Coos Estuary, southern Oregon

Here you will find 1) observational data we have collected or helped collect, 2) grid, forcing, and setup files to run our numerical simulations of the estuary, and 3) a list of what numerical output we have in case it’s of interest. Please contact us if you use these data or the modeling resources, or have suggestions. Enjoy. 

Watch a 2022 webinar (youtube link) on this research given at Hatfield Marine Science Center.

Latest results come from sediment core studies and water temperature modeling of the Coos Estuary, as described in this project. Emily Eidam led a paper on results from long sediment cores, accumulation and sediment transport published in E&C here, examining century long timescales. Molly Keogh has a paper in review looking at Be-7 activity from short cores, thinking more about seasonal scale sediment processes. Finally, Dave Ralston led the modeling of three full years of temperature & salinity in the estuary. See a poster here and more videos showing this modeling effort, while the model description and results are in the project page above.

Results of our Coos Estuary studies are summarized on the NERRS Science Collaborative website, including our first project (2016-2020) and our follow-on (2021-2023). To find info on our realistic hydrodynamic modeling simulations of the Coos Estuary, see details in paper by Ted Conroy (in JPO) and by Emily Eidam here. Ted’s paper validates the model with observations and shows the importance of tidal dispersion in the estuary, despite its significant seasonality, while Emily’s examines estuary function across historic, present-day, and future geometries of the Coos Estuary. Also Maria Jose Marin Jarrin recently wrote a couple papers on the estuary, with one on eelgrass decline and its relationship to water temperature.

VIDEOS: Check out some simulation results at our YouTube Channel!

Observations

CTD Data [File, 2 MB]: A MATLAB file of all the along-estuary conductivity/temperature/depth (CTD) profiles we collected from 2012-2014 (for more recent years please get in touch or see the archived data for Conroy et al. 2020 and Eidam et al. 2021). See the README for information on variables and more details or the publications page for the mentioned papers.

ADCP Data [File1 File2]: A MATLAB file of water velocities, time, and depth from a Sontek 150 kHz ADCP. The ADCP was bottom mounted, upward looking, and deployed by the South Slough west of the main channel near the BLM docks. See the README for information on variables and more details. 

Bathymetry: Many organizations have collected bathymetry data in and around the estuary. These include the USACE channel surveys, USACE Coastal LiDAR, and NOAA DEMs. For our own work, we partnered with Peter Ruggiero at OSU to collect high-resolution transects to fill in gaps. The raw data and merged bathymetry are now being served on github at this link. See the readme at the github site or an example cruise report [8 MB, Word doc] for details of the jet-ski collected data. Our data were collected in 2017-2018. 

Sediment samples & cores

  • For sediment samples, as well as the data listed above, please visit the NCEI database (Accession #0210797), which has archived all data from our recent NERRS Science Collaborative grant (2016-2020).

  • For the dataset for the long sediment cores (>20 cm) see NCEI database here.

  • For the dataset for the short sediment cores (~15 cm) see the NCEI database here.

Please contact us if you use these data or have any comments or questions. 

FVCOM Numerical Simulation Set up

We use the open source Finite Volume Coastal Ocean Model code as our platform for modeling the hydrodynamics of the Coos estuary. Below we have put many of the items needed to successfully setup and run a version of the Coos estuary model using FVCOM v3.2.1.

2014-2016 realistic runs with temperature and salinity: These are the newest runs, led by Dave Ralston at WHOI. See the parameter run file here and his FVCOM code alterations here. For more info, please get in touch or explore this poster with some initial results.

Older runs: 
Grid/Mesh [FILE}: This is the unstructured grid file for our model domain, created using SMS software and a coastline. 
Bathymetry [FILE]: This bathymetry product was built from numerous data sources, starting with the NOAA DEM and adding higher res data on top. It is then smoothed for model purposes. 
Discharge [FILE README file]: Discharge comes mainly from gages maintained by the Coos Watershed Association. The main river source is the Coos River, although numerous small sources of freshwater enter the estuary. 
Tides: We use modeled tides to force the Coos estuary simulations, based on the TPXO/Poseidon inverse tidal model. Specifically, we use 13 constituents (e.g., M2, S2, N2, K2, K1, O1, P1) along the model domain boundary. These tides are checked with sea levels measured at the Charleston, OR, tide gage. 
FVCOM parameter file [FILE]: An example run file from one of our recent simulations, showing the values for common parameters used and input/output flags. 
Notes on setting up FVCOM [File1 File2]: A few files that contain notes created by our group on our progress, challenges, and tips on setting up FVCOM. File1 is mostly from Dave Sutherland on getting FVCOM running on a local server and initial hiccups. File2 will be on getting FVCOM running on a remote cluster, with additional challenges and hiccups discussed. 

Ocean Numerical Simulations

The numerical simulations produce 3-D fields of salinity and velocity throughout the estuary, as well as sea level. The time period available currently runs over the years 2014-2016, which was originally validated by Ted Conroy. We have those variables at hourly time intervals on the numerical model grid for the entire three years. To access these model ‘data’, please contact us, as they are TBs in size. We also have a low-res grid that Maria Jose used in a paper looking at wind influence on the estuary. We have also created:

  • csv files of monthly and weekly time-averaged fields of surface/bottom salinity and temperature

  • time series of T/S at tide gate locations in the estuary

  • accumulated time over certain T&S thresholds specific to Olympia Oysters and eelgrass for modeled locations

  • Suspended sediment concentrations and other sediment variables

These model output results are available on my github page.

External Resources

The links and resources below will allow you to explore more partners and stakeholders interested in the dynamics of the Coos estuary. Some of them also contain data resources. 

Funding for this work has come from Oregon Sea Grant, the National Estuarine Research Reserve Science Collaborative, and the University of Oregon.