Yaquina Bay Environmental Monitoring Forum Summary

April 25, 2006

yaquina bay monitoringIntroduction


Meeting Agenda

Breakout groups

Presentations synopsis

Presentation abstracts

Breakout group recommendations

Next Steps

Participant list

Relevant web links


On April 25th, 2006 a forum was held at the Hatfield Marine Science Center to discuss establishing a long-term environmental monitoring program for Yaquina Bay. Several speakers reviewed historical environmental sampling datasets for Yaquina Bay as well as ongoing research efforts. This was followed by breakout groups to discuss particular sampling issues and a discussion of how we might develop a new, long-term, integrated and holistic environmental monitoring study of the estuary. Both abstracts of the talks and the recommendations of the breakout groups can be found below. 

There were two primary objectives for this meeting:

  1. to examine historical time series of environmental data, from basic physical parameters through sampling of flora and fauna, and
  2. to have a discussion on how best to design, implement, and fund a new, multi-tiered environmental monitoring program of the bay.


The Yaquina Bay estuary is a 4300 acre drowned river mouth estuary located on Oregon’s central coast. It has been used by humans for a variety of purposes over the last 100+ years, with current use focusing on fishing and fish processing, logging, shipping, tourism, aquaculture, and agriculture. It is also home to the Hatfield Marine Science Center, one of the major marine laboratories on the west coast, and the world-class Oregon Coast Aquarium. The estuary has been modified in a variety of ways, being alternately dredged and filled at different locations to suit the needs of development. This, combined with other industrial and recreational uses has the potential to impact the water quality of the bay, and therefore the long-term viability of its waters.

It highlights the need to not only understand the historical environment and environmental change in the estuary, but also the need to have long-term datasets that track the seasonal and annual fluctuations in a variety of physical and biological parameters. These long-term datasets, as unexciting as they are to collect, often prove to be the key to understanding spatial and temporal change as it relates to natural and anthropogenic impacts. It is this motivation that (1) led to our interest in convening this meeting and (2) using HMSC, its associated scientists and facilities, and the many interested partners and stakeholders in Yaquina Bay as a platform to launch a monitoring program that will allow us to understand this estuary now and in the future.


Meeting Agenda

Agenda (PDF)

Guin Library Seminar Room

900 Boehlert, George HMSC Welcome and Introductions


Heppell, Scott OSU/FW Objectives of Workshop, Agenda, and historical Yaquina Bay research
945 Rumrill, Steve SSNERR Background: Considerations on estuarine sampling in the Pacific Northwest, with focus on experience in South Slough. (presentation PDF, 8.3 MB)
1015 Weber, Jeff DLCD Oregon Estuary mapping program
1030 Break    
1050 Brown, Cheryl USEPA Historical and future EPA environmental sampling in Yaquina Bay. (presentation PDF, 6.7 MB)
1105 DeWitt, Ted USEPA EPA's benthic sampling program. (presentation PDF, 5 MB)
1120 Creech, Clay ODFW Atmospheric/meteorological sampling at the HMSC and potential improvements. (presentation PDF, 1.8 MB)
1135 Miller, Charlie OSU/COAS Historical plankton sampling in Yaquina Bay.
1150 Arnold, Gary ODEQ Yaquina Environmental Solutions and related sampling in Yaquina Bay. Summary of regulations in the state of Oregon (presentation PDF, 1.2 MB)
1205 Gallagher, Brett OSU/FW OSU’s “Marine Team” fish and environmental sampling in Yaquina Bay. (presentation PDF)
1220 Plybon, Charlie Surfrider/OCAq Surfrider’s Cooperative Water Quality Sampling Program. (presentation PDF)
1245 Lunch    
1330 Heppell, Scott   Instructions to Breakout Groups
1345 All   Breakout Groups convene
1445 Group leader   Breakout Group Reports (5 min each)
1515 All   Next steps--discussion
1545 Boehlert/Heppell   Closing Comments
1600     Adjourn


Breakout groups

1) Community needs, monitoring needs, logistics and funding sources
2) Biological and habitat monitoring -what parameters, where, how, how often?
3) Physical monitoring of air and water -what parameters, where, how how often?
4) Other monitoring -including pollutants, invasives, estuary use, other metrics
5) Modeling and integration with other programs


