carretta et al. 2007

distribution of marine mammal in CBNMS

CBOMP monthly cruises (ID 19) unpubl. data, PRBO 

Conservation Science at-sea monitoring unpubl. data 

(ID 81); Peterson et al. 2006

krill abundance

Peterson et al. 2006; PRBO Conservation Science atsea monitoring (ID 81), Sydeman et al. 2006, 

Jahncke et al. 2008

Abundance of groundfish stocks NMFS/PFMC stock assessments (PFMC 2006)

Abundance of pelagic juvenile rockfish Peterson et al. 2006; S. Ralston, unpubl. data, 

SWFSC Rockfish Recruitment Surveys

Rockfish fish assemblage

Baskett et al. 2006; Habitat Characterization and 

Biological Monitoring of Cordell Bank submersible 

surveys 2001 - 2005 (ID 77); Anderson et al. 2009

reef-top invertebrates shallower than 60 m photos from 1970s (Schmieder 1991) and 2005 (ID 

77; CBNMS unpubl. data)

soft bottom invertebrates

limited data on continental shelf (CBNMS camera 

sled surveys 2004, 2007 (ID 37)), no data for 

continental slope invertebrates

pelagic invertebrates (including Humboldt 

squid) Zeidberg and Robison 2007

10) What is the status of environmentally sustainable fishing and how is it changing?

impacts of long lines, gillnets and bottom trawls 

on seafloor habitats and benthic organisms 

based on 20 submersible dives in 2002, CBNMS 

unpub data (ID 77)

11) What is the status of non-indigenous species and how is it changing?

Abundance of non-indigenous species Currently no monitoring data

Comprehensive inventory of species within the 

sanctuary Data needed

12) What is the status of key species and how is it changing?

Cassin's Auklet Sydeman et al. 2006, Peterson et al. 2006, Goericke 

et al. 2007, Ainley and Hyrenbach 2007

Black-footed Albatross, Sooty Shearwater

world-wide trend (Naughton et al. 2007, U.S. Fish 

and Wildlife Service 2006); local distribution and 

abundance (Ainley and Hyrenbach 2007, PRBO 

Conservation Science unpubl. data (ID 81), CBOMP 

monthly cruises (ID 19) unpubl. data)

humpback whales, blue whale 

stock-wide trends (Carretta et al. 2007); region-wide 

distribution changes (Peterson et al. 2006, PRBO 

Conservation Science unpubl. data (ID 81), CBOMP 

monthly cruises (ID 19) unpubl. data)
Table 8

40

Questions Indicators Source

Abundance and distribution of California sea 

lion 

stock-wide trends (Carretta et al. 2007); local patterns 

(SWFSC Central California Aerial Surveys (ID 71), 

Lowry and Forney 2005, CBOMP monthly cruises (ID 

19) unpubl. data)

rockfish - abundance trends NMFS/PFMC stock assessments

species composition patterns Anderson et al. 2007

krill abundance PRBO Conservation Science at-sea monitoring (ID 

81), Sydeman et al. 2006, Jahncke et al. 2008

reef-top invertebrates shallower than 60 m photos from 1970s (Schmieder 1991) and 2005 (ID 

77; CBNMS unpubl. data)

leatherback turtle stock population trend and 

local distribution and abundance

worldwide trends (Spotila et al. 2000); local 

distribution and abundance (SWFSC Aerial Surveys 

along the Central California coast (ID 71), Benson et 

al. 2007)

Monthly monitoring of marine mammals and 

seabirds CBOMP monthly cruises (ID 19) unpubl. data

13) What is the condition or health of key species and how is it changing?

lesions on rockfish Okihiro et al. 1992

beach cast marine mammals and seabirds 

linked to HABs Scholin et al. 2000, Work et al. 1993

poor condition of seabirds, marine mammals 

and fishes (related to reduced ocean 

productivity resulting from anomalous 

conditions)

Sydeman et al. 2006

14) What are the levels of human activities that may influence living resource quality and how are they changing?

landings as indicator of fishing activity Scholtz et al. 2005

commercial vessels/month USCG AIS data

marine debris (such as plastics) CBOMP monthly cruises (ID 19) unpubl. data; not 

enough data to determine a trend
Table 9

41

Table 9. Datasets used to assess the current condition of water, habitat, and living resources as 

identified in the draft condition report for the Gulf of the Farallones National Marine Sanctuary 

(ONMS draft). References listed in this table can be found in the “Cited Resources” section of the 

GFNMS condition report. Blue Text = lack of information noted in report. Green Text = Project ID 

# from Appendix 1

Questions Indicators Source

Water 

1) Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting 

water quality?

sedimentation rates, period estero mouths are 

open vs. closed, salinity (Esteros Americano and 

de San Antonio)

Gold Ridge Resource Conservation District 

2007

salinity, sedimentation rates, tidal prism (Bolinas 

Lagoon) State Water Resources Control Board 2006

impaired water bodies State water board 303(d) listing

coliform and bacterial counts at beaches and 

estuaries

California Dept. Public Health, State Water 

Resources Control Board 2006

sedimentation rates and mercury concentration

area of eelgrass beds

chronic oil pollution - oily tarballs and oiled birds on 

shoreline BeachWatch monitoring data (ID 54)

discharges of dredge spoil from transport barges GFNMS enforcement records

chemicals (DDT, PAHs, PCBs) in sediments Hartwell 2004, 2007, 2008; limited data - not 

enough data to determine a trend in estuaries

2) What is the eutrophic condition of sanctuary waters and how is it changing?

nutrient concentration, dissolved oxygen, 

eutrophication, shellfish contamination in Tomales 

and Bodega bays

Airamé 2003

not enough data to determine a trend in 

eutrophic condition for bays and estuaries

precursors of biotoxin-producing phytoplankton in 

water samples and domoic acid toxicity in shellfish

15 years of monitoring data, G. Langlois 

unpub. data. California Department of Public 

Health

3) Do sanctuary waters pose risks to human health?

presence of pathogens in commercial shellfish 

growing areas

monitoring since the mid-1980s (California 

Dept Public Health)

presence of pathogens in swimming areas monitoring for the last 7 years (CA Dept 

Public Health?)

number of shellfish harvesting closures California Department of Public Health data

not enough data to determine a trend in 

estuaries

bacteria counts at beaches, impaired water bodies 303(d) list, State Water Resources Control 

Board 2006

DDT, PAHs and PCBs in sediments Hartwell 2007, 2008

pollutant accumulation in upper trophic level 

organisms a concern, but no data available

4) What are the levels of human activities that may influence water quality and how are they changing?

nutrient and sediment loads in runoff from 

agriculture
Table 9

42

Questions Indicators Source

amount of mudflat and diked marshes in Bolinas 

Lagoon and Tomales Bay

amount of freshwater diversion

urbanization/development in watershed

number of vessel transiting sanctuary Harbor Safety Committee of the SF Bay 

Region 2007

discharges of oil - based on number of oiled wildlife 

and tarballs on outer coast beaches Beach Watch monitoring since 1993 (ID 54)

Habitats 

5) What is the abundance and distribution of major habitat types and how is it changing? 

sedimentation rates in estuaries

change in area of estuarine habitat types, including 

wetlands, eelgrass beds, marsh

volume of tidal prism in Bolinas Lagoon

volume of freshwater input into estuaries

number of harbor seals at haul-outs SEALS monitoring program, Tezak et al. 

2004

abundance of habitat-forming algae and surfgrass 

in rocky intertidal Tenera 2003, 2004; S. Kimura, pers. comm.

shoreline erosion rates (both short-term and longterm) Hapke et al. 2006

beach width Marin County Open Space District 2006

beach profile BeachWatch photo-documentation monitoring 

(ID 54)

number trawl tracks, sediment topography and 

structure, infaunal and epifaunal community 

composition in areas previously trawled

Engel and Kvitek 1998; Lindholm, pers. 

comm.; deMarignac et al. 2009

spills of dredge spoil from barges into GFNMS GFNMS data

location of radioactive waste sidescan and submersible surveys

radioactivity levels in sediments and fish Suchanek 1988, Lindsay 1992, Jones et al. 

2001, Karl 2001; more monitoring is needed

6) What is the condition of biologically-structured habitats and how is it changing?

area of eelgrass beds

California Department of Fish and Game 

2001; Gold Ridge Resource Conservation 

District 2007

abundance native oyster Kimbro and Grosholz 2006

distribution and abundance of beach wrack Beach Watch (ID 54); trend information not 

available

distribution and abundance drift algae

Sanctuary Ecosystem Assessment Surveys -

Pelagic Habitat (SEAS) (ID 28); not enough 

data to determine a trend

impact of trawling on biogenic habitat limited data, not enough data to determine a 

trend for coastal/offshore areas

7) What are the contaminant concentrations in sanctuary habitats and how are they changing?

limited data available to determine status and 

trend in estuaries

levels of mercury in clams Gassell et al. 2004

contaminants in marinas and boat-works in 

Tomales Bay and Bolinas Lagoon data needed

non-point source discharges of chemicals, metals, 

and sediments from SF Bay and Russian River SFPUC 2006
Table 9

43

Questions Indicators Source

concentration of DDT, PAHs, PCBs in sediments Hartwell 2007, Hartwell pers. comm.

organic pollutants (butyltin, chlordane, DDT, 

dieldrin, PAHs, and PCB) and metals (As, Cd, Cu, 

Hg, Ni, Pb , Sn, Zn) in mussels

Mussel Watch Program (ID 88) stations in 

Tomales and Bodega Bays, Kimbrough et al.

2008

limited data makes it difficult to determine a 

status for coastal and offshore habitats

8) What are the levels of human activities that may influence habitat quality and how are they changing?

road construction and maintenance activity levels

boating activity and number of moorings in 

Tomales Bay

location and intensity of fishing and mariculture 

activity

visitation rates at beaches

number of vessel transiting sanctuary Harbor Safety Committee of the SF Bay 

Region 2007

management and enforcement activities to reduce 

chronic oil pollution from sunken vessels and 

discharges of oily bilge water

amount of trawling/area open to trawling

intensity and frequency of road maintenance and 

coastal armoring

Living Resources 

9) What is the status of biodiversity and how is it changing? 

eelgrass abundance/area T. Moore, CDFG, pers. comm.

abundance of forage species such as pacific 

sardine, northern anchovy, pelagic juvenile rockfish

SWFSC Rockfish Recruitment surveys (S. 

Ralston, NMFS-SWFSC, unpubl. data)

breeding success of Cassin's Auklets Abraham 2007

seabird diet composition (krill abundance) Edgar 1997

abundance of sea otters, sea urchin, kelp; sea 

urchin fishery Paul Peilly, CDFG, pers. comm.

abundance of Steller sea lions, northern fur seals

10) What is the status of environmentally sustainable fishing and how is it changing?

aquaculture of oysters; harvest of clams, herring, 

rock crab, perch, halibut 

little information available on status of these 

populations in estuaries

local abundance of Common Murre Manuwal et al. 2001

bycatch of Common Murre, harbor porpoise, sea 

otters in gillnets

Manuwal et al. 2001, Forney 1999, Carretta 

et al. 2005

recreational fish landings and effort California Recreational Fisheries Survey

recreational landings of Humboldt squid no data available

abundance of pelagic juvenile rockfish SWFSC Rockfish Recruitment Surveys (S. 

Ralston, NMFS-SWFSC, unpubl. data, )

abundance of overfished rockfish species NMFS/PFMC stock assessments

number of vessel in the trawl fishery/trawling effort California Fisheries Information Systems 

2007

abundance of 5 abalone species Abalone Recovery and Management Plan

11) What is the status of non-indigenous species and how is it changing?

number of non-indigenous species in the estuaries Byrnes 2007

extent and geographic coverage of non-indigenous 

species

very little is known, no data to determine a 

trend in estuaries

abundance of native gobies USFWS 2005

abundance and distribution of Spartina alterniflora
Table 9

44

Questions Indicators Source

Abundance of green crab and mud snails

non-indigenous planktonic species little data available

abundance of striped bass Bennett, pers. comm.

monitoring in rocky intertidal limited data

12) What is the status of key species and how is it changing?

abundance of eelgrass limited data

abundance of tidewater goby USFWS 2005

abundance of Brandt

abundance of other key estuarine species including 

herring, leopard shark, bat ray, harbor seal, 

Brandt's Cormorant, Snowy Plover

10 species of mammal, 9 species of birds, 1 

species of reptile, 13 species of fish, 11 species of 

invertebrates, 5 species of plant

13) What is the condition or health of key species and how is it changing?

Mercury levels in fish

disturbance of harbor seals in Tomales Bay Tezak et al. 2005, SEALS monitoring

very little data on condition of key estuarine 

species

frequency of domoic acid events

toxin accumulation in pinniped and seabirds 

(organochlorines and domoic acid) as an indicator

gray whale weight S. Swartz, pers. comm.

seabird condition

pinniped population size

14) What are the levels of human activities that may influence living resource quality and how are they changing?

disturbance of harbor seals (clam digging, 

kayaking, boating) Tezak 2005

levels of poaching, boating, anchoring, visitation, 

trampling, oil spills, illegal discharges, runoff from 

agricultural and developed lands, upland 

hydromodification

disturbance at seabird colonies (low flying aircraft, 

boats, human on foot)

flushing of waste and ballast water from vessels

vessel traffic levels

vessel noise no recent data

vessel strikes of whales

impact of lights on crab fishing vessels no data

frequency of illegal discharges (dredge material, 

oily bilge water)

trawling effort

incidence of oiled of birds and mammals
Table 10

45

Table 10. Datasets used to assess the current condition of water, habitat, and living resources as 

identified in the condition report for the Monterey Bay National Marine Sanctuary (ONMS 2009c). 

References listed in this table can be found in the “Cited Resources” section of the MBNMS 

condition report. Blue Text = lack of information noted in report. Green Text = Project ID # from 

Appendix 1.

Questions Indicators Source

Water

1) Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water 

quality?

rates of sediment erosion and deposition Phillip Williams & Associates 1992; Monismith et 

al. 2005

dissolved oxygen levels Beck and Bruland 2000; LOBO (ID 12), Chapin et 

al. 2004

levels of organic matter accumulation ESTWPT 2007

species distribution related to water quality Ritter et al. 2008

waterbodies impaired by levels of pathogens, 

pesticides, sediments, dissolved oxygen, nutrients, 

heavy metals

list of impaired waterbodies (SWRCB 2006)

levels of nutrients and legacy agricultural 

pesticides (e.g., DDT) ESNERR et al. 2009; Phillips et al. 2002

levels of organophosphate pesticides and 

pyrethroid pesticides in coastal watersheds

Hunt et al. 2003, Anderson et al. 2006; Phillips et 

al. 2006

EPA Water Quality Index based on levels of 

dissolved oxygen, dissolved inorganic nitrogen, 

ortho-phosphate, chlorophyll, and water clarity in 

water, sediment and tissue samples

CCAMP monitoring program (ID 30); Sigala et al. 

2007

pollutant concentrations at coastal confluences of 

watersheds Conley et al. 2008

concentration of POPs (e.g., PCBs, PAHs, dieldrin, 

DDT) in rivers that drain to the sanctuary

CCLEAN monitoring program (ID 31); CCLEAN 

2006, 2007

concentration of emerging pollutants (e.g., 

pyrethroid pesticides, fire retardants (PBDEs), 

pharmaceuticals, and personal hygiene products)

a concern, but little information regarding 

presence or effects in the environment and no 

water quality standards have been developed

concentration of nutrients (e.g., nitrate, 

orthophosphate, urea) and POPs (e.g., PAHs, 

PCBs, dieldrin) in water samples

CCLEAN monitoring program (ID 31); CCLEAN 

2007

concentration of POPs (e.g., DDT, PCBs, PAHs) in 

sediments

Hartwell 2008; CCLEAN monitoring program (ID 

31); CCLEAN 2007, 2009

cumulative concentration of POPs and abundance 

of benthic fauna

CCLEAN monitoring program (ID 31); CCLEAN 

2007

concentration of POPs in sea otters Miller et al. 2007

temperature at surface and 60 m, nitrate 

concentration at 60 m, and chlorophyll 

concentration at surface, water column 

stratification 0-20 m

MOOS (ID 6), MBTS Program (ID 66); MBARI 

2006, Tanner 2006

biomass and taxonomic structure of phytoplankton Jester 2008; MBTS Program (ID 66 ); CIMT HAB 

monitoring data (ID 3)

2) What is the eutrophic condition of sanctuary waters and how is it changing?

levels of dissolved oxygen, nutrients list of impaired waterbodies (SWRCB 2006)

dissolved oxygen, chlorophyll-a, and nitrate 

concentrations Bricker et al. 1999, 2007

nitrate levels and turbidity (from phytoplankton 

biomass, suspended sediments)

CCAMP (ID 30), Conley et al. 2008; Elkhorn 

Slough NERR (ID 32), M. Los Huertos, pers. 

comm.

nitrate concentration Elkhorn Slough NERR (ID 32); Caffrey 2002; 

LOBO (ID 12), K. Johnson in prep
Table 10

46

Questions Indicators Source

ecological impacts of eutrophication at Elkhorn 

Slough limited data

waterbodies impaired by elevated nutrient levels list of impaired waterbodies (SWRCB 2006)

nutrient (nitrate, urea, orthophosphate, ammonia) 

concentration in river discharges and wastewater

CCLEAN monitoring program (ID 31); CCLEAN 

2006, 2007

HABs and freshwater runoff events and nutrient 

loading

Kudela and Chavez 2004, Kudela et al. 2008a, 

2008b

toxins in higher trophic level species Fritz et al. 1992, Scholin et al. 2000, Kreuder et al. 

