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​Science Research Program

The Science Program at the South Slough Reserve is focused on understanding estuarine and upland functions, processes and ecological communities, as well links between watersheds, estuaries and nearshore marine environments. We aim to examine patterns and processes that contribute to healthy coastal and estuarine ecosystems, forests and riparian areas in the Lower Columbia biogeographic region and provide science-based information to improve coastal zone and watershed management.

As a National Estuarine Research Reserve (NERR) we also serve as a dedicated site for scientific investigations by our staff, visiting researchers and students, and as a source for long-term water quality and meteorological monitoring data.

Areas of Research

Major components of the Science Program include:

South Slough water quality

The System-Wide Monitoring Program (SWMP) is a nationally coordinated effort that provides long-term weather, water quality, biological community, habitat, and land use/cover information about estuaries and coastal ecosystems for research, education, and coastal management applications. The abiotic components of SWMP include four primary long-term water quality and nutrient monitoring stations, and one weather station. The weather and water quality stations are telemetered to provide near real-time data access (; Additional abiotic elements include hydrologic and sediment dynamic parameters related to the Sentinel Sites. The biotic components of SWMP includes long-term vegetation monitoring transects at tidal marsh, eelgrass, and Sitka spruce swamp habitats located along the estuarine salinity gradient (see Sentinel Sites). The habitat mapping and change elements of SWMP include watershed and reserve scale boundary maps and habitat classification maps to assess changes in habitat condition and quality (see Habitat Mapping). The Centralized Data Management Office (CDMO) provides support for all of the SWMP data management activities, including data access, archiving, protocols, quality assurance/quality control, and training.

Coos Bay water quality

The Reserve expanded its water quality monitoring network to include four additional sites in the Coos estuary, one site in the mid bay at the McCullough Bridge (North Point) and three sites in the upper bay (Isthmus Slough, Catching Slough, and Coos River). The expansion was enabled through the Partnership for Coastal Watersheds project. These secondary SWMP water quality stations continuously monitor physical water parameters, including water temperature, salinity, dissolved oxygen, pH, turbidity, and water depth with the same automated data sonde instruments used at the four core/primary SWMP water quality stations in the South Slough estuary.

Weather stations

The SWMP weather station at the South Slough Reserve provides long-term measurements of air temperature, relative humidity, barometric pressure, wind direction and speed, precipitation, and photosynthetically active radiation to assess impacts on water quality, nutrient dynamics, and biological processes. The weather station was located on the University of Oregon’s Institute of Marine Biology campus from 2001-2015 collecting information near the mouth of the estuary and was relocated in 2016 to the south end of the Reserve at Tom’s Creek Marsh.

The Reserve also serves as a host site for one of NOAA’s US Climate Reference Network stations, located at the south end of the Reserve in Frederickson Marsh. The USCRN, with over 100 stations, provides measurements of air temperature, precipitation, relative humidity, wind speed, solar radiation, infrared surface temperature, and soil conditions (temperature, moisture) for monitoring climate trends and supporting climate-related research.

Learn more​ about environmental monitoring at South Slough Reserve.

​Community, Lands & Waterways Data Source

The Community, Lands & Waterways Data Source is an encyclopedic compilation of all available data describing the socioeconomic and environmental conditions in the Coos Bay (Oregon) area. The Data Source provides in-depth status and trends information about environmental attributes (e.g. water quality, oysters, eelgrass, etc.) in the Coos Watershed and adjacent areas and evaluates our community’s social and economic attributes (e.g., jobs, demographics, schools, etc.) for comparison with other communities. 

Coos Bay estuary shoreland use and zoning analysis

This project (set to being November 2016) will compare actual uses of estuarine and shorelands to zoned uses in the Coos estuary. Local land use plans were developed nearly 40 years ago and have not evolved with the area’s economic and social drivers. The analysis will highlight areas that are underutilized, have conflicting zones, or whose zone designations are now obsolete (e.g., many tracts of shorelands are still zoned as dredge disposal sites despite policy changes that now require dredge spoils to be disposed of at the mouth of the estuary or in the ocean). Technical advisors and stakeholders will then apply a triple bottom line lens (economic, socio-cultural, and environmental) to generate recommendations for Coos County to improve its estuarine and shoreland management.

Coos estuary hydrodynamic​ model

Researchers at the University of Oregon and Woods Hole Oceanographic Institute are working with the Partnership for Coastal Watersheds to develop a water circulation model for the Coos estuary. The model characterizes water current velocities as well as changes in water temperature and salinity over time throughout the estuary. Future work will expand the model to characterize sediment movement and the effects of deepening the shipping channel on changes to water circulation and sediment patterns.​


We are characterizing the spatial and temporal patterns of fish assemblages in tidal habitats of the South Slough and Coos Estuary. Data from this project will be compared to previous assessments to understand long-term trends in habitat use by fish. Project partners include Oregon State University and the US Forest Service. This project is funded through the Pacific Marine and Estuarine Fish Habitat Partnership. 