Presentation synopsis

Steve Rumrill talked about monitoring in SSNERR. He reviewed the how their environmental monitoring program has developed, the types of sensors they use, and how they are using the information. The critical point for monitoring is developing a framework for monitoring, that the objectives for monitoring are clear, and that the monitoring is designed to address those objectives. Jeff Weber discussed the ongoing plan by the Department of Land Conservation and Development to revise and update the estuary plan book, originally published in 1987 but based on maps from the 1970’s. Cheryl Brown discussed the work of her group at the USEPA, working on sampling of biophysical parameters in the bay and developing simulations to model fluxes in the Bay. Ted Dewitt, also from the USEPA, presented a review of historical benthic habitat and biological data that have been collected in the bay over the last 15+ years. Clay Creech gave an overview of HMSC weather monitoring activities, and gave suggestions as to how to improve the system such that it would be more effective for long-term monitoring. Gary Arnold discussed Oregon Department of Environmental Quality’s (DEQ) environmental monitoring programs and criteria, including TMDL limits, and presented how to access information, including Oregon’s administrative rules as they relate to water quality. Many of the web sites to access this information are in his presentation posted on the web site. Brett Gallagher talked about the OSU Marine Team work, which has sampled the bay for ichthyofauna on a monthly basis over the past 4+ years, and is designed to repeat and serve as a comparison to a study that was conducted in the late 1960s. Finally, Charlie Plybon gave a talk on how the Surfrider foundation and Oregon Coast Aquarium have developed a community beach monitoring program, primarily for indications of bacterial presence in the waters around Newport. Charlie Miller was unable to attend and present his work on historical plankton sampling efforts in the bay.


Presentation abstracts

Arnold, Gary

Water Quality Division, Oregon Department of Environmental Quality

Total Maximum Daily Load Presentation (PDF, 1.2 MB)


Brown, Cheryl

Pacific Coastal Ecology Branch, Environmental Protection Agency

Physical and Water Quality Data Presentation (PDF, 6.7 MB)


Creech, Clay and Phil Barbour

Oregon State University: Atmospheric/ meteorological sampling at the HMSC and potential improvements Presentation (PDF,1.8 MB)

weather stationStatus:
The current weather station has been in operation at HMSC since 1996. The weather instrument sensors are mounted on and under the roof of the Guin Library. The sensors are made by Davis instruments, a leading manufacturer of home quality instruments.

It is recommended that the weather station be upgraded to use research quality sensors and that the sensor locations be changed to improve observations. It is also recommended that the observations on the web page continue to be updated with current conditions every minute.


Miller, Charlie

College of Oceanic and Atmospheric Sciences, Oregon State University

Notes on studies of holoplanktonic mesozooplankton in Yaquina Bay, Oregon

Starting in 1959 and reaching full intensity early in the 1960’s, OSU Professor Herbert F. Frolander established a weekly, year-around sampling program for zooplankton in Yaquina Bay. This continued into the early 1970’s. Sampling initially was from small, cabin-cruiser style boats, later from slightly larger craft. It was done entirely with 12.5 cm Clarke-Bumpus nets (with flowmeters) hauled obliquely from near-bottom to the surface with the boat underway. Sampling stations were consistent: under the bridge and at navigation markers 15, 21, 29, 39 and 45. Occasionally sampling continued upstream to a station adjacent to the paper mill in Toledo. Two mesh sizes were used, “12-mesh” (0.112 mm) and “6-mesh” (0.239 mm), although mostly only the latter were counted. Near-surface and bottom temperatures were measured with bucket and reversing thermometers, respectively, and water samples were collected with Nansen bottles and buckets for salinity and oxygen measures. Salinity in early years was from chlorinity titration, later by inductive salinometer. Winkler titrations provided oxygen values. Zooplankton were subsampled by piston pipette for specific identification of 350 to 450 specimens. So far as I can determine, all of the original data books from this study are irretrievably lost. Most of the plankton samples remain, almost all adequately labeled but some dried in their jars, in the COAS biological storage facility in Corvallis. They have been checked in the 1990’s by workers from the University of Washington, led by Jeffery Cordell, interested in invasive species. They did not find the copepods of the genus Pseudodiaptomus known to have been introduced to Yaquina Bay, presumably since the Frolander sampling ended (that is since 1972). I have found those species myself during sampling of the mid-1990’s.