2005, Jester 2008

concentration of urea Cochlan et al. 2008, Anderson et al. 2008

HABs caused by nutrient runoffs Scholin et al. 2000, Ryan et al. 2008

Fluorescence Line Height (FLH) = abundance and 

health of phytoplankton/red tide indicator

Moderate Resolution Imaging Spectrometer 

(MODIS) aboard the Aqua satellite; J. Ryan, 

unpublished monitoring data; Ryan et al. 2008

frequency, spatial extent, and duration of algal 

blooms in Monterey Bay

CIMT monitoring 2002-2006 (ID 3), CIMT 2006, 

Howarth 2008

number of stranded seabirds due to algal bloom Beach COMBERS (ID 2); Jessup et al. 2009

3) Do sanctuary waters pose risks to human health?

levels of pesticides, pathogens list of impaired waterbodies (SWRCB 2006)

DDT and other pesticides in bivalve tissue Phillips et al. 2002

levels of heavy metals and POPs in mussels NOAA's National Status and Trends' Mussel 

Watch program (ID 88) (Kimbrough 2008)

levels of organophosphate in water and toxicity to 

small crustaceans

ESNERR et al. 2009, Hunt et al. 2003, Anderson et 

al. 2004

number of beach warnings and closures Rickers and Peters 2006; NOAA 2008a

Levels of bacterial contamination at local beaches 

and in coastal lagoons

Santa Cruz County Surface Water Quality 

Monitoring Program (ID 33); Rickers and Peters 

2006

incidence of illness likely caused by water contact 

(e.g., earaches, gastrointestinal distress) in 

beachgoers

Santa Cruz County Department of Health (Rickers 

and Peters 2006)

estimated loading of E. coli and Enterococcus

bacteria to nearshore waters

CCLEAN monitoring program (ID 31); CCLEAN 

2007

concentration of chemical contaminants (e.g., 

dieldrin, DDT, PAHs, PCBs) in mussel tissue

CCLEAN monitoring program (ID 31); CCLEAN 

2007

Mercury concentration in tissue of fish and shellfish 

collected from coastal areas SWAMP (ID 41); SWAMP 2005

concentrations of particulate domoic acid and 

Pseudonitzchia at the Monterey Wharf J. Smith, MLML, unpubl. monitoring data

number of shellfish samples with PSP toxin levels 

above regulatory limits; PSP toxins detected in 

planktivorous fish

Jester 2008

contaminants (DDT, PCBs) in killer whales monitoring in Monterey Bay (Black et al. 2003)

contaminants (DDT, PCBs) in Black-Footed 

Albatross Finkelstein et al. 2006

contaminants (DDT, PCBs) in Califonria sea lion Kannan et al. 2004

mercury concentration in water and large pelagic 

fishes little monitoring data available

biotoxins in planktivorous fishes Fritz et al. 1992, Scholin et al. 2000, Jester 2008

domoic acid in beached birds and mammals Fritz et al. 1992, Scholin et al. 2000; Beach 

COMBERs data (ID 2)

4) What are the levels of human activities that may influence water quality and how are they changing?
Table 10

47

Questions Indicators Source

levels of non-point source pollution from 

agriculture, urbanization and other human activities limited data

levels of nutrients and legacy organochlorines 

pesticides in watershed wetlands ESNERR et al. 2009; Phillips et al. 2002

levels of organophosphate pesticides in watershed Hunt et al. 2003

levels of pyrethroid pesticides in watershed 

sediments Anderson et al. 2006; Phillips et al. 2006

alteration of sediment and freshwater flows (e.g., 

construction of levees, diversion of freshwater) Van Dyke and Wasson 2005

changes in water quality in response to 

management practices to reduce pollution sources limited data

nutrient loads from heavily cultivated watersheds CCLEAN monitoring program (ID 31); CCLEAN 

2007; Los Huertos et al. 2003

levels of regulation of non-point source 

contaminants

level of implementation of better management 

practices

sources of bacterial pollution (e.g., condition of 

sewer systems, stormwater drainage) County of Santa Cruz 2006

application of nutrient management practices Monterey County 2002

application of nutrient, pesticide, erosion, and 

irrigation management practices RWQCB 2007

frequency and persistence of algal blooms in 

Monterey Bay CIMT (ID 3)

nutrient loading from human activities Glibert et al. 1995, CIMT 2006 

number of deep draft vessels entering San 

Francisco Bay

Harbor Safety Committee of the San Francisco 

Bay Region 2007

deposition of oiled seabirds on beaches in MBNMS

monitored by BeachCOMBERS program (ID 2)

since 1997 (Nevins et al. in prep), PRBO 

monitoring program 1971-1985 (Nevins et al. 

2003)

oil slicks on water surface in MBNMS

recorded since 2001 during SWFSC Central 

California aerial surveys (ID 71) (K. Forney, 

NMFS-SWFSC, unpubl. data)

Habitats

5) What is the abundance and distribution of major habitat types and how is it changing?

relative abundance of estuarine habitat types Van Dyke and Wasson 2005, ESNERR unpubl. 

data

volume of exported sediment Sampey 2006

tidal prism volume Broenkow and Breaker 2005, Sampey 2006

bank erosion rates ESNERR Tidal Erosion Monitoring Program, Van 

Dyke and Wasosn 2005

mean cross sectional area of main channel Dean 2003, Malzone 1999

sediment composition of main channel Kvitek et al. 1996

abundance and distribution of fishes and 

invertebrates Yoklavich et al. 2002, Lindquist 2008

shoreline habitat type

NOAA-Office of Response and RestorationEnvironmental Sensitivity Index (Research 

Planning Inc. 2006)

rate of change of sandy shoreline habitat Hapke et al. 2006

percentage of shoreline that is armored California Coastal Commission 2005

location and impacts of burial of rocky intertidal and 

subtidal habitats MBNMS Rocky Shores Monitoring Project
Table 10

48

Questions Indicators Source

Erosion at the head of the Monterey Submarine 

Canyon Wong 2006

benthic habitat type - low resolution multibeam NOS

benthic habitat type - med and high resolution 

multibeam data

MBARI Monterey Bay Multibeam Survey (ID 20), 

CSUMB Seafloor Mapping Lab (ID 17), Fugro 

Pelagos International

benthic habitat type - sidescan sonar USGS U.S. Pacific Coast habitat mapping 

program (ID 47)

impacts to benthic habitat and associated species 

by submerged cable Kogan et al. 2006

abundance of microtopographic structures

Central California Habitat Characterization (ID 

37); deMarignac et al. 2009; Engel and Kvitek 

1998

trawling gear footprint PacFIN trawl logbook data 1997-2007 (from 

California Department of Fish and Game)

6) What is the condition of biologically-structured habitats and how is it changing?

abundance and distribution of eelgrass MacGinitie 1935; Zimmerman and Caffrey 2002; 

ESNERR unpubl. data

abundance and distribution of native oysters MacGinitie 1935; Heiman 2006; Heiman et al. 

2008

recruitment rates of juvenile oysters K. Heiman, unpubl. data

abundance and distribution of non-native tubeworm Heiman 2006, Heiman et al. 2008

abundance and distribution of subtidal structureforming species PISCO (ID 59), CRANE (ID 76), MBNMS rocky 

shores monitoring programs

aerial extent of kelp canopy CA Annual Kelp Surveys (ID 10)

abundance and distribution of rocky intertidal 

structure-forming species 

PISCO (ID 59) and MARINe (ID 91) monitoring 

programs, Pete Raimondi, pers. comm.

levels of human visitation and abundance and 

diversity of intertidal structure-forming species Tenera Environmental 2003

abundance and distribution of biologicallystructured habitats limited data available

distribution of structure-forming species on the 

continental shelf, slope and submarine canyons

MBARI ROV survey data (Jim Barry, unpublished 

data); NWFSC Groundfish Surveys (ID 67); NMFS 

2004; Central California Habitat Characterization 

(ID 37)

occurrence of deep-sea corals Etnoyer and Morgan 2003, Morgan et al. 2005

distribution of cold seep communities MBARI ROV surveys of cold seeps (Barry 1996, 

Paull 2005)

species composition on whale falls Monitoring of whale falls in Monterey Bay 

(Goffredi et al. 2004)

extent of trawling footprint PacFIN trawl logbook data (from California 

Department of Fish and Game)

impacts of trawling and other human activities little data available

7) What are the contaminant concentrations in sanctuary habitats and how are they changing?

distribution and concentration of contaminants in 

Elkhorn Slough and Monterey Bay area literature review (Hardin et al. 2007)

concentrations of dieldrin, DDT and PCB in 

mussels from Elkhorn Slough and Moss Landing Hardin et al. 2007

concentration of DDT and contaminants in Caspian 

Tern eggs and embryos Parkin 1998

toxicity of sediments in Moss Landing Harbor to 

crustaceans

Anderson et al. 2004

concentration of POPS (e.g., PCB, DDT, 

chlordane) and metals (e.g., arsenic, mercury, 

lead) in sediment and tissue samples from harbors

CCAMP monitoring program (ID 30); Sigala et al. 

2007
Table 10

49

Questions Indicators Source

concentration of contaminants (e.g., oxychlordane, 

DDT, PCBs) in sand crabs Dugan et al. 2005

concentration of DDT in mussels CCLEAN monitoring program (ID 31); CCLEAN 

2006

concentration of POPs in stranded sea otters California Department of Fish and Game study 

from 2000-2005 (Miller et al. 2007)

concentration of POPs (e.g., DDT, dieldrin, PAH, 

PCB) in sediment samples from shelf, slope and 

canyon habitats

CCLEAN monitoring program (ID 31); CCLEAN 

2009, Hartwell 2008, Paull et al. 2002

impacts of contaminants in sediments on living 

resources

limited data available

abundance of infaunal species and cumulative 

concentration of POPs

CCLEAN monitoring program (ID 31); CCLEAN 

2006

POPs in demersal fish and invertebrate samples Froescheis et al. 2000, Looser et al. 2000

8) What are the levels of human activities that may influence habitat quality and how are they changing?

changes in land use practices to decrease inputs 

from agricultural fields ESNERR et al. 2009

land acquisition for conservation or restoration ESNERR et al. 2009

acres under cultivation ESNERR et al. 2009

levels of human visitation at rocky intertidal sites Tenera Environmental 2003

levels of human harvesting of mussels PISCO (ID 59) and MARINe (ID 91) monitoring 

program, Pete Raimondi, pers. comm.

intensity and frequency of coastal armoring activity

location and volume of sand mining PWA 2008

volume of kelp harvested from beds in MBNMS CDFG Kelp Harvesters Monthly Reports

location and intensity of fishing with trawl gear PacFIN trawl logbook data 1997-2007 (from 

California Fish Landings)

installation of submerged cables MBNMS submerged cable permitting information 

impacts of ATOC/Pioneer Seamount cable Kogan et al. 2006

distribution, abundance and composition of benthic 

marine debris in Monterey Bay surveyed in 1993-1994 (Watters et al. 2008)

distribution and abundance of pelagic marine 

debris no data available

Living Resources

9) What is the status of biodiversity and how is it changing?

overall native species richness (including plants, 

algae, fish, birds, invertebrates) and biodiversity Caffrey et al. 2002

loss of once common invertebrate species comparison of historical accounts to recent 

surveys (summarized in Wasson et al. 2002)

biodiversity in benthic invertebrate fauna (including 

sediment cores) Wasson et al. 2002

relative abundance of prey organisms in the 

stomachs of benthic foraging fish Lindquist 1998

relative abundance of clam species Oliver et al. unpublished data

relative abundance of large fish and mammalian 

predators Yoklavich et al. 2002, Harvey 2002

relative abundance and biodiversity of fish Yoklavich et al. 1991, Oxman 1995

fish assemblages in different habitat types Yoklavich et al. 2002

biodiversity in the rocky intertidal Wasson et al. 2005; PISCO (ID 59) and MARINe 

(ID 91) monitoring data, P. Raimondi pers. comm.

composition of intertidal community in relation to 

black abalone abundance

PISCO (ID 59) and MARINe (ID 91) monitoring 

data (Miner et al. 2006)
Table 10

50

Questions Indicators Source

relative abundance of fish species Starr et al. 2004, PISCO (ID 59) subtidal 

monitoring data, M. Carr pers. comm.

biodiversity in the rocky subtidal and kelp forest PISCO (ID 59) monitoring data

relative abundance of shallow subtidal fishes inside 

and outside marine reserves PISCO (ID 59) monitoring data

rockfish recruitment levels SWFSC rockfish recruitment surveys; PISCO (ID 

59) monitoring data 

species distribution along the coast Lonhart and Tupen 2001

biodiversity in subtidal soft bottom MLML 2006; very limited data

abundance of sand crabs LiMPETS program data (ID 48), George 2008

abundance of marine mammal stocks NMFS stock monitoring and assessments (Angliss 

and Allen 2009, Carretta et al. 2008)

abundance of locally breeding seabirds

Goericke et al. 2007; PRBO Conservation 

Science breeding colony monitoring (including 

surveys on SE Farallon)

abundance of Sooty Shearwater Ainley and Hyrenbach, unpubl. seabird data from 

SWFSC rockfish recruitment surveys

abundance of Marbled Murrelets in central 

California Peery et al. 2008

relative abundance of groundfishes (e.g., flatfishes, 

cartilaginous fishes, rockfishes)

Levin et al. 2006 based on NWFSC Groundfish 

Surveys (ID 67)

abundance of jumbo squid Field et al. 2007 based on SWFSC rockfish 

recruitment survey

relative abundance of jumbo squid and Pacific 

hake

Zeidberg and Robison 2007 based on MBARI 

ROV mid-water monitoring data

composition and distribution of midwater 

assemblage MBARI Midwater Ecology ROV surveys

composition and distribution of deep benthic 

assemblage MBARI Benthic Ecology ROV surveys

10) What is the status of environmentally sustainable fishing and how is it changing?

levels of take of shellfish and mudflat invertebrates Wasson et al. 2002; regulated by CDFG

abundance and distribution of elasmobranchs 

based on catch records from elasmobranch 

derbies

Carlisle et al. 2007

level of recreational hook -and-line fishing Yoklavich et al. 2002; limited data available

impacts of extraction no data available

local abundance of large, mobile species in areas 

open or closed to public access

PISCO (ID 59) and MARINe (ID 91) monitoring 

data

size frequency of large, mobile species in areas 

open or closed to public access

PISCO (ID 59) and MARINe (ID 91) monitoring 

data, Sagarin et al. 2007

levels of poaching of black abalone PISCO (ID 59) intertidal monitoring data, Pete 

Raimondi, pers. comm.

abundance of targeted nearshore fish stocks

stock assessments when available; stock 

assessments not available for many targeted 

nearshore fish stocks

local abundance of targeted species in open and 

closed areas

PISCO (ID 59) monitoring data; Mason 1998, 

Paddack and Estes 2000, Dorn 2002, Starr et al. 