Invasive European green​ crabs

European green crabs (Carcinus maenas) are aggressive invaders and are known to have significant impacts on native ecological communities. We are studying the spatial distribution and recruitment patterns of green crabs in the Coos Estuary. Abundance has been steadily increasing since 2016, and is now at high enough densities in some areas to expect negative effects on eelgrass meadows, native crab populations, and oysters and clams. We will continue to monitor green crab populations and assess potential negative effects and management methods.​ Read the 2020 European green crabs monitoring report​.

Native Olympia oysters

Native oysters (Ostrea lurida) experienced a local extinction from the Coos estuary before the 20th century. They have since returned to the estuary, but there is limited data on their population dynamics. We are planning monitoring, modeling, and experiments to better understand where, when, and how to restore Olympia oysters to Coos Bay and South Slough Reserve.

Habitat mapping​

The South Slough Reserve has created habitat maps to classify all wetland, aquatic, and upland habitats, as well as all cultural land covers in the South Slough estuary in order to characterize changes to estuarine habitat due to impacts from climate change, land use pressures, and changes to local tidal inundation patterns.

Restoration of Eelgrass beds

The South Slough Reserve lost large areas of eelgrass meadows in 2016-2017. Since then, we have been investigating causes of the decline. In 2020, we started an experiement to restore areas of eelgrass. We are studying planting elevation and seasons to determine whether restoration is feasible. We expect to continue this experiment for several years with additional plantings and regular monitoring.​Eelgrass map​ping

As part of the eelgrass restoration project we are also investigating the use of UAVs (unmanned aerial vehicles) to map eelgrass in the estuary. In 2019 and 2020 we tested different sensors and different elevations. We found that both NIR (near infrared) and regular RGB (red, green, blue) imagery at 60 foot elevation produced satisfactory​ maps of eelgrass cover, but algal mats were frequently mistaken for eelgrass cover. We will try to improve this method over the next several years.        


The South Slough Reserve is one of a 126 sites that participate in SeagrassNet, a global monitoring program to document the status and health of seagrass meadows. The Reserve has been monitoring trends and changes of a Zostera marina eelgrass bed at Valino Island since 2004. Seagrasses are underwater flowering plants that provide essential habitat for invertebrates and fish, improve water quality, protect and stabilize shorelines from erosion, and store carbon in their sediments. ​​

NERRS Sentinel Sites Program

The South Slough Reserve is one of many “Sentinel Sites” across the country, set up to monitor long-term changes to estuaries due to climate change. In particular, South Slough is trying to understand how changing sea levels will affect coastal inundation rates, erosion rates and vegetation in emergent marsh and eelgrass communities in Oregon’s estuaries.​​

Blue carbon

Coastal and ocean ecosystems are increasingly being recognized as important stores for carbon (known as blue carbon), yet virtually no work has been done to evaluate blue carbon stocks in the Pacific Northwest. As a member of the Pacific Northwest Blue Carbon Working Group, the South Slough Reserve is involved in a project to quantify carbon stocks and sequestration rates, and identify ecosystem drivers that influence carbon storage potential in estuarine wetland habitats across the Pacific Northwest. Additional blue carbon projects have involved partnerships with the US Environmental Protection Agency to quantifying carbon storage and sequestration rates from sediment cores taken at high and low intertidal marshes throughout the Coos estuary and with the University of New Hampshire to quantify carbon in cores collected at eelgrass beds within the Reserve.

Wasson Restoration Project

The South Slough Reserve is working towards restoring the ridge-top to estuary function of the Wasson Creek watershed. This watershed has a long history of timber extraction and lowland agricultural activities that have significantly changed the quality of its wetland, stream, and forest habitats. The main objectives of this restoration project are to: 

  1. Reestablish hydrologic connectivity between the historical stream and its floodplain  
  2. Increase the amount and suitability of wetlands and upland habitats
  3. Document and protect cultural resources 
  4. Increase the complexity and heterogeneity of the forested uplands
  5. Reestablish native plant communities
This project is supported by a Technical Assistance grant from the Oregon Watershed Enhancement Board. 
 Wasson Restoration Project Final Plans​
 Appendix A - Revised Permits
 Appendix B -  Floodplain Hydrology Plan
 Appendix C - Vegetation Plan
 Appendix D - Commission Approved Uplands Plan
 Appendix F​ - Inadvertent Discovery Plan for Cultural Resources  
​ ​

Indian Point Restoration Plan

The South Slough Reserve is planning a restoration project for 240 acres of uplands on Indian Point in the South Slough estuary. Restoration planning will focus on expanding habitat availability for multiple endangered species through the removal of non-native species and modifications to adjacent forested areas.

Funds from the United States Fish and Wildlife Services Coastal Wetlands Conservation Grant Program were used to purchase Indian Point and will be used for the restoration project. 