Publications specifically regarding this work include two published papers and it was included in book chapters and other publications.


DeWitt, Ted

EPA’s Benthic Habitat Data for Yaquina Estuary Presentation (PDF, 5 MB)

yaquina bay habitatsScientists at EPA’s National Health and Environmental Effects Research Laboratory, Western Ecology Division (WED) have been studying seafloor (benthic) habitats in Yaquina estuary for several years. Those studies were conducted as parts of several research projects, including: effects of contaminated sediments on benthic invertebrates, effects of nutrient enrichment on estuarine ecosystems, effects of habitat loss on estuarine resources, and environmental monitoring and assessment of coastal environments. Each project required different data, although some data sets supported multiple projects. Since the mid-1990’s, most data collected by WED were spatially referenced so that the data could be incorporated into geographic information system databases. Sampling sites were often randomly-distributed within the estuary, although the selection of study sites for any given study was determined by the experimental design of the study. Types of benthic habitat data that WED has collected or compiled for Yaquina estuary include: aerial photographs of the estuary at low tide (most as color infrared images) orthorectified and mosaicked into maps of the estuary; bathymetry based on hydroacoustic data; sediment properties, such as grain size; distribution and abundance of seagrass, green macroalgae, and benthic invertebrates; and maps of seagrass and burrowing shrimp populations. Current and former staff at WED who have contributed to the collection of benthic habitat data include Bruce Boese, Faith Cole, Ted DeWitt, Steve Ferraro, Walter Frick, Jim Kaldy, Mary Kentula, Janet Lamberson, Henry Lee, Walt Nelson, David Specht, David Young, Rick Swartz (retired), John Chapman (OSU), Tony D’Andrea (OSU), Scott Larned (NIWA), and Brad Robbins (Mote Marine Lab).


Gallagher, Brett

OSU Marine Team: Long-term sampling of ichthyofauna in Yaquina Bay Presentation (PDF)

people on small boatMarine Team is a student effort to examine spatial and temporal variation of fish species within Yaquina Bay. Marine Team was developed at OSU as a seminar course with a field sampling component, to help students of marine ecology get “hands on” experience with data collection and analysis. We set out to recreate a historical survey of Yaquina Bay, conducted by the EPA in 1967-68 (De Ben et al. 1990). Monthly monitoring of abiotic and biotic parameters at 5 sites within Yaquina Bay has been ongoing since November 2002. Preliminary results indicate changes in fish diversity and abundance between 1967-68 and 2002-2005. Total species diversity has decreased within Yaquina Bay. Seasonal changes in diversity and abundance indicate variations in community structure, evidenced by numerous juvenile and migratory species inhabiting Yaquina Bay seasonally. Further analysis will concentrate on examining fine scale variations in abundance and diversity on numerous spatial and temporal scales, while correlating strong trends with local hydrographic and oceanic conditions.


Plybon, Charlie

Surfrider Foundation and Oregon Coast Aquarium: Surfrider’s Cooperative Water Quality Sampling Program Presentation (PDF)

wq on coast

  • In the spring of 2003 the Surfrider foundation presented the blue water task force program at the aquarium
  • The program is a grassroots, volunteer based water quality monitoring network
  • Originally formed in/around high use beaches to monitor fecal bacteria contamination (ie. Surfers were getting sick)
  • This was really a problem of poor planning and overdevelopment in coastal communities and was eventually addressed in the Clean Water Act
  • All states were mandated to monitor water quality particularly in areas of high public use and recreation
  • The Blue Water Task force is a volunteer based group that exists to promote clean water, augment state testing, and bring public awareness to possible health threats.

In the fall of 2003, the Oregon Coast Aquarium’s youth volunteers and the Surfrider Foundation teamed up to create a Blue Water Task Force to monitor water quality along a 20 mile stretch of coastline from Ona Beach to Otter Rock. Surfrider volunteers drop off the water samples at the Aquarium each weekend and the samples are run for Enterococcus counts. Enterococcus is the EPA adopted indicator bacteria for mammalian waste. With the assistance of an Aquarium staff member, the youth volunteers are ale to perform, incubate, and read the test results. The results are posted locally at two different surf shops in Newport, within the Aquarium and on the Surfrider website. The aquarium and the youth volunteers are open to testing other beaches, estuaries, or areas of point and non point source pollution. Please contact via information below if you are interested in having your waterfront tested.