2004

size frequency of targeted species in open and 

closed areas

Mason 1998, Paddack and Estes 2000, Dorn 

2002, Starr et al. 2004

impacts of reduced abundance on community and 

ecosystem function

Berkeley et al. 2004, Palumbi 2004, PISCO 2007; 

very little information available

market squid landings Porzio and Brady 2008

direct and indirect impacts of squid harvesting on 

the ecosystem very little information available
Table 10

51

Questions Indicators Source

population size of assessed groundfish stocks

groundfish stock assessments (various authors) 

based in part on NWFSC Groundfish Surveys (ID 

67) and SWFSC rockfish recruitment surveys

average body size of targeted rockfish species Steve Ralston, SWFSC, unpublished data based 

on data available in the California Fish Landings

abundance of Pacific hake stock assessment (Helser and Martell 2007)

population size of sardine and mackerel stocks NMFS stock assessments

population size of market squid and anchovy 

stocks CDFG/PFMC stock assessments

sustainability of Dungeness crab fishery Hankin et al. 2004 (no formal population 

assessment)

sustainability of spot prawn fishery Larson and Reilly 2008 (no formal population 

assessment)

abundance of benthic invertebrate fauna MBARI ROV survey data (Jim Barry, unpublished 

data)

Composition of the fish assemblage on the 

continental shelf and slope

Levin et al. 2006 based on NWFSC Groundfish 

Surveys (ID 67)

Fish assemblage composition and relative density 

of large and small bodied rockfish Yoklavich et al. 2000

Mean body size of harvested rockfish Mason 1998

11) What is the status of non-indigenous species and how is it changing?

number of non-indigenous, cryptogenic, and native 

invertebrate species in Elkhorn Slough Wasson et al. 2005

number of non-native fish species in Elkhorn 

Slough Yoklavich et al. 2002

relative abundance of native horn snail and 

Japanese mud snail Byers 1999, 2000

distribution and abundance of non-native tube 

worm and associated invertebrate assemblage Heiman et al. 2008

abundance and distribution of the European green 

crab ESNERR monitoring data

presence of non-indigenous species in the rocky 

intertidal one-time surveys (Wasson et al. 2005)

presence of non-indigenous species in the sandy 

and rocky intertidal, and sandy and rocky subtidal one-time surveys (Maloney et al. 2006)

amount of Undaria pinnatifida removed from 

Monterey Harbor S. Lonhart, MBNMS monitoring data

abundance and distribution of Japanese bryozoan 

Watersipora subtorquata, Asian kelp Sargassum 

muticum, and red algae Caulacanthus ustalatus

S. Lonhart, MBNMS monitoring program

presence of non-indigenous species in infaunal 

samples one-time surveys (Maloney et al. 2006)

12) What is the status of key species and how is it changing?

status of native oysters MacGinitie 1935; Heiman et al. 2008, Heiman 

2006; K. Wasson and K. Heiman, pers. comm.

status of eelgrass

MacGinitie 1935; Zimmerman and Caffrey 2002; 

analysis of aerial photographs (ESNERR 

unpublished data)

status of pickleweed salt marsh analysis of aerial photographs (ESNERR 

unpublished data), Zimmerman and Caffrey 2002

abundance of non-native species on native 

biodiversity Wasson et al. 2002

abundance of black abalone, mussels and 

structure-forming algae

PISCO (ID 59) and MARINe (ID 91) monitoring 

data
Table 10

52

Questions Indicators Source

trampling of algae and invertebrates Tenera 2003

status of subtidal kelp and sea urchins PISCO (ID 59) and CRANE (ID 76), and MBNMS 

monitoring data

abundance of rockfishes, cabezon, lingcod stock assessments when available

abundance of California sea otter California Sea Otter Surveys (ID 7)

abundance of Pismo clams Kim et al. 2006

status of sand dollars no available data

status of ornate tubeworm Diopatra ornate no available data

abundance of Sooty Shearwaters 

in Monterey Bay (Adams and Harvey 2006); in 

central California (Ainley and Hyrenbach, unpubl. 

seabird data from SWFSC rockfish recruitment 

surveys)

abundance of marine mammal stocks

Carretta et al. 2008, Angliss and Allen 2009; 

based on SWFSC Shipboard Cetacean Surveys 

(ID 60)

Steller sea lion population size NMFS stock assessments (Angliss and Allen 

2009)

Steller sea lion pup counts at Año Nuevo SWFSC Pinniped Aerial Surveys, M. Lowry, per. 

comm. 

Chinook salmon abundance

abundance of market squid Porzio and Brady 2008

relative abundance of phytoplankton groups MOOS (ID 6), MBTS Program (ID 66); Pennington 

et al. 2007

13) What is the condition or health of key species and how is it changing?

turbidity Elkhorn Slough NERR water quality monitoring 

program (ID 32); M. Los Huertos, pers. comm.

levels of contaminants Hardin et al. 2007

health of key estuarine species not being monitored, very little data available

trend in abundance of black abalone and incidence 

of withering syndrome at monitoring sites in central 

California

PISCO (ID 59) and MARINe (ID 91) intertidal 

monitoring data; Raimondi et al. 2002

trend in abundance of sea otters California Sea Otter Surveys (ID 7)

cause of death in beach cast southern sea otters Kreuder et al. 2003, Tinker et al. 2006

POPs in tissues of beach cast sea otters Miller et al. 2007

incidence of food limitation in southern sea otter 

population Tinker et al. 2006

domoic acid poisoning in sea lions Scholin et al. 2000

deposition of seabirds and mammals on area 

beaches BeachCOMBERS (ID 2) data

monitoring of pinnipeds entangled in synthetic 

materials

PRBO Conservation Science Monitoring data 

(Hanni and Pyle 2000)

number of stranded pinnipeds injured by 

entanglement in synthetic materials

Marine Mammal Center data (Goldstein et al. 

1999)

proportion of seabird carcasses with plastic in 

stomach

Beach COMBERS (ID 2) data, Nevins et al. 2005, 

Zabka et al. 2006, Phillips et al. 2007

contaminants in marine mammals, seabirds, and 

seabird eggs

Jarman et al. 1996, Calambokidis and Barlow 

1991, Black et al. 2003, Krahn et al. 2007, 

Finkelstein et al. 2006, Pyle 1999; lack of 

consistent monitoring and long-term data

14) What are the levels of human activities that may influence living resource quality and how are they changing?

land use, agriculture and development, in 

surrounding watershed
Table 10

53

Questions Indicators Source

run-off of nutrients and contaminants from 

agricultural activities Caffrey et al. 2002

levels of aquaculture in Elkhorn Slough area

boating activity in Moss Landing Harbor

harvest of living resources little data available

entrainment of fish and invertebrates larvae in 

power plant intake pipes Wasson, pers. comm.

human visitation to rocky intertidal Tenera 2003, PISCO (ID 59) and MARINe (ID 91)

monitoring data, P. Raimondi pers. comm.

extraction of rocky intertidal organisms PISCO (ID 59) and MARINe (ID 91) monitoring 

data, P. Raimondi pers. comm.

distribution and intensity of fishing effort

impacts of landslide-caused burial of intertidal and 

subtidal organisms CRANE (ID 76) monitoring data (Carr et al. 2006)

activities that impact sandy beach and subtidal: 

coastal armoring, sand mining, beach grooming, 

dredge disposal, discharge from outfalls, 

recreational use

location and intensity of fishing with trawl gear PacFIN trawl logbook data 1997-2007 (from 

California Fish Landings)

level of fishing with bottom contact fishing gear

level of bycatch of sensitive or protected species Forney et al. 2001

Number of commercial fishermen and fishing 

vessels MLPA 2005, CDFG 2007

Total Landings and total value MLPA 2005, CDFG 2007

volume and composition of trash in storm drains California Department of Transportation pilot 

study (CIWMB 2004)

volume and composition of trash on beaches U.S. Coastal Cleanup Day

length of submerged cables in MBNMS MBNMS submerged cable permitting information 

impacts of ATOC/Pioneer Seamount cable Kogan et al. 2006

impacts of increasing pH on living resources limited data

impacts of acoustic pollution on living resources NRC 2005; limited data
Table 11

54

Table 11. Datasets used to assess the current condition of water, habitat, and living resources as 

identified in the condition report for the Channel Islands National Marine Sanctuary (ONMS 

2009a). References listed in this table can be found in the “Cited Resources” section of the 

CINMS condition report. Blue Text = lack of information noted in report. Green Text = Project ID # 

from Appendix

Questions Indicators Source

Water

1) Are specific or multiple stressors, including changing oceanographic and atmospheric conditions, affecting water 

quality?

satellite images of sediment plumes from mainland 

rivers Otero and Siegel 2004

sediment toxicity

on-going monitoring by SCCWRP Southern 

California Bight Regional Surveys (ID 26), 

Bay et al. 2005

DDT in sediment

on-going monitoring by SCCWRP Southern 

California Bight Regional Surveys (ID 26), 

Schiff et al. 2006

DDT in birds Sydeman et al. 2001, on-going monitoring by 

Channel Islands National Park 

DDT in fish and other organisms Jarvis et al. 2007

intensity and length of Pseudo-nitzschia blooms Anderson et al. in press, Busse et al. 2006, 

Schnetzer et al. 2007

domoic acid mortality events Gulland 2000, Scholin et al. 2000

effects of global warming (e.g., sea level rise, 

changes in ocean chemistry, sea water temperature 

increases)

Not well understood

withering syndrome pathogen in red abalone CDFG 2007

2) What is the eutrophic condition of sanctuary waters and how is it changing?

nutrient input (from mainland streams/rivers)

On-going monitoring Santa Barbara Coastal 

Long Term Ecological Research Program (ID 

51), McPhee-Shaw et al. 2007

amount of nutrient enrichment (from island streams)

frequency and intensity of harmful diatom blooms Anderson et al. in press

nutrient inputs and HABs Schnetzer et al. 2007

3) Do sanctuary waters pose risks to human health?

number of human illnesses reported due to shellfish 

consumption

concentration of biotoxins in harvested shellfish Novelli et al. 1991

human fecal pollution in sanctuary waters

concentration of harmful bacteria (from vessel 

discharges)

Santa Barbara ChannelKeeper (ID 93), 

Altstatt 2007

4) What are the levels of human activities that may influence water quality and how are they changing?

number of cargo ship transits

effects of vessel discharges little information available

concentration of airborne contaminants from shipping 

traffic little information available

contaminants (e.g., DDT) in sediment

on-going monitoring by SCCWRP Southern 

California Bight Regional Surveys (ID 26), 

Schiff et al. 2006
Table 11

55

Questions Indicators Source

abundance of brown pelicans and bald eagles

Sydeman et al. 2001, Engle 2006, H. Carter 

personal communication 2007, on-going 

monitoring by Channel Islands National Park

satellite images of mainland runoff from agriculture 

and development Otero and Siegel 2004

Habitats

5) What is the abundance and distribution of major habitat types and how is it changing?

health of deep water habitats J. Engle (UCSB) personal communication 

2007; not well studied

area closed to fishing with bottom-tending gear

impacts of fish traps

impacts of marine debris

6) What is the condition of biologically-structured habitats and how is it changing?

abundance of giant kelp and understory habitatforming algae

Channel Islands National Park Kelp Forest 

Monitoring Program, Behrens and Lafferty 

2004, Lafferty 2004

abundance/health of deeper hard-bottom coral 

communities

J. Engle (UCSB) personal communication 

2007; not well studied

area closed to trawling and trapping

eelgrass abundance on-going monitoring, Engle and Miller 2005

frequency of recreational anchoring

mussel bed thickness, biomass, and community 

diversity Smith et al. 2006a, Smith et al. 2006b

7) What are the contaminant concentrations in sanctuary habitats and how are they changing?

DDT concentrations in sediments

on-going monitoring by SCCWRP Southern 

California Bight Regional Surveys (ID 26), 

Schiff et al. 2006

DDT influence on nesting birds

Channel Islands National Park on-going 

monitoring, Sydeman et al. 2001, Engle 2006, 

H. Carter personal communication 2007

area/geographic extent of plumes of suspended 

sediments Otero and Siegel 2004

illegal discharge from vessels no data available

frequency of vessel groundings

8) What are the levels of human activities that may influence habitat quality and how are they changing?

area closed to trawling and trapping activity in the 

CINMS

commercial and sport harvesting of community 

dominant species (historic and current)

marine debris Richards 1993, National Park Service marine 

debris surveys

illegal vessel discharges

anchoring

commercial and recreational fishing activities on-going monitoring, Senyk et al. 2008

visitation by non-consumptive users on-going monitoring, Senyk et al. 2008

enforcement of marine reserves

public awareness of marine reserve regulations
Table 11

56

Questions Indicators Source

number of boats/boating disturbance of wildlife

oil production and transport

Living Resources

9) What is the status of biodiversity and how is it changing?

abundance and size structure of key species (e.g., 

sheephead, kelp bass, rockfishes, shark, swordfish, 

lobster, abalone)

Channel Islands National Park Kelp Forest 

Monitoring Program, D. Richards personal 

communication 2007

biodiversity in kelp forest

Channel Islands National Park Kelp Forest 

Monitoring Program, D. Kushner personal 

communication 2007

fishing pressure Channel Islands National Park monitoring, D. 

Kushner personal communication 2007

abundance of kelp and eelgrass

Channel Islands National Park Kelp Forest 

Monitoring Program, J. Altstatt personal 

communication 2007, Engle personal 

communication 2007

abundance of urchins and brittle stars

Channel Islands National Park Kelp Forest 

Monitoring Program, J. Altstatt 2005, J. 

Altstatt personal communication 2007, J. 

Engle personal communication 2007

biodiversity (in areas dominated by brittle stars) J. Altstatt personal communication 2007

abundance and diversity of mussel bed communities Smith et al. 2006a, Smith et al. 2006b

10) What is the status of environmentally sustainable fishing and how is it changing?

location and intensity of gill netting

ghost fishing by lobster and fish traps

abundance of sea otter, sharks, giant sea bass, 

swordfish, rockfishes, abalone

on-going monitoring by CDFG, Leet et al. 

2001, Rogers-Bennet et al. 2004

size structure of red sea urchin, sheephead

Channel Islands National Park Kelp Forest 

Monitoring Program, D. Richards personal 

communication 2007

relative abundance of lobster, urchin, kelp

Channel Islands National Park Kelp Forest 

Monitoring Program, Behrens and Lafferty 

2004

abundance and distribution of anchovy and sardine 

(as prey for Brown Pelican)

bycatch rates of cormorants and alcids in gill nets

bycatch rates of pelicans in recreations fishing gear

rates of avian predation, nest abandonments, and 

collisions with lighted structures and vessels due to 

light pollution

significant gaps in our knowledge of fishery 

effects and basic life history that impede 

management

11) What is the status of non-indigenous species and how is it changing?

abundance and distribution of several algal species 

(including Undaria pinnatifida, Sargassum filicinum, 

and Caulacanthus ustulatus)

on-going monitoring, Miller et al. 2006

12) What is the status of key species and how is it changing?

relative abundance of echinoderms, kelp, lobster, and 

fishes (e.g., sheephead and rockfishes)

Channel Islands National Park Kelp Forest 

Monitoring Program, Lafferty and Kushner 

2000, Lafferty 2004, D. Kushner personal 

communication 2007
Table 11

57

Questions Indicators Source

giant seabass abundance Leet et al. 2001

distribution and abundance of giant kelp

Channel Islands National Park Kelp Forest 

Monitoring Program, Lafferty and Behrens 

2004

abundance of red abalone

abundance of sea otters

abundance of Brown Pelicans

abundance of Peregrine Falcons

abundance of Bald Eagles

abundance of Brandt's Cormorant

on-going monitoring, Capitolo et al. 2004 

unpublished data, as reported in CINMS 

Biogeographic Report

abundance of cormorant

abundance of Cassin's Auklet on-going monitoring, Carter et al. 2007

abundance of Xantus's Murrelets on-going monitoring, Whitworth et al. 2006

abundance of Ashy Storm-Petrels on-going monitoring, Wolf 2007

abundance of Tufted Puffins

abundance of fin whale, humpback whale, gray whale on-going monitoring, J. Calambokidis 

personal communication 2007

abundance of blue whales

on-going monitoring including Shipboard 

Cetacean Survey (ID 60), Barlow and Forney 

2007

13) What is the condition or health of key species and how is it changing?

withering syndrome disease in red abalone CDFG 2007

abundance of black abalone and incidence of disease

diseases in echinoderms

size structure of spiny lobster on-going monitoring, CINP unpublished data, 

D. Kushner personal communication 2007

abundance and size structure of sheephead and kelp 

bass

on-going monitoring, D. Kushner personal 

communication 2007

nest failure rates of Cassin's Auklet on-going monitoring, Carter et al 2007

timing of nesting of Xantus's Murrelets on-going monitoring, Whitworth et al 2006

nesting rates of Ashy Storm-Petrels on-going monitoring, Carter et al 2007

14) What are the levels of human activities that may influence living resource quality and how are they changing?

extraction rates for exploited species

number of recreational kayaker

trampling rates of nests and intertidal animals

amount of recreational boating/anchoring

amount of shipping traffic

runoff/storm events on mainland - pollutants and 

marine debris
Table 12

58

Table 12. Observing datasets that are being used by one or more of the on-going ecosystem assessment efforts in the California Current 

Ecosystem. Datasets that are currently hosted by PaCOOS (http://www.pacoos.org/DataMgt.htm) are indicated. A project identification number is 

provided for observing datasets identified by the West Coast Sanctuary Data Inventory project (see Appendix I). 

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

West Coast 

Observatories (WCObs)

WCObs deals with oceanographic data collected at the five west 

coast sanctuaries. The project began in 2004 and focuses on 

various data streams collected at instrument moorings.

X 1

Beach COMBERS Beach COMBERS (Coastal Ocean Marine Mammal & Bird 

Education and Research Surveys) uses volunteers to survey 

beached marine birds and mammals monthly at selected beach 

segments in central and southern portions of Monterey Bay 

sanctuary.

MB X 2

Center for Integrated 

Marine Technologies 

(CIMT)

CIMT simultaneously collected data on physical, chemical, and 

biological (from phytoplankton to marine mammals) via moorings, 

shipboard surveys, apex predator tagging and tracking, and 

satellite, aircraft, and land-based remote sensing in Monterey Bay 

from 2002-2007 and was built on a foundation of data collection 

initiated in 1997.