For more information, please contact: Bree Yednock, Reserve Manager, 541-888-8270, ext. 302

Invasive species management

Current work focuses on the control and restoration of invaded landscapes to improve habitat complexity and resiliency. Over the next several years, work will include characterizing and monitoring the extent of invasive species impacting the Reserve; measuring and tracking those impacts; and reducing impacts of invasive species affecting or threatening the Reserve. A list of the Reserve’s top priority invasive species to target for control includes: 
Terrestrial species
  • Gorse, Ulex europaeus
  • Pampas grass, Cortaderia selloana
  • Purple loosestrife, Lythrum salicaria
  • English ivy, Hedera helix
  • Scotch broom, Cytisus scoparius
  • Reed canary grass, Phalaris arundinacea
  • Nutria, Myocastor coypus
Aquatics species
  • Carpet sea squirt, Didemnum vexeillum
  • European green crab, Carcinus maenas

Land acquisition

One of the responsibilities of the Reserve is to ensure that high quality estuarine and coastal ecosystems continue to be available for long-term research, education and interpretation. From time to time lands become available that, if acquired, would help the Reserve further its mission. If you are interested in learning more about the Reserve’s land acquisition program or priorities contact the Reserve Manager. The Reserve acquires land only on a willing buyer/willing seller basis.

Past restoration work

Over the past two decades, the South Slough Reserve has engaged in a series of experimental wetland restoration projects to address the need for more information about restoring estuaries in the Northwest. Published in 2005, this set of case histories is designed to share concepts, methods, and lessons that have been learned at the Reserve with landowners, watershed councils, wetland managers, other restoration practitioners who may be planning estuarine restoration projects, students, and the general public. 

Recently Published Research

Status of the European Green Crab, Carcinus maenas, (aka 5-spine crab) in Oregon Estuaries.
Sylvia Behrens Yamada, Integrative Biology, Oregon State University
Report for 2022 

Mapping the Distributions of Pacific and Western Brook Lampreys Along the Oregon South Coast using eDNA and Community Science 

Community volunteers and South Slough Reserve scientists are testing a new method that involves using environmental DNA (eDNA) to detect the presence or absence of Pacific and western brook lampreys in Oregon South Coast steams.

Read the 2019 - 2022 report

Fish Assemblage of the South Slough Estuary

This report offers a 30-year look into the fish assemblage of the South Slough estuary. South Slough Reserve scientists and others look at trends of declining productivity and biodiversity in an Oregon estuarine reserve.
Read the 2022 report.

5-Spine (aka Green) Crab Numbers Continue to Rise in Coos Bay
Researchers at South Slough Reserve recently concluded annual reporting on the status of the 5-spine (aka green) crab (Carcinus maenas) in Oregon's Coos Bay Estuary. The research suggests 5-spine crab populations continue to grow, threatening Oregon coastal species and habitats. Read the 2022 report.  Check out a culinary guide to preparing and cooking green crabs.

Navigating data sources

NANOOS Visualization System (for real-time water quality and weather data)
  • Navigate to: Data Explorer, Fixed Platforms, scroll down to Fixed Shore Platform under the Fixed Platform tab (stations listed alphabetically - NERRS), about 1/3 the way down our sites are alphabetically listed NERRS SOS (NERRS SOSCWQ, SOSECWQ, SOSWIWQ, SOSVAWQ).  Scroll further down to Land Station, South Slough’s weather station is NERRS sostcmet.  
NERRS database (for real-time and downloadable water quality and weather data, reserve and watershed boundaries and reserve habitat map, vegetation monitoring data)
  • NERRS Database: Get Data, scroll to third application: Real Time Data Application, click To  launch the Real Time Data Application, click here, at top under Quick search of all real-time stations listed: click drop down arrow and scroll (stations listed alphabetically) to select SOSCHWQ (Charleston Bridge water quality), SOSECWQ (Elliot Creek water quality), SOSTCMET (Weather station), SOSVAWQ (Valino Island water quality), or SOSWIWQ (Winchester Creek water quality).
  • Select See Latest Observations in the Green box (Datasets) at bottom center of page, scroll down (alphabetically listed) to OR Coos Bay 8 SW and click on blue text. 

Interested in conducting research in the reserve?

The South Slough Reserve Science Center is located in Charleston, Oregon, on the campus of the Oregon Institute of Marine Biology. Its location provides direct access to the South Slough, greater Coos estuary, and coast.  For more information on conducting research in the reserve please see our application for doing work in the reserve and direct all inquiries to Shon Schooler (541-888-8270, ext. 315).

Researchers at South Slough looking into pails



South Slough Reserve Science Center
63466 Boat Basin Rd. 
Charleston, OR 97420
Phone: 541-888-8270

Shon Schooler
Lead Scientist and Research Coordinator
Phone: 541-888-8270 Ext. 315