Blue Water Task Force Data available here.

Oregon Beach Monitoring Program – All State historical data available here.


Rumrill, Steve

South Slough NERR: Environmental Monitoring within Pacific Northwest Estuaries: Question-Based Monitoring in the South Slough National Estuarine Research Reserve, OR Presentation (PDF, 8.3 MB)



Abstract: A case history of ambient status and trends monitoring is presented for the South Slough estuary (southern Oregon). Datasets collected over the past decade by the South Slough National Estuarine Research Reserve / System-Wide Monitoring program (SWMP) include real-time measurements (every 5 min) of several meteorological parameters (air temperature, relative humidity, wind speed & direction, barometric pressure, precipitation, solar radiation), near real-time measurements (every 30 min) of water parameters (depth, temperature, conductivity, salinity, dissolved oxygen, pH, turbidity, fluorescence), and monthly measurements of estuarine nutrients (nitrate, nitrite, ammonium, phosphate, chlorophyll a, phaeopigments).

Measurements collected by the SWMP are compiled to address the primary question: “to what extent are chlorophyll levels and nutrient dynamics within the South Slough estuary driven by oceanic forcing and seasonal upwelling events versus watershed inputs?” Real-time data collection activities are carried out within the South Slough estuary in cooperation with the US Integrated Coastal Ocean Observing System (ICOOS) and the Northwest Association of Networked Ocean Observing Systems (NANOOS). Datasets generated by the South Slough SWMP are archived and displayed on a website managed by the NERR Centralized Data Management Office (CDMO), and they are handled locally by incorporation into a common integrated EQWin relational database. The South Slough NERR has also developed protocols for biomonitoring of salt marshes, eelgrass beds, and estuarine non-indigenous species, and maintains a long-term program for monitoring the effectiveness of tidal habitat restoration projects.

estuary researchFuture monitoring efforts will focus on data acquisition and modeling to address the question: “how well does the South Slough serve as a small-scale model for understanding the greater Coos estuary?” This new initiative will capitalize on the datastreams generated by the existing array of SWMP monitoring stations and add them to information generated by several new stations. Finally, it should be emphasized that question-based estuarine monitoring is an important element of the emerging effort to adopt an ecosystem-based approach to coastal management, and that the cooperative work carried out by federal and state agencies, academic scientists, ICOOS and NANOOS provide a timely opportunity to monitor, investigate and understand the physical and biotic connectivity between the nearshore, estuarine, and watershed elements of the Pacific northwest land-margin ecosystem.


Weber, Jeff

Department of Land Conservation and Development

blue tides

The Oregon Coastal Management Program published a compilation of local estuary management plans in The Oregon Estuary Plan Book in 1987. The Estuary Plan Book contains the maps of benthic habitats and local estuary management plan designations for seventeen Oregon estuaries. The plan book represents the culmination of a broad coastal resource management, planning and protection initiative that began in 1971, when the Oregon Coastal Conservation and Development Commission (OCC&DC) was appointed. In a 1975 report to the Oregon legislature that consisted of a series of recommendations for the management of a broad suite of coastal resources, including estuaries and coastal shorelands, the OCC&DC provided the framework and foundation for what was to become the federally-approved Oregon Coastal Management Program (OCMP). In 1976, based in part on the work of the OCC&DC, the Land Conservation and Development Commission (LCDC) adopted Statewide Planning Goal 16 for Estuarine Resources. Goal 16 in part directed local governments to develop policies for the conservation and development of estuarine resources as part of their local comprehensive land use plans. At the time, there was very little comprehensive information available to local governments about estuarine resources. In 1978, the Department of Land Conservation and Development (DLCD) contracted with the Oregon Department of Fish and Wildlife to compile the available data on estuarine resources into a form that could be used by local officials in implementing Goal 16. In 1979, ODFW published a report called Habitat Classification and Inventory Methods for the Management of Oregon Estuaries (commonly known to users as the “Raccoon Reports”) and a series of supplemental reports on the natural resources of several Oregon estuaries. These reports were accompanied by a series of habitat maps and data notebooks (which are not yet available on the web) that became the informational basis for local estuary management plans, which were adopted in the early 1980s and are still in effect today.


ocean frontOregon’s estuary management framework has been far-reaching and effective in conserving and protecting estuarine resources and areas. However, the informational basis for the management system, which was developed in the late 1970s, largely remains the informational base for estuary management decisions today. That is, the habitat and resource inventories have not been updated since 1979. The Oregon Coastal Management Program (OCMP) recently convened a workshop to discuss the need for a new information base for estuary management. Based on the results of that workshop and subsequent discussions to occur starting in the fall of 2006, the OCMP anticipates developing a new web-based estuary management information system. 