CTD & Chloro 

only MB X X 3

MBARI Ocean 

Observing System 

(MOOS)

Since 1989 Monterey Bay Aquarium Research Institute (MBARI) 

has operated a mooring observing system in Monterey Bay. X MB X 6

California Sea Otter 

Survey

Bi-annual aerial and land-based standardized surveys of Southern 

sea otters have been conducted in California (from Santa Barbara 

to Half Moon Bay) during late spring and early fall since 1983.

MB X 7

Naval Postgraduate

School HF Radar

HF radar hardware and software have allowed examination of 

circulation in Monterey Bay since 1994. X 8

WA Annual Kelp 

Surveys

Aerial photographs taken in the late summer are used to monitor 

maximum bed extent of floating kelp along the Strait of Juan de 

Fuca and outer coast in the Olympic Coast sanctuary. Data 

collected by Washington State Department of Natural Resources in 

1989-1992 and 1994-present.

X OC 9

CA Annual Kelp 

Surveys

Aerial photographs taken in the late summer have been used to 

monitor maximum bed extent of floating kelp along the California 

mainland coast. Data collected by California Department of Fish and 

Game in 1989 and 1999-present.

MB X 10

Land/Ocean 

Biogeochemical 

Observatory in Elkhorn 

Slough (LOBO)

The LOBO project uses in situ chemical sensors to determine 

chemical fluxes into, within, and out of Elkhorn Slough in the 

Monterey Bay sanctuary. The primary focus is to measure nutrients, 

such as nitrate, ammonium, and phosphate. Data collected since 

2003.

MB 12

Coastal Observation 

and Seabird Survey 

Team (COASST)

COASST, which began in 1999, uses volunteers to survey beached 

marine birds at selected beach segments in Washington and 

northern Oregon. Beach segments are surveyed either monthly or 

2006 data only OC 15
Table 12

59

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

every two weeks.

CSUMB Seafloor 

Mapping Lab (SFML)

The CSUMB SFML specializes in high-resolution acoustic remote 

sensing for coastal habitats. Data collection in coastal California 

began in 1993.

CB, MB 17

OCNMS Habitat 

Mapping

In August 2004 and May and July 2005, OCNMS imaged several 

regions of the sea floor in the northern OCNMS. Video from a towed 

camera sled, bathymetry data, sedimentary samples and side scan 

sonar mapping were integrated to describe geological and biological 

aspects of habitat.

X OC 18

Cordell Bank Ocean 

Monitoring Program 

(CBOMP)

A monthly census of birds, marine mammals, krill and physical 

oceanographic conditions in the CBNMS began in 2004. Data 

collection methods were designed so that data could be integrated 

with CIMT.

CB 19

MBARI Monterey Bay 

Multibeam Survey

In June 1998 MBARI completed surveys of selected areas of the 

Monterey Bay sanctuary and surrounding features using a 

multibeam echo sounder.

MB 20

Essential Fish Habitat 

(EFH)

The EFH data set contains physical seafloor characteristics 

considered important for identifying essential habitat for groundfish. 

Seafloor feature data sets include side-scan sonar, bottom samples, 

seismic data, and multibeam bathymetry. The Active Tectonics and 

Seafloor Mapping Lab, College of Oceanic and Atmospheric 

Sciences, Oregon State University developed the data for Oregon 

and Washington. The Center for Habitat Studies, Moss Landing 

Marine Laboratories developed the data for California.

X OC X X 21

OCNMS multi-agency 

census of sea otters

Monitoring the sea otter population in Washington state since 1995. 

Annual surveys in July. OC 25

SCCWRP Southern 

California Bight 

Regional Surveys

Beginning in 1994 and repeating every 5 years, Southern California 

Coastal Water Research Project (SCCWRP) has led a consortium 

of 13 organizations in conducting a integrated, coordinated regional 

monitoring survey for the Southern California Bight. The surveys 

include measurement of chemistry, toxicity, benthic infauna, and 

fish assemblages at 261 sites between Point Conception and the 

Mexican border.

CI 26

Sanctuary Ecosystem 

Assessment Surveys 

(SEAS)

SEAS collect data on the abundance and distribution of bird, 

mammals, turtles, jellyfish, krill, vessel activities, harmful algal 

blooms, and location of surface fronts and convergent zones. 2005-

2008 annual 10 day cruise

GF 28

Central Coast Ambient 

Monitoring Program 

(CCAMP)

A water quality monitoring and assessment program for the central 

California region that began in 1998. MB 30
Table 12

60

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

Central Coast Long 

Term Environmental 

Network (CCLEAN)

A long-term regional monitoring program for central California that 

began in 2000. Water quality is monitored in watersheds that flow 

into coastal regions, in estuarine coastal confluences, and at coastal 

sites. Monitoring persistent organic pollutants in water and 

sediment, nutrients, pathogens, and suspended sediments in rivers.

MB X 31

National Estuarine 

Research Reserve 

(NERR) System-Wide 

Monitoring Program

Part of a system-wide long-term monitoring program that focuses on 

short-term variability and long-term changes in key properties of 

water quality. Monthly sampling in Elkhorn Slough since 1988 and in 

San Francisco NERR since 2005.

MB 32

Santa Cruz County

Surface Water Quality 

Monitoring Program

The Santa Cruz County Surface Water Quality Monitoring Program 

began in 1975, and is conducted by the Santa Cruz County 

Environmental Health Services Agency. Measures baseline water 

quality and identifies sources of water quality degradation in the 

marine and fresh waters of Santa Cruz County.

MB 33

OCNMS intertidal 

monitoring

Bi-annual monitoring of baseline information and trends over time 

for intertidal living resources along the Olympic Coast began in 

1996. Conducted by OCNMS and Olympic National Park.

OC 35

Central California 

Habitat Characterization

Starting in 2004, this project has been mapping the seafloor and 

characterizing habitats and associated benthic macroinvertebrates 

and fish assemblages in the three West Coast national marine 

sanctuaries.

MB, CB 37

Statewide Water 

Ambient Monitoring 

Program (SWAMP)

SWAMP data currently consists of field observations, discrete field 

measures and laboratory, bacteria indicators, and toxicity results for 

sediment and water samples throughout the state of California. 

Tissue, bioassessment (organisms and physical habitat) and time 

series data are being added to the database.

MB 41

OCNMS offshore 

cetacean and seabird 

surveys

Binocular and naked-eye surveys using ship-based line transects 

following permanent east-west tracklines; photo ID catalogue 

collected. Annual surveys in late May to July since 1995.

OC 42

Deep Sea Corals Expeditions to inventory deep sea corals from Olympic Coast NMS 

(in 2006) and the Davidson Seamount (in 2002 and 2006). OC 43

USFW seabird colony 

surveys

Annual surveys of seabird colonies in the Olympic Coast sanctuary 

conducted by USFW. OC 46

USGS Pacific Coast 

habitat mapping 

program

Various remotely-sensed data available for download. Primarily 

sidescan. X MB 47

Long-term Monitoring 

Program & Experiential 

Training for Students 

(LiMPETS)

The LiMPETS program began in 2002. Middle school, high school, 

and other volunteer groups monitor rocky intertidal and sandy shore 

areas in four of the west coast National Marine Sanctuaries. MB 48

Santa Barbara Coastal 

Long Term Ecological 

The primary research objective of the SBC LTER is to investigate 

the relative importance of land and ocean processes in structuring CI 51
Table 12

61

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

Research Program 

(SBC LTER)

giant kelp forest ecosystems. This monitoring program began in 

2000.

Beach Watch Beach Watch is a long-term shoreline monitoring project that was 

founded in 1993. Volunteers conduct monthly surveys of assigned 

beaches within the Gulf of the Farallones and Monterey Bay 

National Marine Sanctuaries. Data is collected on live and dead 

species of birds and marine mammals as well as oil pollution.

GF 54

Partnership for the 

Interdisciplinary Study 

of Coastal Oceans 

(PISCO)

PISCO conducts experiments & long-term monitoring of west coast 

nearshore ecosystems (e.g., rocky intertidal, kelp forest and rocky 

reef). Components include nearshore oceanography, larval 

dispersal, recruitment, physiology, ecological interactions, 

community structure. Began in 1999.

MB 59

SWFSC Shipboard 

Cetacean Survey

Survey to assess the abundance and distribution of marine 

mammals and to characterize the pelagic ecosystem off the U.S. 

West Coast out to a distance of approximately 300 nautical miles. 

Surveys occurred in 1991, 1993, 1996, 2001, 2005, and 2008. The 

2005 cruise, called the Collaborative Survey of Cetacean 

Abundance and the Pelagic Ecosystem (CSCAPE), was a 

collaboration with ONMS and included additional fine-scale surveys 

within the NMS boundaries.

CTD data only MB, CI X 60

California Cooperative 

Oceanic Fisheries 

Investigations 

(CalCOFI)

CalCOFI are a series of shipboard surveys along fixed transect lines 

off central and southern California to collect physical and chemical 

oceanographic data and to census populations from phytoplankton 

to avifauna. Began in 1949. Some transects are still sampled 

annually through a partnership including SIO, SWFSC and CDFG

Biological data: 

Phytoplankton, 

fish eggs and 

larvae only

X X 65

Monterey Bay Time 

Series (MBTS) Program

Shipboard measurements of physical, chemical and biological 

parameters are made during quarterly MBARI cruises. Data 

collection in Monterey Bay began in 1989. Data collection was 

expanded offshore into the California Current (along CalCOFI 

transect line 67) in 1997 under the name SECRET (Studies of 

Ecological and Chemical Responses to Environmental Trends). 

X MB X X 66

NWFSC Groundfish 

Surveys

Annual trawl groundfish surveys are conducted by NMFS NWFSC 

from the Canadian border to the Mexican border along the West 

Coast of the U.S. These surveys provide information about 

distribution, relative abundance, and age structure of important 

groundfish populations. Occurrence of structure-forming 

invertebrates in trawls is recorded when possible.

X OC, MB X X X 67

NOAA National Data 

Buoy Center (NDBC)

The NOAA NDBC collects recent and historical buoy data and 

observations from various types of buoys around the world, 

including the entire U.S. West Coast

X 68

Humboldt Line Survey Monitoring of ocean structure and the spatial distribution of plankton 

species including egg and larval stages of fish and select 

invertebrate species along a 60 nautical mile cross-shelf transect off 

Trinidad Head. Quarterly sampling by NOAA and Humboldt State 

69
Table 12

62

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

University starting April 2006.

SWFSC Central 

California Aerial 

Surveys

Aerial surveys to quantify the spatial and temporal distribution of 

marine mammals, seabirds and leatherback turtles in coastal waters 

of central California. Began in 1997.

CB X 71

Cooperative Research 

and Assessment of 

Nearshore Ecosystems 

(CRANE)

CRANE, which began in 2002, is a collaborative effort to gather 

data for fishery management and performance of marine protected 

areas in central and southern California. Data collection includes 

wide-scale survey of fish and invertebrate populations in shallow, 

rocky habitats accessible to divers (Monterey to San Diego, 

including the Channel Islands).

MB 76

Habitat Characterization 

and Biological 

Monitoring of Cordell 

Bank

In 2001, Cordell Bank sanctuary, in partnership with the SWFSC, 

USGS, and CDFG, initiated a long-term study to classify habitats 

and monitor fishes and macro-invertebrates on and around Cordell 

Bank. Underwater surveys of fishes, invertebrates, and their 

habitats are conducted on and around Cordell Bank using direct 

observation and video-transect methods from an occupied research 

submersible (Delta).

CB 77

Coastal Ocean Currents 

Monitoring Program 

(COCMP)

COCMP uses an integrated set of high frequency radar systems to 

measure and map surface currents over large areas of the coastal 

ocean in central and southern California.

Monterey Bay, 

San Francisco 

Bay and outlet

79

PRBO At-Sea Marine 

Mammal and Seabird 

Surveys

Surveys in the Gulf of the Farallones to determine the distribution 

and abundance of marine birds and mammals, to quantify the 

distribution and abundance of euphausiids and other bird/mammals 

prey, to characterize the zooplankton community in the upper water 

column, and to characterize the physical oceanographic conditions.

CB 81

Mussel Watch Program The NOAA National Status and Trends Mussel Watch Program 

monitors chemical contamination in the coastal United States. Since 

1986 mussels and oysters have been annually collected at more 

than 200 sites around the nation and analyzed for a suite of 

chemical contaminants.

OC, GF, 

MB X 88

Multi-Agency Rocky 

Intertidal Network 

(MARINe)

MARINe monitors sites along the Pacific Coast using two different 

approaches—target assemblage monitoring (biannually at 80 

locations in California and Oregon), and biodiversity community 

monitoring (less frequent at 91 locations from Alaska to Mexico). 

Sites are selected to provide data about different rocky habitats, 

different exposure variables, different public uses.

MB 91
Table 12

63

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

Santa Barbara 

Channelkeeper Stream 

Team monitoring 

program

Channelkeeper has run a volunteer-based water quality monitoring 

program - Stream Team - since 2001 in the Ventura River 

watershed (in partnership with the Ventura County chapter of the 

Surfrider Foundation), and since 2002 in the Goleta Slough 

watershed. Water quality is tested monthly at every major reach and 

junction to locate the 'trouble' spots.

CI 93

PRBO Snowy Plover 

monitoring

PRBO Conservation Science has two monitoring projects for Snowy 

Plover, one in Monterey Bay and one at Point Reyes. Since 1976, 

the Monterey project has monitored Snowy Plovers nesting in 

coastal habitats of Santa Cruz and Monterey counties. Since 1996, 

the Point Reyes project has been protecting and monitoring nesting 

Snowy Plovers within the Point Reyes National Seashore.

X 96

Line P Department of Fisheries and Oceans Canada (DFO) & others. 

Oceanographic sampling off British Columbia, Canada. 

Hydrography, nutrients and lower trophic level productivity is 

measured. Seabirds and marine mammals are also surveyed. Ongoing monitoring began in 1949.

X X

SWFSC Rockfish 

Recruitment Survey

NMFS-SWFSC and other collaborators have conducted annual midwater trawl surveys in the greater Gulf of the Farallones (Monterey 

Bay to Bodega Bay) region off central California. Hydrography and 

estimates of recruitment for young-of-the-year (age-0) Sebastes are 

priorities for this survey. On-going monitoring began in 1983. Data 

on abundance of seabirds and marine mammals is also collected.

CTD and 

Thermosal data 

only

CB, GF, 

MB X X

Southeast Farallon 

Island Seabird Ecology 

Surveys

Under contract with USFWS, PRBO Conservation Science monitors 

and studies the ecology of 12 seabird species and 5 pinniped 

species at this site. Daily measurements of SST, salinity, and 

weather are also made. On-going monitoring began in 1971.

CB, MB X

cenCA 

model 

only

X

Channel Islands 

Seabird Ecology 

Surveys

The California Center for Environmental Studies initiated research 

on Brown Pelicans in the Channel Islands in the late 1960s. In 

1985, the Channel Islands National Park initiated long-term studies 

of a variety of seabirds at Santa Barbara, Anacapa, and San Miguel 

islands. On-going monitoring began in 1968.

CI X

Vancouver Island 

Zooplankton

Since 1979, DFO Canada has measured zooplankton and 

hydrographic conditions on the Vancouver Island continental 

margin. 

X

Newport Hydrographic 

Line

Biweekly surveys of this line have been conducted by NMFSNWFSC off Newport, Oregon since 1996. Priorities for this survey 

include hydrography and zooplankton (copepods and euphausiids) 

and more recently seabirds.

hydrography 

data X X

Oregon and 

Washington Forage 

Fish

Hydrography, nutrients, chlorophyll-a, zooplankton and pelagic 

forage fish are sampled by NMFS-NWFSC at six stations along 

each of eight transects ranging from Newport, Oregon to the 

Washington-Canadian border. 1998 - present

X TBD
Table 12

64

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

Tatoosh Island Seabird 

Ecology Study

Studies of the breeding success and diet of seabirds that inhabit 

Tatoosh Island, WA, focused on Common Murres began in 1990 by 

University of Washington.

X

Triangle Island Seabird 

Ecology

Canadian Wildlife Service and Simon Fraser University are studying 

the breeding success and diet of the seabirds that inhabit Triangle 

Island. Focus on Rhinoceros Auklet and Cassin’s Auklet. On-going 

monitoring began in 1994.

X

SWFSC Pinniped Aerial 

Surveys Project

SWFSC conducts censuses of five species of pinnipeds.. Pups and 

other age/sex classes are counted from color photographs taken at 

rookeries and haulouts during aerial surveys of islands and the 

mainland coast of California.

MB X X

CINP Monitoring Subsurface temperature and biological monitoring data at numerous 

subtidal sites in the Channel Islands National Park (CINP).