The Oregon Estuary Plan Book is available here.

Data in the Plan Book can be acquired from The Oregon Coastal Atlas, click on the Search tab or the binoculars to access the data archives.

See Oregon’s Statewide Planning Goals here.


Breakout group recommendations

There were originally five breakout groups defined, but because of a lack of participation in Modeling and integration with other programs, this group was disbanded and other groups were instructed to consider these points in their general discussions

1) Community needs, monitoring needs, logistics and funding sources
The community needs group was led by Ginny Goblirsch. They commented that community vision is currently lacking with regard to the use and long-term viability of the estuary. This makes planning difficult. This group recommended that any monitoring program have relevance and provide benefit to the users of the bay, although it should be noted that not all monitoring may have direct utility to evaluating current activities. Information should be made available to enhance the decision making process about uses in the bay, including the ability to respond to proposals about new uses for the estuary’s waters and habitats. As a corollary, once we have a better understanding of processes in the Yaquina estuary, proposals for appropriate uses could be made. This group identified critical knowledge needs including water quality, pollutants, and invasives. Potential funding sources were discussed, including non-profit organizations such as the Gates Foundation, Georgia Pacific, Walmart, and others. Finally, this group recommended that from a logistics standpoint that information be made available through a centralized website to foster community participation.

2) Biological and habitat monitoring -what parameters, where, how, how often?
Work Group Members: Ted DeWitt, Steve Rumrill, Fran Recht, Jim Kaldy, Cheryl Brown, Brett Gallagher, Brett Dumbauld, Mark Camara, Dave Fox

The biological habitat and monitoring group identified three questions that need to be addressed with regard to biological and habitat monitoring:

1. What do we want to know?
2. What would we measure to monitor what we want to know?
3. How often and at what spatial scale should we measure?

With regard to estuarine habitats, status and trends monitoring are important. Aerial photography and a defined classification system can help delineate different habitat types and changes in percent cover of each type, while functions of these habitats requires on-site research. Estuary Health – again status & trends: Functional roles of the estuary, and identification of measurable indicators, including trophic ecology (multiple trophic levels), the impacts of sub-lethal stressors, assessments of fisheries and invasive species, impact studies including examination of the impacts of bioaccumulation of pollutants. Interaction with outside world are important, including land use changes in watershed, transport of materials and water to/from watershed and the ocean, and the response of the estuary ecosystem to climate change. Impacts on human health should be evaluated, including bioaccumulation issues, food safety, and presence and density of potentially harmful bacteria

This group raised questions as to how often and at what locations measurements be taken, as well as at what spatial scales should these measurements take place. There is a need for flexibility to examine status and trends at multiple spatial scales (estuary scale versus localized impacts, etc). It is critical to develop data & sample archives as well. A meta-database, used to describe the types of data that have been collected, is essential. Consistent methodologies should be used, and as needs dictate changes in methods, a comparative analysis should be conducted to develop relevant conversions from old datasets to new. Finally, there should be a rigorous QA/QC program for any monitoring program.

Ultimately, a list of questions regarding what we would like to know about the biological components of the system was developed by this group:

1. Early warning of estuary change
2. Sub-lethal effects and stress indicators
3. Effects of Invasive Species
4. Counting Organisms is too late
5. Is this estuary health? Improving? Degrading?
6. Evaluation of habitat changes (increasing, decreasing, stable)
7. How is the estuary functioning now, compared to how it functioned in the past?
8. Watershed changes -influence on estuary (landuse impacts)
9. Effects of sea level rise on estuarine communities
10. Production of target species (clams, crabs, fish)
11. Habitat types – how much is present?
12. Is the estuary safe for human use? Shellfishing, swimming, fishing, bacteria, contaminants.
13. Trophic indicators of ecosystem function
14. Has function of habitats changed
15. Biotic links between watershed, estuary, and nearshore.
16. Suite of indicators for multiple layer evaluation
17. Bioaccumulation of persistent organics, contaminants.