Temp, kelp, 

inverts and fish 

data

CI

GLOBEC GLOBEC (Global Ocean Ecosystem Dynamics) was initiated in 

1991. Oceanographic data including temperature, salinity, oxygen, 

nutrients, phytoplankton, birds, cetaceans.

X X

World Ocean Database 

(WODB)

The World Ocean Database is a collection of scientifically qualitycontrolled ocean profiles from the National Oceanographic Data 

Center (NODC). This dataset contains measurements of 

temperature, salinity, oxygen, chlorophyll.

X

NOAA Habitat Use 

Database (HUD)

This NWFSC database Includes Fish Occurrence Details, Fish 

Species Details, Predators and Prey, References. X

West Coast Groundfish 

Observer Program

This NWFSC Observer Program conducts sampling of groundfish 

discarded by commercial fisheries along the entire continental U.S. 

West Coast. The seventeen species included in this data product 

are those of most interest to fisheries management and commercial 

fishing communities. Data available for both trawl and fixed gear.

X X

Integrated Acoustic and 

Trawl Surveys of Pacific 

Hake

Shipboard acoustic Doppler current profiler data collected by 

NWFSC during the Integrated Acoustic and Trawl Surveys of Pacific 

Hake, years: 1995, 1998, 2001, 2003, and 2005.

ADCP data only X

NGDC Coastal Relief 

Gridded database

The National Geophysical Data Center (NGDC) Coastal Relief 

model provides bathymetry from the coastal state boundaries to as 

far offshore as the NOS hydrographic data will support a continuous 

view of the seafloor.

X ?

WOCE World Ocean Circulation Experiment (WOCE) in-situ tide gauge 

data (data on sea level) as part of the Global Sea Level Observing 

System (GLOSS) network

X

POES Polar Operational Environmental Satellites (POES) provide ocean 

surface temperature data. X
Table 12

65

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

California Fish Landings Database includes commercial landings of fish and invertebrates 

caught off California and landed in California. Landing receipt data 

began in 1928. Includes PacFIN database which began in 1981. 

Also includes length and age compositions.

X MB X X X

SF-BEAMS The San Francisco Bay Environmental Assessment and Monitoring 

Station (SF-BEAMS) continuously monitors San Francisco Bay 

water quality and weather conditions at a location approximately 

200 ft offshore on the Romberg Tiberon Center pier. SF-BEAMS is 

part of CICORE.

X

COADS Comprehensive Ocean-Atmosphere Data Set (COADS) Project 

provides monthly time series (1854-1993) of atmospheric variables 

including SST, Sea Level Pressure, Wind.

X X

usSEABED usSEABED provides data from seafloor samples on sediment and 

rock distributions in the waters off the United States. Part of the 

USGS Coastal & Marine Geology Program

X

NMFS Cold Water

Corals

The location of some observations of cold-water/deep-sea corals off 

the west coast of the United States. Records of coral catch originate 

from bottom trawl surveys conducted from 1980 to 2001 by the 

Alaska Fisheries Science Center (AFSC) and 2001 to 2005 by the 

Northwest Fisheries Science Center (NWFSC).

X OC, MB

EPA Toxic Release 

Inventory

The EPA Toxics Release Inventory contains information on toxic 

chemical releases and waste management activities reported 

annually by certain industries as well as federal facilities. 

X

California Recreational 

Fisheries Survey 

(CRFS)

CRFS is a coordinated sampling survey designed to gather catch 

and effort data from anglers in all modes of marine recreational 

finfish fishing. It can be used to estimate total marine recreational 

finfish catch and effort in California

GF X

VOS Scheme World Meteorological Organization Voluntary Observing Ship (VOS) 

Scheme provides information on commercial shipping traffic 

patterns.

X

FAO Fisheries timeseriesThe Food and Agriculture Organization (FAO) of the United Nations 

Fisheries and Aquaculture department collects data on demersal 

and pelagic fisheries 

X

DOT Ferry Traffic Data on ferry traffic available from the state Department of 

Transportation (California and Washington) X

Shipping Tonnage data available from the US Army Corps of Engineers 

Navigation Data Center X

Oil Rigs Data available from Pacific States Marine Fisheries Commission X

Platts energy database Location of power plants and desalination plants. Provided by Platts 

(part of McGraw-Hill Companies) X
Table 12

66

Project Name Project Description

Available 

though 

PaCOOS 

ONMS 

SWiM 

Condition 

Reports

Module I, 

CCE IEA

Atlantis 

NCCE 

model

NCEAS 

CCME 

Human 

Impact 

Assessment

MBCO

RC 

Report 

Card

ID #

California Coastal 

Commission Public 

Education Program

Data on coastal pollution including marine debris (other than fishing 

gear) and oil, chemicals, etc. X

AVHRR Pathfinder 

Satellite data

Sea surface temperature data produced by NOAA’s National 

Oceanographic Data Center and the University of Miami’s 

Rosenstiel School of Marine and Atmospheric Science.

? X

Human access to 

beaches, intertidal

California: California Coastal Access Guide (MLPA); Oregon: 

Oregon Geospatial Enterprise Office; Washington: Washington 

State Department of Ecology BEACH (Beach Environmental 

Assessment, Communication and Health) Program

X

PDO index The Pacific Decadal Oscillation (PDO) index (1900-2006). Data 

courtesy Nate Mantua (Joint Institute for the Study of the 

Atmosphere and Ocean, UW). 

http://jisao.washington.edu/pdo/PDO.latest

X

MEI The Multivariate El Niño Index (MEI), 1950-2006. Data courtesy 

Klaus Wolter (NOAA-Earth System Research Laboratory). The MEI 

is a composite index constructed using 7 environmental variables. 

http://www.cdc.noaa.gov/people/klaus.wolter/MEI/table.html.

X

SWFSC Upwelling 

Index

The SWFSC Pacific Fisheries Environmental Laboratory generates 

indices of the intensity of large-scale, wind-induced coastal 

upwelling and along-shore transport at 15 standard locations along 

the west coast of North America.

X X x x
67

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appendices.

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Marine Sanctuary final management plan. U.S. Dept. of Commerce, National Oceanic and 

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Marine Sanctuary Management Plan / Final Impact Statement. U.S. Dept. of Commerce, 

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Atmospheric Administration, Office of National Marine Sanctuaries, Silver Spring, MD. 72pp. 

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Appendix 1

70

Appendix 1 - West Coast Sanctuary Data Inventory

A west coast sanctuary data inventory was built by identifying monitoring programs in the five west coast sanctuaries: Olympic Coast, 

Cordell Bank, Gulf of the Farallones, Monterey Bay, and Channel Islands National Marine Sanctuaries. Initial requirements for

inventory inclusion were subjectively based on (in no particular order) geographic range, monitoring frequency, duration, future 

longevity, variables measured, and ONMS participation. Since PaCOOS primarily seeks to integrate data from the relatively large area 

of the U.S. Pacific west coast Exclusive Economic Zone (EEZ; from shore out to 200 nautical miles), monitoring efforts with a small 

footprint were considered lower priority. Emphasis was placed on monitoring efforts that were multi-year with frequent data 

collection. Future longevity of a project was also a key consideration.

ONMS Site Biological data Physical data

ID Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile inverts

Adult inverts

Ichthyoplankton

Juvenile fish

Adult fish

Marine mammals

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents (ADCP)

Transmittance

Weather

Barometric pres

PAR

Wind

Wave direction

Aerial/sat photos

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

1 West 

Coast 

Observa

tories 

(WCObs

)

WCObs deals with 

oceanographic data 

collected at all five 

sanctuary sites located 

on the west coast. The 

project began in 2004 

and focuses on various 

data streams collected 

at instrument moorings.

1, 

2

x x x x x x x x x x x x

Turbidity, sigma-t

http://www.sanctuarysi

mon.org/regional_sect

ions/obs/

2 Beach 

COMBE

RS

Beach COMBERS 

(Coastal Ocean Marine 

Mammal & Bird 

Education and 

Research Surveys) 

uses volunteers to 

survey beached marine 

birds and mammals 

monthly at selected 

sections of beaches in 

the central and 

southern portions of the 

Monterey Bay 

sanctuary.

8 x x x x

tar balls

http://sanctuarysimon.

org/monterey/sections

/marineMammals/proj

ect_info.php?projectID

=100143&sec=mm
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

71

3 Center 

for 

Integrat

ed 

Marine 

Technol

ogies 

(CIMT)

CIMT simultaneously 

collected data on 

physical, chemical, and 

biological (from 

phytoplankton to marine 

mammals) via 

moorings, shipboard 

surveys, apex predator 

tagging and tracking, 

and satellite, aircraft, 

and land-based remote 

sensing in Monterey 

Bay from 2002-2007 

and was built on a 

foundation of data 

collection initiated in 

1997.

1, 

2, 

8, 

14, 

15

x x x x x x x x x x x x x

harmful algal blooms

http://sanctuarysimon.

org/monterey/sections

/oceanography/project

_info.php?projectID=1

00155&sec=o

4 R/V 

Fulmar 

and R/V 

Shearw

ater 

data 

logger

Weather and ocean 

surface variables 

measured continuously 

when the research 

vessel is moving 

greater than 1kt. Data 

collection began in 

2006.

1 x x x x x x x x x x

5 USGS 

Stream 

Gauge 

Network

The US Geological 

Survey Stream Gauge 

Network provides 

historical and real-time 

river/stream level and 

flow information.

2, 

5

x x x x x

flow rate

http://waterdata.usgs.

gov/nwis/rt

6 MBARI 

Ocean 

Observi

ng 

System 

(MOOS)

Since 1989 Monterey 

Bay Aquarium 

Research Institute 

(MBARI) has operated 

a mooring observing 

system in Monterey 

Bay.

1 x x x x x x x x http://www.mbari.org

/bog/Projects/MOO

S/default.htm
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

72

7 Californi

a Sea 

Otter 

Survey

Bi-annual aerial and 

land-based 

standardized surveys of 

Southern sea otters 

have been conducted in 

California (from Santa 

Barbara to Half Moon 

Bay) during late spring 

and early fall since 

1983.

12, 

15

x x x x x x http://sanctuarysimon.

org/monterey/sections

/marineMammals/proj

ect_info.php?projectID

=100172&sec=mm

8 Naval 

Postgra

duate 

School 

HF 

Radar

HF radar hardware and 

software have allowed 

examination of 

circulation in Monterey 

Bay since 1994.

1, 

2

x x http://www.oc.nps.nav

y.mil/~radlab/radar.ht

ml

9 WA 

Annual 

Kelp 

Surveys

Aerial photographs 

taken in the late 

summer are used to 

monitor maximum bed 

extent of floating kelp 

along the Strait of Juan 

de Fuca and outer 

coast in the Olympic 

Coast sanctuary. Data 

collected by 

Washington State 

Department of Natural 

Resources in 1989-

1992 and 1994-present.

9, 

12

x

kelp

x x http://www3.wadnr.go

v/dnrapp6/dataweb/m

etadata/dnr_kelp.htm

1

0

CA 

Annual 

Kelp 

Surveys

Aerial photographs 

taken in the late 

summer have been 

used to monitor 

maximum bed extent of 

floating kelp along the 

California mainland 

coast. Data collected by 

California Department 

of Fish and Game in 

1989 and 1999-present.

9, 

12

x x x

kelp

x x
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

73

1

1

MBARI 

cruise 

data

Monterey Bay Aquarium 

Research Institute 

(MBARI) vessels 

continuously record 

oceanographic 

variables.

1 x x x x

1

2

Land/Oc

ean 

Biogeoc

hemical 

Observa

tory in 

Elkhorn 

Slough 

(LOBO)

The LOBO project uses 

in situ chemical sensors 

to determine chemical 

fluxes into, within, and 

out of Elkhorn Slough in 

the Monterey Bay 

sanctuary. The primary 

focus is to measure 

nutrients, such as 

nitrate, ammonium, and 

phosphate. Data 

collected since 2003.

2, 

5, 

8

x x x x x x x x x x x x x

NO4, PO4

http://www.mbari.org/l

obo/

1

3

Structur

e of 

Populati

ons, 

Levels 

of 

Abunda

nce and 

Status 

of 

Humpba

cks 

(SPLAS

H)

SPLASH conducted a 

dedicated sampling 

program of humpback 

whales in the entire 

North Pacific from 

2003-2007. Subsequent 

analysis is determining 

a current estimate of 

overall abundance for 

the North Pacific 

(including estimates for 

specific wintering and 

feeding areas).

15 x x x x x x

skin and blubber

x x x http://www.cascadiare

search.org/SPLASH/s

plash.htm

1

4

Coastal 

Data 

Informat

ion 

Program 

(CDIP)/

Wave 

Rider 

buoys

CDIP was established 

in 1975 to measure, 

analyze, archive and 

disseminate coastal 

environmental data 

including wave models 

and forecasts for the 

United States.

1, 

2

x x x x x x x x x http://cdip.ucsd.edu/?

nav=recent&sub=obse

rved
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

74

15Coastal 

Observa

tion and 

Seabird 

Survey 

Team 

(COASS

T)

COASST, which began 

in 1999, uses 

volunteers to survey 

beached marine birds at 

selected sections of 

beaches in Washington 

and northern Oregon. 

Beach segments are 

surveyed either monthly 

or every two weeks.

8xxxxx http://coasst.org

16Network 

for 

Environ

mental 

Observa

tions of 

the 

Coastal 

Ocean 

(NEOC

O)

NEOCO, established in 

2001, is a observing 

network that monitors 

coastal oceanographic 

conditions. Active sites 

are Bodega Head, La 

Jolla, Newport Beach, 

Santa Barbara, and 

Santa Cruz. 

1, 

2, 

5, 8

xxxxxxxxx http://www.es.ucsc.ed

u/~neoco/instruments.

html

17Californi

a State 

Universi

ty 

Montere

y Bay -

Seafloor 

Mapping 

Lab 

(SFML)

The CSUMB-SFML 

specializes in high-

resolution acoustic 

remote sensing for 

coastal habitats. Data 

collection in coastal 

California began in 

1993.

4xxxxxxxxx http://seafloor.csumb.

edu/index.html

18OCNMS 

Habitat 

Mapping

In August 2004 and 

May and July 2005, 

OCNMS imaged 

several regions of the 

sea floor in the northern 

OCNMS. Video from a 

towed camera sled, 

bathymetry data, 

sedimentary samples 

and side scan sonar 

mapping were 

integrated to describe 

geological and 

biological aspects of 

habitat.

4xxxxx http://www.sanctuarie

s.noaa.gov/science/co

nservation/oc_mappin

g.html
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

75

1

9

Cordell 

Bank 

Ocean 

Monitori

ng 

Program 

(CBOM

P)

A monthly census of 

birds, marine mammals, 

krill and physical 

oceanographic 

conditions in the Cordell 

Bank NMS began in 

2004. Data collection 

methods were designed 

so that data could be 

integrated with CIMT.

1, 

14, 

15

x x x x x x x x x x x x http://sanctuarysimon.

org/cordell/sections/op

enOcean/project_info.

php?projectID=84&se

c=oo

2

0

MBARI 

Montere

y Bay 

Multibea

m 

Survey

In June 1998 Monterey 

Bay Aquarium 

Research Institute 

(MBARI) completed 

surveys of selected 

areas of the Monterey 

Bay sanctuary and 

surrounding features 

using a multibeam echo 

sounder.

4 x x x x http://www.mbari.org/d

ata/mapping/monterey

/default.htm

2

1

Essentia

l Fish 

Habitat 

(EFH)

The EFH data set 

contains physical 

seafloor characteristics 

considered important 

for identifying essential 

habitat for groundfish. 

Seafloor feature data 

sets include side-scan 

sonar, bottom samples, 

seismic data, and 

multibeam bathymetry. 

The Active Tectonics 

and Seafloor Mapping

Lab, College of Oceanic 

and Atmospheric 

Sciences, Oregon State 

University developed 

the data for Oregon and 

Washington. The 

Center for Habitat 

Studies, Moss Landing 

Marine Laboratories 

developed the data for 

California.

4 x x x x x x x http://www.nmfs.noaa.

gov/habitat/habitatprot

ection/efh/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

76

2

2

Tagging 

of 

Pacific 

Predator

s 

(TOPP)

Archiving tags collect 

data on the movements 

of pelagic nekton and 

seabirds in the North 

Pacific and record the 

physical conditions of 

their surroundings.

1, 

14, 

15

x x x x x x x x x

sea turtles

x x x x x http://www.toppcensu

s.org, 

http://sanctuarysimon.

org/monterey/sections

/marineMammals/proj

ect_info.php?projectID

=100137&sec=mm

2

3

Tracking 

Blackfooted 

Albatros

s

This project uses 

satellite tracking to 

explore the postbreeding movements 

and ocean habitats of 

Black-footed Albatross 

tagged in National 

Marine Sanctuaries off 

central California during 

summer / fall. Started in 

2004.