3) Physical monitoring of air and water -what parameters, where, how, how often?
Kipp Shearman presented the discussion from this group. The important question for this group was “How does physical variability impact water quality and ecosystem dynamics from tidal to inter-annual cycles? What are the relative impacts of unpredictable vs. predictable changes, including tides, seasons, spills, storms, the Pacific decadal oscillation, El niño, etc.? Water quality parameters to be measured should include temperature, pressure, dissolved oxygen, turbidity, wave conditions, bathymetry, river inflows, mixing and dispersion, and other water quality parameters such as salinity.
This group discussed both the use of fixed platforms and mobile bases. Fixed platforms should be used at key sites that are regularly monitored, such as at the ocean mouth, mid-estuary, and in a riverine environment. Placement should be guided by models, but they note that monitoring the along-estuary gradient is more important than across-estuary gradients. This type of monitoring can be used to understand the impacts of both short term and long term cycles and change, and should allow for rapid sampling intervals over long time periods. The systems should be essentially self-contained and automated, reporting information back to a centralized location while allowing for additional human sampling efforts. An adaptive sampling strategy should be incorporated into monitoring, such that if an unusual environmental event is occurring, the sampling rate could be increased to capture any potential change in monitored parameters.
Mobile platforms, including dedicated research vessels, community boats, and autonomous underwater vehicles (AUV’s) can be deployed to collect many of the same pieces of data, and can be used to fill in the gaps both physically between fixed stations as well as temporally between sampling periods at the fixed stations. The OSU College of Oceanography and Atmospheric Sciences has been successful in deploying AUV’s for coastal science to collect many of these data.

4) Other monitoring -including pollutants, invasives, estuary use, other metrics
Gary Arnold presented the results from the discussions of this group. They raised two primary questions:

  1. How do you get consensus on monitoring a resource?
  2. How do you separate out human and natural effects?
    a. What would it look like in a pristine state
    b. What influences do humans have on the system?

Land use was raised as an important monitoring metric. A GIS-based analysis approach should be used to characterize changes in land use practices, including the number of building permits being issued, soil disturbance, dredge and fill permits, storm water flow and impervious surface change. They point out that some of these datasets already exist, but should be integrated into a single location.

For pollution, in addition to monitoring potential pollutants in the system and identifying potential major compounds to be monitored, issues of bioaccumulation in both sessile and mobile organisms should be addressed. With regard to invasive species, changes in community composition for both plants and animals should be monitored. Finally, the scale at which we are working should be defined. Do we just want to know about the estuary, or the estuary and watershed? Do we just care about understanding water quality in the estuary, or do we need to know something about air and land quality as well?

Next Steps

Several recommendations were made in the general discussion at the end. First of all, there was a comment that the cards are in our favor to develop an effective monitoring plan because of (1) the current interest in the bay, (2) the resources available (both intellectual and physical) to monitor the bay, and (3) the potential to build on existing programs within the bay. It was recommended that any project be developed with appropriate vision and scale, and that designed properly a Yaquina environmental monitoring program could serve as a conceptual monitoring model for other estuaries in the Pacific Northwest. A monitoring program would be well served to follow upon some standardized protocols such as the USEPA EMAP protocol, for at least some of the data collection in order to generate standardized information. Finally, a comment was made that the results from any environmental monitoring program should be made available to the Newport government, the chamber of commerce, and the community at large so that they have an understanding of the processes and changes that are occurring in their back yard.

At this point in time it seems that given proper leadership and funding a monitoring program could be developed immediately that would at least cover changes in physical parameters in the bay. These parameters would include dissolved oxygen, salinity, temperature, phytoplankton concentrations, currents, benthic characteristics and the like. More involved monitoring, including for biological parameters such as nutrient loading, fish abundance and diversity, invasive species, pollutants, and benthic organisms, would take either a dedicated funding source and a crew of qualified researchers in order to be accomplished, or excellent coordination between research groups as they pursue each of these issues independently through the course of their own studies. Regardless of currently available resources, this more integrated level of monitoring should be the goal of any program that seeks to understand the processes and changes in Yaquina Bay.


For further information, contact Scott Heppell