15 x x x x http://www.oikonos.or

g/projects/albatross.ht

m, 

http://sanctuarysimon.

org/monterey/sections

/birds/project_info.php

?projectID=100305&s

ec=ss

2

4

City of 

San 

Diego 

Ocean 

Monitori

ng 

Program

The City of San Diego's 

Ocean Monitoring 

Program has two 

distinct monitoring 

programs (beginning in 

2004): 1) the National 

Pollutant Discharge 

Elimination System 

mandated program 

surrounding the Point 

Loma Ocean Outfall, 

and 2) the monitoring 

program surrounding 

the South Bay Ocean 

Outfall. 350 sampling 

days per year from 2 

vessels

6, 

13

x x x x

bacterial samples

x x x x x

sediment, pH

http://www.sandiego.g

ov/mwwd/environment

/oceanmonitor.shtml

2

5

OCNMS 

multiagency 

census 

of sea 

otters

Monitoring the sea otter 

population in 

Washington state since 

1995. Annual surveys in 

July.

12, 

15

x x x
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

77

2

6

SCCWR

P 

Souther

n 

Californi

a Bight 

Regiona

l 

Surveys

Beginning in 1994 and 

repeating every 5 years, 

Southern California 

Coastal Water 

Research Project 

(SCCWRP) has led a 

consortium of 13 

organizations in 

conducting a integrated, 

coordinated regional 

monitoring survey for 

the Southern California 

Bight. The surveys 

include measurement of 

chemistry, toxicity, 

benthic infauna, and 

fish assemblages at 

261 sites between Point 

Conception and the 

Mexican border.

1, 

5, 

6, 

7, 

13, 

14

x x x x x x x x

toxicity, grain size

http://www.sccwrp.org

/view.php?id=545

2

7

El Nino 

Coastal 

Erosion 

study

NASA's Wallops Flight 

Facility, NOAA's 

Coastal Services 

Center, and the USGS 

Coastal & Marine 

Program surveyed 1200 

km of representative 

areas of the west coast 

both prior to and 

following the El Niño 

winter storms using 

scanning airborne laser 

altimetry to determine 

the magnitude, spatial 

patterns, and causative 

processes of El Niñoinduced change.

4 x x x x http://www.mbnmssimon.org/sections/ge

ology/project_info.php

?pid=100188&sec=g
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

78

2

8

Sanctua

ry 

Ecosyst

em 

Assess

ment 

Surveys 

(SEAS)

SEAS collect data on 

the abundance and 

distribution of bird, 

mammals, turtles, 

jellyfish, krill, vessel 

activities, harmful algal 

blooms, and location of 

surface fronts and 

convergent zones. 

2005-2008 annual 10 

day cruise

1, 

8, 

14, 

15

x x x x x x x x x

sounds

x x x x x x http://www.sanctuarie

s.noaa.gov/missions/2

006gfnms/welcome.ht

ml

3

0

Central 

Coast 

Ambient 

Monitori

ng 

Program 

(CCAM

P)

A water quality 

monitoring and 

assessment program 

for the central California 

region that began in 

1998.

5 x x x

various

http://www.ccamp.org/

3

1

Central 

Coast 

Long 

Term 

Environ

mental 

Network 

(CCLEA

N)

A long-term regional 

monitoring program for 

central California that 

began in 2000. Water 

quality is monitored in 

watersheds that flow 

into coastal regions, in 

estuarine coastal 

confluences, and at 

coastal sites. Monitoring 

persistent organic 

pollutants in water and 

sediment, nutrients, 

pathogens, and 

suspended sediments 

in rivers.

2, 

5, 

6, 

7, 

8

x x x x x x x x x

various

http://www.amarine.co

m/information/cclean/c

clean.html
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

79

32National 

Estuarin

e 

Researc

h 

Reserve 

(NERR) 

System-

Wide 

Monitori

ng 

Program

Part of a system-wide 

long-term monitoring 

program that focuses 

on short-term variability 

and long-term changes 

in key properties of 

water quality. Monthly 

sampling in Elkhorn

Slough since 1988 and 

in San Francisco NERR 

since 2005.

2, 5xxxxxxxx

various

http://www.elkhornslo

ugh.org/research/wate

rquality_stations.htm

33Santa 

Cruz 

County 

SWQM P

The Santa Cruz County 

Surface Water Quality 

Monitoring Program 

(SWQMP) began in 

1975, and is conducted 

by the Santa Cruz 

County Environmental 

Health Services 

Agency. Measures 

baseline water quality 

and identifies sources 

of water quality 

degradation in the 

marine and fresh waters 

of Santa Cruz County.

2, 5xxxxxxx

various

http://sccounty01.co.s

anta-cruz.ca.us/eh/

34Central 

Coast 

Watersh

ed 

Studies 

(CCoW

S)

CCoWS, which began 

in 2001, is conducting 

watershed and 

landscape ecological 

research and education 

that supports 

sustainable land 

management in 

California's Central 

Coast region.

2, 5xxxxxxx

various

http://ccows.csumb.edu/

35OCNMS 

intertidal 

monitori

ng

Bi-annual monitoring of 

baseline information 

and trends over time for 

intertidal living 

resources along the 

Olympic Coast began in 

1996. Conducted by 

OCNMS and Olympic 

National Park.

10xxx
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

80

3

6

Physical 

Oceano

graphic 

RealTime 

System 

(PORTS

)

PORTS provides realtime information to 

mariners, oil spill 

response teams, 

coastal managers, and 

others about San 

Francisco Bay water 

levels, currents, salinity, 

and winds. Includes 

nowcasts and 

predictions. 

NOAA/National Ocean 

Service CO-OPS

x x x x x x x

tides

http://tidesandcurrents

.noaa.gov/ports.html

3

7

Central 

Californi

a 

Habitat 

Charact

erization

Starting in 2004, this 

project has been 

mapping the seafloor 

and characterizing 

habitats and associated 

benthic 

macroinvertebrates and 

fish assemblages in the 

three West Coast 

national marine 

sanctuaries.

4, 

13

x x x x x x x x x http://www.mbnmssimon.org/sections/sa

ndyFloor/project_info.

php?pid=100237&sec

=sf

3

8

Plumes 

and 

Blooms 

(PnB 

Project)

The PnB project 

provides data on the 

Santa Barbara 

Channel's ever

changing environment, 

including temperature, 

salinity, chlorophyll 

concentrations, and 

phytoplankton blooms. 

Since 1996.

1, 

5, 

8

x x x x x x x x x x http://www.icess.ucsb.

edu/PnB/PnB.html
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

81

3

9

EPA 

Californi

a 

Coastal 

Project

Various projects 

throughout California: 

Sediment samples 

taken from 80 estuaries 

in 1999; sediment 

samples from 50 

stations in SF Bay 

taken in 2000; Los 

Angeles County 

dredging sediment 

samples taken since 

1997; continental shelf 

sediment samples 

taken around Southern 

CA bight in 1998; 

several others

x x x x x x x x x x http://www.sccwrp.org

/

4

0

CDFG/C

INP 

White 

abalone 

surveys

Surveys in the 1980's 12 x x x x

4

1

Statewid

e Water 

Ambient 

Monitori

ng 

Program 

(SWAM

P)

SWAMP data currently 

consists of field 

observations, discrete 

field measures and 

laboratory, bacteria 

indicators, and toxicity 

results for sediment and 

water samples 

throughout the state of 

California. Tissue, 

bioassessment 

(organisms and 

physical habitat) and 

time series data are 

being added to the 

database.

5, 

6, 

7

x x x

mussel tissue, bacteria

x x x x x

pH, sediment

http://www.swrcb.ca.g

ov/water_issues/progr

ams/swamp/
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

82

42OCNMS 

offshore 

cetacea

n and 

seabird 

surveys

Binocular and naked-

eye surveys using ship-

based line transects 

following permanent 

east-west tracklines; 

photo ID catalogue 

collected. Annual 

surveys in late May to 

July since 1995.

15xxxx

43Deep 

Sea 

Corals

Expeditions to inventory 

deep sea corals from 

Olympic Coast NMS (in 

2006) and the Davidson 

Seamount (in 2002 and 

2006).

9xxxxxxxx http://olympiccoast.no

aa.gov/research/resea

rch_feat/welcome.htm

44Sanctua

ry Aerial 

Monitori

ng and 

Spatial 

Analysis 

Program 

(SAMSA

P)

Aerial surveys over the 

Channel Islands NMS 

from 1999-2004 

primarily for looking at 

vessel use/traffic of all 

vessel, but marine 

mammal sightings are 

also taken.

15xx

x

45Coastal

LIDAR 

Collectio n

Light Detection and 

Ranging (LIDAR) is 

being used by NOAA 

and NASA scientists to 

document topographic 

changes along 

shorelines. LIDAR data 

collected along the U.S. 

west coast since 1997. 

2, 3xxxxxxhttp://www.csc.noaa.g

ov/crs/tcm/about_ldart

.html

46USFW 

seabird 

colony 

surveys

Annual surveys of 

seabird colonies in the 

Olympic Coast 

sanctuary conducted by 

USFW.

15xx

47USGS 

Pacific 

Coast 

habitat 

mapping 

program

Various remotely-

sensed data available 

for download. Primarily 

sidescan.

4xxxxxxx http://kai.er.usgs.gov/r

egional/contusa/westc

oast/
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

83

48Long-

term 

Monitori

ng 

Program 

& 

Experie

ntial 

Training 

for 

Student

s 

(LiMPE

TS)

The LiMPETS program 

began in 2002. Middle 

school, high school, and 

other volunteer groups 

monitor the rocky 

intertidal, sandy shore 

and offshore areas of 

the five west coast 

National Marine 

Sanctuaries.

10, 

11

xxxxx

algae

http://limpetsmonitorin

g.org/

49USGS 

Water 

Quality 

Monitori

ng

The USGS collects and 

analyzes chemical, 

physical, and biological 

properties of water, 

sediment and tissue 

samples from across 

the Nation. The 

NWISWeb discrete 

sample data base is a 

compilation of over 4.4 

million historical water 

quality analyses in the 

USGS district data 

bases through 

September 2005. 1958-

present.

xxxxxxx http://waterdata.usgs.

gov/nwis/qw

50Pacific 

Jets 

Experim

ent 

(PACJE

T)

The goal of PACJET

was to understand land-

falling winter storms 

and test the use of new 

observing systems to 

understand these 

storms and generate 

products to improve 

National Weather 

Service (NWS) 

predictions of rainfall 

and runoff. This project 

ran 3 storm seasons 

(2001-2003) in 

California and Oregon.

xxxxxxx

precip

http://www.etl.noaa.go

v/programs/2003/pacj

et/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

84

5

1

Santa 

Barbara 

Coastal 

Long 

Term 

Ecologic

al 

Researc

h 

Program 

(SBC 

LTER)

The primary research 

objective of the SBC 

LTER is to investigate 

the relative importance 

of land and ocean 

processes in structuring 

giant kelp forest 

ecosystems. This 

monitoring program 

began in 2000.

x x x x x

flow

http://sbc.lternet.edu/

5

2

Automat

ed 

Surface 

Observi

ng 

System

(ASOS)

ASOS stations are 

automated weather 

stations designed to 

provide pilots and 

meteorologists with 

near real-time weather 

conditions. This system 

began data collection in 

1998.

1 x x x http://www.weather.go

v/ost/asostech.html

5

3

Advanc

ed 

Global 

Atmosp

heric 

Gases 

Experim

ent 

(AGAG

E)

Continuous highfrequency gas 

chromatographic 

measurements of two 

biogenic/anthropogenic 

gases and five 

anthropogenic gases to 

determine the source 

and circulation. The 

stations are located at 

coastal sites around the 

world, with one site at 

Trinidad Head, 

California. 1995-

present.

x

atm gases

http://agage.eas.gatec

h.edu/
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

85

54Beach 

Watch

Beach Watch is a long-

term shoreline 

monitoring project that 

was founded in 1993. 

Volunteers conduct 

monthly surveys of 

assigned beaches 

within the Gulf of the 

Farallones and 

Monterey Bay National 

Marine Sanctuaries. 

Data is collected on live 

and dead species of 

birds and marine 

mammals as well as oil 

pollution.

8, 

11

xxxx

human activity, dog activity, live bird 

and mammal counts

xx

relevant stream conditions, tar balls

http://www.farallones.

org/volunteer/beach_

watch.htm

55Spatial 

Ecologic

al 

Analyse

s of 

Megave

rtebrate 

Populati

ons 

(SEAMA

P)

As part of Ocean 

Biological Information 

System (OBIS), 

SEAMAP is a digital 

database of marine 

mammal, seabird, and 

sea turtle distribution 

and abundance data. 

The web-based system 

allows the interactive 

display, query, and 

analysis of Digital 

Archive in conjunction 

with environmental 

data.

1xxxxxxxxxxxxx http://seamap.env.duk

e.edu/

56First 

Flush

First Flush is a 

volunteer water quality 

sampling program run 

by the Monterey Bay 

Sanctuary Citizen 

Watershed Monitoring 

Network. Beginning in 

2000, runoff has been 

sampled after the first 

rain each year at 12 

different sites in the 

cities of Monterey, 

Pacific Grove and 

Capitola, CA.

5xxx

pH

http://www.coastal-

watershed.org/Progra

ms/First_Flush/index.

htm
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

86

5

7

Montere

y Inner 

Shelf 

Observa

tory 

(MISO)

MISO is part of the 

Rapid Environmental 

Assessment Lab 

(REAL) at the Naval 

Postgraduate School in 

Monterey, California. 

The MISO instruments, 

which record nearshore 

oceanographic 

conditions, are located

on shore and 600m out 

from the beach adjacent 

to the Naval 

Postgraduate School at 

the southern end of 

Monterey Bay.

2 x x x x x x x http://www.oc.nps.nav

y.mil/~stanton/miso/

5

8

Bodega 

Marine 

Laborat

ory 

Coastal 

Observi

ng 

System 

(BMLCOS)

Meteorological and 

oceanographic 

conditions on the 

Bodega Marine 

Reserve and adjacent 

coastal waters have 

been continuously 

monitored since 1988.

1 x x x x x x x

CO

http://www.bml.ucdavi

s.edu/boon/

5

9

Partners

hip for 

the 

Interdisc

iplinary 

Study of 

Coastal 

Oceans 

(PISCO)

PISCO conducts 

experiments & longterm monitoring of west 

coast nearshore 

ecosystems (e.g., rocky 

intertidal, kelp forest 

and rocky reef). 

Components include 

nearshore 

oceanography, larval 

dispersal, recruitment, 

physiology, ecological 

interactions, community 

structure. Began in 

1999.

9, 

10, 

12, 

14

x x x x x x x x x x http://www.piscoweb.o

rg/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

87

6

0

SWFSC 

Shipboa

rd 

Cetacea

n 

Survey

Survey to assess the 

abundance and 

distribution of marine 

mammals and to 

characterize the pelagic 

ecosystem off the U.S. 

West Coast out to a 

distance of 

approximately 300 

nautical miles. Surveys 

occurred in 1991, 1993, 

1996, 2001, 2005, and 

2008. The 2005 cruise, 

called the Collaborative 

Survey of Cetacean 

Abundance and the 

Pelagic Ecosystem 

(CSCAPE), was a 

collaboration with 

ONMS and included 

additional fine-scale 

surveys within the NMS 

boundaries.

1, 

15

x x x x x x x x http://www.mbnmssimon.org/other/gen/p

roject_info.php?pid=1

00273&query=cscape

&form=kw

6

1

Aerial 

Monitori

ng of 

Kelp 

Canopy 

(CINMS

)

CINMS discontinued 

this monitoring program 

that surveyed 

presence/absence of 

kelp canopy. See 

CDFG kelp monitoring 

for on-going monitoring 

effort.

x x x

6

2

Montere

y Bay 

Cable 

Survey

Survey of infauna and 

epibenthic organisms 

for cable instillation, 10 

- 2,000 m Monterey Bay

x x
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

88

6

3

USGS 

SF Bay 

and 

Delta 

monitori

ng

The US Geological 

Survey (USGS) has 

continuously monitored 

suspended-solids 

concentrations, 

temperature, salinity, 

and water level at many 

sites throughout the 

San Francisco Bay and 

Delta since 1989. Data 

availability varies 

among the sites and is 

limited to time series 

between 1989 and 

2001. 

5 x x x

sediment

6

4

CoastW

atch

CoastWatch, a NOAA 

program that began in 

1979, collects remotely 

sensed satellite and 

other environmental 

data along the west 

coast. Data is provided 

to government decision 

makers and academic 

researchers.

1 x x x x x x x http://coastwatch.noaa

.gov/cw_index.html

6

5

Californi

a 

Coopera

tive 

Oceanic 

Fisherie

s 

Investig

ations 

(CalCO

FI)

CalCOFI are a series of 

shipboard surveys 

along fixed transect 

lines off central and 

southern California to 

collect physical and 

chemical 

oceanographic data and 

to census populations 

from phytoplankton to 

avifauna. Began in 

1949. Some transects 

are still sampled 

annually through a 

partnership including 

SIO, SWFSC, and 

CDFG

1, 

14

x x x x x x x x x x x x

PO4 NO3

http://www.calcofi.org l
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

89

6

6

Montere

y Bay 

Time 

Series 

(MBTS) 

Program

Shipboard 

measurements of 

physical, chemical and 

biological parameters 

are made during 

quarterly MBARI 

cruises. Data collection 

in Monterey Bay began 

in 1989 and was 

expanded offshore into 

the California Current 

(along CalCOFI 

transect line 67) in 

1997.

1, 

14

x x x x x http://www.mbari.org/b

og/Projects/secret/def

ault.htm

6

7

NWFSC 

Groundfi

sh 

Surveys

Annual trawl groundfish 

surveys are conducted 

by NFMS NWFSC from 

the Canadian border to 

the Mexican border 

along the West Coast of 

the U.S. These surveys 

provide information 

about distribution, 

relative abundance, and 

age structure of 

important groundfish 

populations. 

Occurrence of 

structure-forming 

invertebrates in trawls is 

recorded when 

possible.

13 x x x x http://www.nwfsc.noaa

.gov/research/division

s/fram/survey.cfm

6

8

NOAA 

National 

Data 

Buoy 

Center 

(NDBC)

The NOAA NDBC 

collects recent and 

historical buoy data and 

observations from 

various types of buoys 

around the world, 

including the entire U.S. 

West Coast

1 x x x x x x x x x x http://www.ndbc.noaa.

gov/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

90

6

9

Humbol

dt Line

Monitoring of ocean 

structure and the spatial 

distribution of plankton 

species including egg 

and larval stages of fish 

and select invertebrate 

species along a 60 

nautical mile cross-shelf 

transect off Trinidad 

Head. Quarterly 

sampling by HSU and 

SWFSC, starting April 

2006.

1 x x x x x x x x x www.pacoos.org

7

0

Remote 

Automat

ed 

Weather 

Stations 

(RAWS)

There are nearly 2,200 

interagency RAWS 

strategically located 

throughout the United 

States. These landbased stations collected 

meteorological data.

x x http://www.fs.fed.us/ra

ws/

7

1

SWFSC 

Central 

Californi

a Aerial 

Surveys

Aerial surveys to 

quantify the spatial and 

temporal distribution of 

marine mammals, 

seabirds and 

leatherback turtles in 

coastal waters of 

central California. 

Began in 1997.

15 x x x x x x
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

91

72REEF 

Volunte

er 

Survey 

Project

The Reef 

Environmental 

Education Fund (REEF) 

Volunteer Survey 

Project enlists volunteer 

SCUBA divers and 

snorkelers to collect 

and report information 

on marine fish 

populations (Fish 

Survey Project) as well 

as selected invertebrate 

and algae species 

(Invertebrate & Algae 

Monitoring Program) 

along the West Coast of 

the US and Canada. 

The Project was 

developed in 1990. 

Surveys are completed 

annually in MBNMS, 

OCNMS, and CINMS.

12xxxxxx http://www.reef.org/

74CCSF 

Beach 

and 

Ocean 

Monitori

ng

The City and County of 

San Francisco (CCSF) 

owns and operates the 

Oceanside Water 

Pollution Control Plant 

that discharges 

municipal wastewater 

and storm water 

approximately 3.75 

miles offshore of Ocean 

Beach. Approximately 

55 stations are sampled 

annually for sediment 

quality and benthic 

infauna community 

analyses (sampled 

since 1997). Five 

stations fall within the 

GFNMS and ten 

stations fall within the 

MBNMS.

13xxxxx

PCB, metals

http://www.mbnms-

simon.org/sections/sa

ndyFloor/project_info.

php?pid=100212&sec

=sf
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

92

7

5

Center 

for 

Integrati

ve 

Coastal 

Observa

tion, 

Researc

h and 

Educati

on (CICORE)

CI-CORE examines 

watershed alteration, 

erosion, chemical 

contamination, 

depletion of fish stocks, 

toxic plankton blooms, 

marine-borne 

pathogens, and nonindigenous species 

along the California 

coast.

2 x x x http://www.cicore.org/

7

6

Coopera

tive 

Researc

h and 

Assess

ment of 

Nearsho

re 

Ecosyst

ems 

(CRANE

)

CRANE, which began in 

2002, is a collaborative 

effort to gather data for 

fishery management 

and performance of 

marine protected areas 

in central and southern 

California. Data 

collection includes 

wide-scale survey of 

fish and invertebrate 

populations in shallow, 

rocky habitats 

accessible to divers 

(Monterey to San 

Diego, including the 

Channel Islands).

12 x x x x x x x http://sanctuarysimon.

org/monterey/sections

/kelpForests/project_i

nfo.php?projectID=10

0154&sec=kf
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

93

7

7

Habitat 

Charact

erization 

and 

Biologic

al 

Monitori

ng of 

Cordell 

Bank

In 2001, Cordell Bank 

sanctuary, in 

partnership with the 

SWFSC, USGS, and 

CDFG, initiated a longterm study to classify 

habitats and monitor

fishes and macroinvertebrates on and 

around Cordell Bank. 

Underwater surveys of 

fishes, invertebrates, 

and their habitats are 

conducted on and 

around Cordell Bank 

using direct observation 

and video-transect 

methods from an 

occupied research 

submersible (Delta).

9, 

12

x x x x x x x x http://www.mbnmssimon.org/other/gen/p

roject_info.php?pid=1

00163&proid=&form=

pi

7

8

Love 

Lab 

subtidal 

surveys 

Subtidal surveys at San 

Miguel and Santa Rosa 

Islands using the 

CRANE protocol. 

Includes monitoring of 

marine reserves. Began 

in 1995. 

12 x x

7

9

Coastal 

Ocean 

Currents 

Monitori

ng 

Program 

(COCM

P)

COCMP uses an 

integrated set of high 

frequency radar 

systems to measure 

and map surface 

currents over large 

areas of the coastal 

ocean in central and 

southern California. 

Began in 2004.

1 x x x x http://www.cocmp.org/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

94

8

0

Pacific 

Whiting 

Conserv

ation 

Coopera

tive 

(PWCC) 

surveys

To improve estimates of 

whiting recruitment, the 

PWCC partners with 

NMFS to conduct an 

annual survey. Started 

in 1999, this 

cooperative survey 

investigates the 

abundance and 

distribution of juvenile 

whiting and rockfish in 

the California Current.

14 x x http://www.pacificwhiti

ng.org/

8

1

PRBO 

At-Sea 

Marine 

Mammal 

and 

Seabird 

Surveys

Surveys in the Gulf of 

the Farallones to 

determine the 

distribution and 

abundance of marine 

birds and mammals, to 

quantify the distribution 

and abundance of 

euphausiids and other 

bird/mammals prey, to 

characterize the 

zooplankton community 

in the upper water 

column, and to 

characterize the 

physical oceanographic 

conditions.

x x x x x x x x x x x x x x http://www.sanctuarysi

mon.org/farallones/se

ctions/marineMammal

s/project_info.php?pro

jectID=91&sec=mm

8

2

PIER 

Acoustic 

Telemet

ry 

Monitori

ng

PIER has installed an 

array of acoustic 

receivers at Anacapa, 

Santa Rosa, west end 

of Santa Cruz Island to 

monitor the movement 

of tagged fishes (e.g., 

kelp bass, California 

sheephead). Began in 

2004.

x x
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

95

8

3

Pioneer 

Seamou

nt 

Acoustic 

Observa

tory

A hydrophone array 

was installed on the 

summit of the Pioneer 

seamount (998m depth) 

and sounds from 

earthquakes, weather, 

whales, ships, etc. were 

continuously recorded 

between June 2001 and 

September 2002.

x x x

sound

http://www.mbari.org/it

d/retrospective/algal.h

tml

8

4

Point 

Lobos 

Montere

y Bay 

Time 

Series

Bio-optical, physical, 

meteorological, 

chemical, and biological 

time series data from 

moorings and ships are 

used document annual 

and ENSO-related 

variability. Began in 

1997.

1 x x x x x

8

5

Remote 

Sensing 

of 

CINMS

Various - multibeam 

and LiDAR Channel 

Islands and southern 

CA

x x x x x

8

6

San 

Francisc

o 

Estuary 

Researc

h 

Institute'

s 

Regiona

l 

Monitori

ng 

Program 

(SFEI 

RMP)

SFEI RMP monitors 

contaminant 

concentrations in water, 

sediments, and fish and 

shellfish tissue in San 

Francisco Bay and 

Delta. Began in 1994.

5, 

6, 

7

x x

sediment
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

96

8

7

Shore 

Station 

Program

The Shore Stations 

Program, which began 

in 1916, collects and 

provides access to 

current and historical 

data records of sea 

surface temperature 

and salinity 

measurements 

observed at shoreline 

stations along the west 

coast of the United 

States. Historically, 

stations ranged from 

the southern most 

station in La Jolla, 

California, up to the 

northern most point on 

the western coast, 

Neah Bay, Washington. 

All active stations are 

located in California.

x x x x x http://shorestation.ucs

d.edu/

8

8

Mussel 

Watch 

Program

The NOAA National 

Status and Trends 

Mussel Watch Project 

monitors chemical 

contamination in the 

coastal United States. 

Since 1986 mussels 

and oysters have been 

annually collected at 

more than 200 sites 

around the nation and 

chemically analyzed for 

a suite of chemical 

contaminants.

6, 

8

x x x

mussel tissue

grain/sediment, dioxin, PCB

http://www.sfei.org/ca

mp/servlet/DisplayPro

gram?which=General

&pid=1SF01NSTMW
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

97

8

9

MBARI 

Environ

mental 

Sample 

Process

or (ESP)

The ESP was 

developed at the 

Monterey Bay Aquarium 

Research Institute 

(MBARI) and is 

designed to 

autonomously collect 

discrete subsurface 

water samples, 

concentrate 

microorganisms or 

particles, and identify 

and quantify the 

species captured. The 

ESP has also been 

used to detect the onset 

and development of a 

harmful algal bloom 

(HAB). One trial was 

conducted in Monterey 

Bay in 2002 and a 

second generation ESP 

was deployed in spring 

2006.

8 x x x

DNA seq

x x x x x

HAB

http://www.mbari.org/

ESP/

9

0

ESNER

R bird 

monitori

ng 

program

s

The Elkhorn Slough 

National Estuarine 

Research Reserve 

(ESNERR) has seven 

distinct, volunteer-run 

bird monitoring projects 

including: Monitoring 

the Rookery, Monitoring 

the Caspian Tern 

Colony, Shorebird and 

Waterfowl Monitoring 

on the Reserve (and 

Elkhorn Slough), 

Monitoring Habitat Use 

in the south marsh.

15 x x http://www.elkhornslo

ugh.org/research/biom

onitor_bird.htm
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

98

9

1

MultiAgency 

Rocky 

Intertidal 

Network 

(MARIN

e)

MARINe monitors sites 

along the Pacific Coast 

using two different 

approaches - target 

assemblage monitoring 

(biannually at 80 

locations in California 

and Oregon), and 

biodiversity community 

monitoring (less 

frequent at 91 locations 

from Alaska to Mexico). 

Sites are selected to 

provide data about 

different rocky habitats, 

different exposure 

variables, different 

public uses.

10 x x x x

algae

wave exposure

http://www.marine.gov

9

2

ESNER

R 

elasmob

ranch 

monitori

ng 

program

s

Elkhorn Slough National 

Estuarine Research 

Reserve (ESNERR) has 

been monitoring the 

elasmobranch 

assemblage in Elkhorn 

Slough since 2002. The 

general focus is to 

investigate the affect of 

tides on elasmobranch 

assemblages and 

abundances at various 

points along the Elkhorn 

Slough. These sampling 

sites included the main 

channel at the mouth of 

the slough and several 

of the tidal creeks and 

lagoons throughout the 

reserve.

11 x x x x http://www.pelagic.org

/slough/
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

99

9

3

Santa 

Barbara 

Channel

keeper 

Stream 

Team 

monitori

ng 

program

Channelkeeper has run 

a volunteer-based water 

quality monitoring 

program - Stream Team 

- since 2001 in the 

Ventura River 

watershed (in 

partnership with the 

Ventura County chapter 

of the Surfrider 

Foundation), and since 

2002 in the Goleta 

Slough watershed. 

Water quality is tested 

monthly at every major 

reach and junction to 

locate the 'trouble' 

spots.

5, 

6

x

bacteria

x x x x http://streamteam.org/index.html

9

4

PRNS 

Pinnipe

d 

Monitori

ng 

Six species of pinnipeds 

have been documented 

in the Point Reyes 

National Seashore 

(PRNS). Two species, 

Northern elephant seals 

and harbor seals, have 

been monitored on a 

regular basis during 

their breeding and 

pupping seasons since 

1971. The other four 

species (California sea 

lions, Steller sea lions, 

Guadalupe fur seals, 

and Northern fur seals) 

have been censused 

weekly at the Point 

Reyes Headlands since 

1995.

15 x x http://www.mbnmssimon.org/sections/ma

rineMammals/project_

info.php?pid=100242

&sec=mm
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

100

9

5

PRNS 

Intertidal 

Monitori

ng

The Point Reyes 

National Seashore 

(PRNS) intertidal 

monitoring program 

began in 1996. Sites 

are surveyed twice a 

year, usually around 

November and May, 

during a low tide series. 

Surveys are conducted 

on the rocky intertidal in 

three locations. The 

objective of this 

monitoring is to create a 

system for long-term 

tracking of the Point 

Reyes intertidal 

environment integrity.

10 x x

algae

http://www.nps.gov/ar

chive/pore/science_cu

rrent_resmgt.htm

9

6

PRBO 

Snowy 

Plover 

monitori

ng

PRBO Conservation 

Science has two 

monitoring projects for 

Snowy Plover, one in 

Monterey Bay and one

at Point Reyes. Since 

1976, the Monterey 

project has monitored 

Snowy Plovers nesting 

in coastal habitats of 

Santa Cruz and 

Monterey counties. 

Since 1996, the Point 

Reyes project has been 

protecting and 

monitoring nesting 

Snowy Plovers within 

the Point Reyes 

National Seashore.

11 x x x http://www.prbo.org/c

ms/index.php?mid=12

6
ID

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

101

97Olympic 

Region 

Harmful 

Algal 

Blooms 

(ORHA

B)

Since summer 2000, 

ORHAB has been 

investigating the origins 

of blooms of toxic 

algae, monitoring where 

and when the blooms 

occur, and exploring 

methods that can be 

used to reduce HAB 

impacts on humans and 

the environment. The 

ORHAB project 

monitors plankton, 

toxins, and water quality 

along the WA coast to 

determine the 

environmental 

conditions associated 

with blooms.

1, 8xxx

demonic acid

http://www.orhab.org/i

ndex.html

98MLML 

class 

trawls 

project

Since the early 1970s, 

faculty and students in 

Marine Ecology, 

Invertebrate Zoology, 

and Ichthyology 

courses at Moss 

Landing Marine 

Laboratories (MLML) 

have participated in 

class cruises aboard 

several research 

vessels to survey the 

fishes and invertebrates 

in shallow-benthic, 

deep-benthic and 

midwater habitats in 

Monterey Bay. All fishes 

and invertebrates were 

identified to the lowest 

possible taxon. The 

results of these 

surveys, originally 

recorded on data 

sheets, are available in 

a Microsoft Access 

database.

13, 

14

xxxxxxx http://www.mbnms-

simon.org/other/gen/p

roject_info.php?pid=1

00170&proid=&form=

pi
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

102

9

9

ESNER

R 

inverteb

rate 

monitori

ng 

program

s

The Elkhorn Slough 

National Estuarine 

Research Reserve 

(ESNERR) is 

monitoring crabs and 

large burrowing 

invertebrates (e.g., 

clams, fat innkeeper 

worms, ghost shrimp) -

two groups of large, 

relatively easy to 

identify invertebrates. 

The goals are to detect 

dramatic changes in 

abundance, species 

diversity, and 

distribution. 

11 x x http://www.elkhornslo

ugh.org/research/biom

onitor_invert.htm

1

0

0

Snapsh

ot Day

Each years since 2003 

watershed groups from 

across the state 

participate in the 

California Coast-Wide 

Snapshot Day, with the 

goal of collecting 

important information 

about the health of 

coastal waters flowing 

into the Pacific Ocean. 

Snapshot Day 

volunteers collected 

water samples at 565 

creeks, rivers, wetlands, 

and beaches from the 

Oregon border to 

Ensenada, Mexico.

5, 

6

x x x x

PO4, NO3

http://www.mbnmssimon.org/other/gen/p

roject_info.php?pid=1

00142&query=snapsh

ot&form=kw
I

D

Project 

Name

Project Description

Charact. ID #

OC

CB

GF

MB

CI

Chlorophyll

Fluorescence

Phytoplankton

Zooplankton

Juvenile 

Adult inverts

Ichthyoplankt

Juvenile fish

Adult fish

Marine 

Seabirds

Other - bio

Nutrients

Dissolved O2

Salinity

Density

Water temp

Depth

Air temp

Currents 

Transmittance

Weather

Barometric 

PAR

Wind

Wave 

Aerial/sat 

Sidescan

Multibeam

Habitat type

LiDAR

Other-physical

Project URL

103

1

0

1

OSPR 

and 

MMS 

Santa 

Barbara 

Channel 

Aerial 

Surveys

These surveys are 

conducted as part of a 

program to maintain 

readiness for oil spill 

response. Aerial 

surveys are conducted 

frequently throughout 

the year to ensure that 

trained and experienced 

aerial observers are 

available in the event of 

an oil spill in California 

offshore waters. Data 

available 1994-1998 

and 2001-present.

x x x x x http://ccmaserver.nos.

noaa.gov/products/bio

geography/canms_cd/

htm/birds/EFFLOC_ae

rial.htm
104

Appendix 2 – Background Information on IEA Efforts in CCE

Atlantis Model for CCE

Atlantis is a simulation modeling approach developed by Commonwealth Scientific and 

Industrial Research Organization (CSIRO) scientists in Australia (Fulton 2004, Fulton et 

al. 2005). In Atlantis, ecosystem dynamics are represented by spatially-explicit submodels that simulate hydrographic processes (light- and temperature-driven fluxes of 

water and nutrients), biogeochemical factors driving primary production, and foodweb

relations among functional groups. The Atlantis approach has been adapted to the 

California Current Ecosystem by scientists at the Northwest Fisheries Science Center 

(Brand et al. 2007). Currently, the Northwest Fisheries Science Center is creating an 

Atlantis ecosystem model at the Central California sub-regional scale. The central 

California model is including additional sub-regional scale data and monitoring 

information. The modeling team has built a network of collaborators and has identified 

management scenarios and data outputs that will be relevant to the management needs of 

their state and federal collaborators.

The CCE and central California Atlantis models are intended as a strategic management 

tools that will allow the identification of trade-offs and to identify direct and indirect 

effects of management policies. The Atlantis framework will be used in management 

strategy evaluation, in which management policies and assessment methods are tested 

against simulations that represent a real ecosystem and its complexities. The ecosystem 

model can serve as a filter to identify which policies (e.g., marine protected areas 

placement and monitoring) and methods (e.g., stock assessment techniques) are 

promising and which are flawed or likely to be ineffective. In addition the model can be 

used to develop a range of scenarios that consider tradeoffs and benefits of the multiagency management of the fisheries (state, fisheries council, and National Marine 

Sanctuaries). Within the context of IEAs, the model will be used for performance testing 

of indicators, development of ecologically-based management targets, monitoring 

strategy evaluation, and possibly for semi-quantitative risk assessment.

Module I, CCE (Sydeman and Elliott 2008)

The Module I California Current Ecosystem IEA by Sydeman and Elliot (2008) takes a 

biological indicator approach to developing an IEA. They have compiled time-series data 

sets of both physical oceanography and key biological organisms. Key biological 

organisms include forage species (e.g., krill, plankton) top-level vertebrate predators of 

significant management concern, such as salmon and seabirds. The objectives of this 

effort are used to determine trends in the abundance of indicator species to understand 

both recent and long-term changes in the ecosystem. An additional goal of this initial 

effort was to identify gaps in knowledge. Module I does not include socio-economic data 

and other human-related data, though this type of data may be included in subsequent 
105

modules. Module I did not forecast future conditions, but this is a likely direction for 

subsequent modules. 

NCEAS CCME Human Impact Assessment (Halpern et al. 2009)

This project aims to understand and map how human activities are affecting marine 

ecosystems in the California Current, a region defined in this study as the coastal marine 

area between the U.S.-Canada border and central Baja, Mexico. The project builds upon 

previous work by collaborators from the National Center for Ecological Analysis and 

Synthesis (NCEAS) and Stanford University, which mapped human impacts on marine 

ecosystems globally. One objective of this study is the synthesis of spatial data on the 

distribution and intensity of human activities and the overlap of their impacts on marine 

ecosystems. The authors identified anthropogenic drivers of ecological change for 18 

marine ecosystems in the California Current and then determined the availability of data 

sets to model the impacts of those drivers (Table 5). This project aims to help determine 

how to allocate conservation and management resources, to implement ecosystem-based 

management, and to inform marine spatial planning, education, and basic research.

ONMS SWiM Condition Reports

Each site in the Office of National Marine Sanctuaries (ONMS) is in the process of 

developing, reviewing and issuing their condition reports. The reports are part of the 

ONMS System-Wide Monitoring framework that facilitates the development of effective, 

ecosystem-based monitoring programs that address management information needs using 

a design process that can be applied in a consistent way at multiple spatial scales and to 

multiple resource types. The condition reports are developed based on a Pressure-StateResponse framework (PSR) – they provide a summary of natural and anthropogenic 

pressures on resources in the National Marine Sanctuaries, the current status and trends of 

resource conditions, and management responses to the anthropogenic pressures affecting 

resources. The PSR framework allows managers to both prioritize management actions 

and evaluate their effectiveness in meeting conservation or restoration goals. 

The “state” section of the condition reports centers on a set of questions used as 

evaluation criteria to assess resource conditions and trends within each sanctuary. The 

questions derive from the Office of National Marine Sanctuaries mission and a systemwide monitoring framework. Resource status relating to each question is rated on a scale 

from good to poor and trends in the status of resources are also reported. In order to 

address the set of questions and thereby evaluate the status and trends of resources, 

sanctuary staff selected and consulted outside experts familiar with water quality, living 

resources, habitat, and maritime archaeological resources. 

The ONMS condition reports may be accessed from the ONMS Web site: 

http://sanctuaries.noaa.gov/science/condition.
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Background Information on MBCORC Report Card and Virtual Monterey Bay

The mission of the Monterey Bay Crescent Ocean Research Consortium (MBCORC) is 

to promote the scientific understanding of coastal and marine systems and to facilitate the 

application of that knowledge for public policy, environmental awareness, and decision 

making. MBCORC achieves its objectives by creating, coordinating, promoting, and 

endorsing research, education, and outreach activities, using the Monterey Bay as a 

natural laboratory. This group meets periodically to discuss projects of joint regional 

effort. Two of those projects are:

• Monterey Bay Ecosystem Report Card: Producing an ecosystem report card/set of 

ecosystem indicators for the Monterey Bay region/Central California. This effort has 

been focused on identifying indicators of interest and determining the availability of 

associated monitoring data for the Monterey Bay area.

• Oceanographic Modeling Workshop: Conducting one or more oceanographic 

modeling workshops to foster sharing and transfer of knowledge and expertise among 

MBCORC members. The first workshop was held in 2007.
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Appendix 3 – Acronyms and Abbreviations

AFSC: Alaska Fisheries Science Center

Beach COMBERS: Coastal Ocean Marine Mammal & Bird Education and Research 

Surveys

CalCOFI: California Cooperative Oceanic Fisheries Investigations

CBNMS: Cordell Bank National Marine Sanctuary

CBOMP: Cordell Bank Ocean Monitoring Program

CCAMP: Central Coast Ambient Monitoring Program

CCE: California Current Ecosystem

CCLEAN: Central Coast Long Term Environmental Network

CCSF: City and County of San Francisco

CIMT: Center for Integrated Marine Technologies

CINMS: Channel Islands

CINP: Channel Island National Park

COASST: Coastal Observation and Seabird Survey Team

COCMP: Coastal Ocean Currents Monitoring Program

CRANE: Cooperative Research and Assessment of Nearshore Ecosystems 

CRFS: Recreational Fisheries Survey

CSUMB: California State University, Monterey Bay

DPSIR: Driver, Pressure, State, Impact, Response

DFO: Department of Fisheries and Oceans Canada

EAM: Ecosystem Approach to Management

EFH: Essential Fish Habitat

EPA: Environmental Protection Agency

FAO: Food and Agriculture Organization of the United Nations

GFNMS: Gulf of the Farallones National Marine Sanctuary

HABs: Harmful Algal Blooms

IEA: Integrated Ecosystem Assessment

IOOS: Integrated Ocean Observing System 

LOBO: Land/Ocean Biogeochemical Observatory

MARINe: Multi-Agency Rocky Intertidal Network 

MBARI: Monterey Bay Aquarium Research Institute

MBCORC: Monterey Bay Crescent Ocean Research Consortium

Monterey Bay Time Series (MBTS) Program

MBNMS: Monterey Bay National Marine Sanctuary

MEI: Multivariate El Niño Index

MOOS: MBARI Ocean Observing System

NCCE: Northern California Current Ecosystem

NCEAS: National Center for Ecological Analysis and Synthesis

NDBC: National Data Buoy Center

NERR: National Estuarine Research Reserve

NGDC: National Geophysical Data Center

NMFS: National Marine Fisheries Service

NMS: National Marine Sanctuary
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NOAA: National Oceanic and Atmospheric Administration

NODC: National Oceanographic Data Center

NWFSC: Northwest Fisheries Science Center

OCNMS: Olympic Coast National Marine Sanctuary

ONMS: Office of National Marine Sanctuaries

ORHAB: Olympic Region Harmful Algal Blooms

PaCOOS: Pacific Coast Ocean Observing System

PDO: Pacific Decadal Oscillation

PISCO: Partnership for the Interdisciplinary Study of Coastal Oceans 

PnB: Plumes and Blooms

POES: Polar Operational Environmental Satellites

PRBO: Point Reyes Bird Observatory

PSR: Pressure-State-Response

SCCWRP: Southern California Coastal Water Research Project

SEAS: Sanctuary Ecosystem Assessment Surveys

SECRET: Studies of Ecological and Chemical Responses to Environmental Trends

SF-BEAMS: San Francisco Bay Environmental Assessment and Monitoring Station

SFML: Seafloor Mapping Laboratory

SIO: Scripps Institution of Oceanography

SWAMP: Statewide Water Ambient Monitoring Program 

SWFSC: Southwest Fisheries Science Center

SWiM: System-Wide Monitoring

USGS: United States Geological Survey

USFW: United States Fish and Wildlife

WCObs: West Coast Observatories

WOCE: World Ocean Circulation Experiment
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ONMS CONSERVATION SERIES PUBLICATIONS

To date, the following reports have been published in the Marine Sanctuaries Conservation Series. All 

publications are available on the Office of National Marine Sanctuaries website 

(http://www.sanctuaries.noaa.gov/).

Reconciling Ecosystem-Based Management and Focal Resource Conservation in the Papahānaumokuākea 

Marine National Monument (ONMS-09-04)

Preliminary Comparison of Natural Versus Model-predicted Recovery of Vessel-generated Seagrass 

Injuries in Florida Keys National Marine Sanctuary (ONMS-09-03) 

A Comparison of Seafloor Habitats and Associated Benthic Fauna in Areas Open and Closed to Bottom 

Trawling Along the Central California Continental Shelf (ONMS-09-02) 

Chemical Contaminants, Pathogen Exposure and General Health Status of Live and Beach-Cast 

Washington Sea Otters (Enhydra lutris kenyoni) (ONMS-09-01) 

Caribbean Connectivity: Implications for Marine Protected Area Management (ONMS-08-07) 

Knowledge, Attitudes and Perceptions of Management Strategies and Regulations of FKNMS by 

Commercial Fishers, Dive Operators, and Environmental Group Members: A Baseline Characterization and 

10-year Comparison (ONMS-08-06) 

First Biennial Ocean Climate Summit: Finding Solutions for San Francisco Bay Area's Coast and Ocean 

(ONMS-08-05) 

A Scientific Forum on the Gulf of Mexico: The Islands in the Stream Concept (NMSP-08-04) 

M/V ELPIS Coral Reef Restoration Monitoring Report Monitoring Events 2004-2007 Florida Keys 

National Marine Sanctuary Monroe County, Florida (NMSP-08-03)

CONNECTIVITY Science, People and Policy in the Florida Keys National Marine Sanctuary (NMSP-08-

02) 

M/V ALEC OWEN MAITLAND Coral Reef Restoration Monitoring Report Monitoring Events 2004-2007 

Florida Keys National Marine Sanctuary Monroe County, Florida (NMSP-08-01) 

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate 

maps from James Island to Ozette Lake, Washington Outer Coast. (NMSP-07-05) 

Observations of Deep Coral and Sponge Assemblages in Olympic Coast National Marine Sanctuary, 

Washington (NMSP-07-04) 

A Bioregional Classification of the Continental Shelf of Northeastern North America for Conservation 

Analysis and Planning Based on Representation (NMSP-07-03) 

M/V WELLWOOD Coral Reef Restoration Monitoring Report Monitoring Events 2004-2006 Florida Keys 

National Marine Sanctuary Monroe County, Florida (NMSP-07-02) 

Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat 

classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic 

Coast National Marine Sanctuary (NMSP-07-01) 
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2002 - 03 Florida Keys National Marine Sanctuary Science Report: An Ecosystem Report Card After Five 

Years of Marine Zoning (NMSP-06-12) 

Habitat Mapping Effort at the Olympic Coast National Marine Sanctuary - Current Status and Future Needs 

(NMSP-06-11)

M/V CONNECTED Coral Reef Restoration Monitoring Report Monitoring Events 2004-2005 Florida Keys 

National Marine Sanctuary Monroe County, Florida (NMSP-06-010) 

M/V JACQUELYN L Coral Reef Restoration Monitoring Report Monitoring Events 2004-2005 Florida 

Keys National Marine Sanctuary Monroe County, Florida (NMSP-06-09) 

M/V WAVE WALKER Coral Reef Restoration Baseline Monitoring Report - 2004 Florida Keys National 

Marine Sanctuary Monroe County, Florida (NMSP-06-08) 

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of side scan 

sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01 (NMSP-06-07) 

A Pilot Study of Hogfish (Lachnolaimus maximus Walbaum 1792) Movement in the Conch Reef Research 

Only Area (Northern Florida Keys) (NMSP-06-06) 

Comments on Hydrographic and Topographic LIDAR Acquisition and Merging with Multibeam Sounding 

Data Acquired in the Olympic Coast National Marine Sanctuary (ONMS-06-05) 

Conservation Science in NOAA's National Marine Sanctuaries: Description and Recent Accomplishments 

(ONMS-06-04) 

Normalization and characterization of multibeam backscatter: Koitlah Point to Point of the Arches, 

Olympic Coast National Marine Sanctuary - Survey HMPR-115-2004-03 (ONMS-06-03) 

Developing Alternatives for Optimal Representation of Seafloor Habitats and Associated Communities in 

Stellwagen Bank National Marine Sanctuary (ONMS-06-02) 

Benthic Habitat Mapping in the Olympic Coast National Marine Sanctuary (ONMS-06-01) 

Channel Islands Deep Water Monitoring Plan Development Workshop Report (ONMS-05-05) 

Movement of yellowtail snapper (Ocyurus chrysurus Block 1790) and black grouper (Mycteroperca bonaci

Poey 1860) in the northern Florida Keys National Marine Sanctuary as determined by acoustic telemetry 

(MSD-05-4) 

The Impacts of Coastal Protection Structures in California's Monterey Bay National Marine Sanctuary 

(MSD-05-3) 

An annotated bibliography of diet studies of fish of the southeast United States and Gray's Reef National 

Marine Sanctuary (MSD-05-2) 

Noise Levels and Sources in the Stellwagen Bank National Marine Sanctuary and the St. Lawrence River

Estuary (MSD-05-1) 

Biogeographic Analysis of the Tortugas Ecological Reserve (MSD-04-1) 

A Review of the Ecological Effectiveness of Subtidal Marine Reserves in Central California (MSD-04-2, 

MSD-04-3) 

Pre-Construction Coral Survey of the M/V Wellwood Grounding Site (MSD-03-1) 
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Olympic Coast National Marine Sanctuary: Proceedings of the 1998 Research Workshop, Seattle, 

Washington (MSD-01-04) 

Workshop on Marine Mammal Research & Monitoring in the National Marine Sanctuaries (MSD-01-03) 

A Review of Marine Zones in the Monterey Bay National Marine Sanctuary (MSD-01-2)
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Distribution and Sighting Frequency of Reef Fishes in the Florida Keys National Marine Sanctuary (MSD01-1) 

Flower Garden Banks National Marine Sanctuary: A Rapid Assessment of Coral, Fish, and Algae Using the 

AGRRA Protocol (MSD-00-3) 

The Economic Contribution of Whalewatching to Regional Economies: Perspectives From Two National 

Marine Sanctuaries (MSD-00-2) 

Olympic Coast National Marine Sanctuary Area to be Avoided Education and Monitoring Program (MSD00-1) 

Multi-species and Multi-interest Management: an Ecosystem Approach to Market Squid (Loligo 

opalescens) Harvest in California (MSD-99-1)