Upgrade to the Coastal Margin Observation and Prediction (CMOP) Program’s Estuary and Ocean Monitoring and Modeling Capacity

Salmonid Restoration Planning and Assessments

Salmonid Habitat Assessment / Inventory
Project ID23-CRITFC-02
Recovery DomainsLower Columbia River
Start Date03/01/2024
End Date06/30/2028
Last Edited05/03/2024
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This project will support climate change-focused monitoring and modeling of the Columbia River estuary and coastal waters by the Coastal Margin Observation and Prediction (CMOP) program. The estuary provides critical migratory and rearing habitat for Columbia Basin salmon and steelhead populations, including all ESA-listed salmon runs in the Columbia Basin. Over the past century, development and land use have reduced the extent and quality of habitat within the Columbia River estuary, and climate change is expected to further degrade habitat quality. Understanding environmental changes in estuary and ocean habitats is needed to protect salmon throughout their lifecycle, which is a critical component of the Columbia River Anadromous Fish Restoration Plan (https://plan.critfc.org).

CMOP includes an observatory comprised of stations collecting continuous biogeochemical data, as well as a modeling program that predicts conditions throughout the region and forecasts future scenarios. CMOP focuses on water properties that affect salmon survival and habitat suitability, including temperature, restricts estuary habitat during summer and fall, dissolved oxygen, which drops low enough to cause physiological stress during summer, and ocean acidification, which restricts ocean prey availability and may impair olfactory responses.

This project takes a three-pronged approach to investigate climate change and other disturbances in the estuary and ocean. First, CMOP will operationalize a continuous ocean acidification analysis system. A state-of-the-art instrument was recently purchased (non-PCSRF funding) and will be maintained through necessary staff hours for weekly maintenance, data assessment, and data interpretation from 2024-2028.

Second, CMOP will conduct a pilot study using environmental DNA (eDNA) for ecological monitoring. The CMOP observatory currently lacks the ecological data needed to assess how environmental conditions affect salmon and their prey. eDNA-based techniques are increasingly being used as non-invasive, cost-effective methods to track fish populations and conduct ecological monitoring. Seawater for eDNA will be collected from CMOP’s Point Adams station using existing pumps and infrastructure (non-PCSRF funding). Samples will be collected during 2024 and 2025, with targeted sampling to characterize the tidal cycle, seasonal changes, upwelling/downwelling conditions, and high/low river flow. eDNA from filtered seawater samples will be extracted and sequenced using metabarcoding approaches to characterize the diversity of phytoplankton, zooplankton, and fish communities. Salmon genes will also be quantified after conducting a needs assessment to determine valuable target species for CRITFC-member tribes. Data will be analyzed to examine ecosystem shifts in the context of environmental variability.

Finally, the CMOP Virtual Columbia River modeling program will be used to spatially extend observations throughout the estuary and to interpret the results in the context of climate change scenarios. The Virtual Columbia River model is an established tool for analyzing conditions in the Columbia River estuary under modern, historical, and future scenarios and is currently being improved (non-PCSRF funding) to better represent tidal wetlands, which provide habitat for resident juvenile salmon and food sources for migratory juvenile salmon. The program has been applied to questions of salmon habitat and survival through salmon habitat opportunity metrics, through individual based-models. CMOP will apply the program to updated climate change scenarios incorporating sea level rise, increased water temperature and modified hydrographs using established techniques and will explore the development of new methods of analysis. Model results will be incorporated into salmon lifecycle modeling.

Please see attached proposal for a complete list of references

Project Benefit    

Pacific salmon spend a large fraction of their lives in the ocean, a heterogeneous environment that is often described as a ‘black box’ where the distributions, diets, growth rates, and mortality rates of salmon are largely unknown (Weitkamp & Sturdevant, 2008). Poor ocean survival is thought to be a major cause of recent declines in Columbia River Chinook salmon populations, along with overharvest and the construction of dams (Hilborn, 2013). Furthermore, life cycle modeling predicts that future climate change may lead to a ~90% decline in marine life stage survival and ultimately cause the extinction of Snake River spring/summer Chinook populations by 2060 (Crozier et al., 2021). Monitoring and forecasting of physical, biogeochemical, and ecological properties of the estuary and ocean is fundamentally needed to understand the factors controlling salmon survival under current conditions and to predict changes with future climate scenarios.

This project benefits Columbia Basin salmon populations (including all ESA-listed populations) by increasing salmon-relevant climate change monitoring and modeling by the CMOP program. Operationalizing CMOP’s ocean acidification analysis system will produce new data on ocean acidification, a climate change process expected to negatively impact salmon by restructuring the ocean food web, reducing prey availability, and impairing olfactory systems. These ocean acidification data will be freely available in real-time, thus providing important information for regional marine resource managers. The eDNA pilot study will establish baseline ecological information that will allow ocean conditions and biogeochemical measurements from CMOP’s Point Adams station to be directly linked to semi-quantitative salmon abundance data and to the structure of the salmon food web, setting the stage for a climate change ecological monitoring program. CMOP staff will work with NOAA oceanographers to determine whether these new ocean acidification data and/or eDNA data can help inform the NOAA ‘stoplight’ chart indicators of salmon returns. Finally, improvements to CMOP’s modeling program will enable predictions of how climate change will impact habitats throughout the Columbia River estuary. This will constitute an important long-term salmon management tool by enabling effective target restoration and habitat protection efforts that will increase habitat for resident juvenile salmon and food supplies for migrating juvenile salmon.

Overall outcomes for this project include:

• Collection of continuous ocean acidification data starting in summer 2024. Data will be published on the CMOP website.

• Completion of eDNA pilot study, including collecting samples (2024-2025), running lab analyses (2025-2026), and analyzing data (2026-2028). Data analysis will be used to optimize methods and assess their utility, and to investigate how community composition, ecosystem structure, and/or salmon abundance vary with environmental conditions. Results will be discussed with CRITFC and the tribes so that management actions or revisions in return estimates can be conducted, as appropriate (by 2028).

• Predict changes in estuary salmon habitat using climate change scenarios incorporating sea level rise, increased water temperature and modified hydrographs (by 2027) and incorporate results into salmon lifecycle modeling (by 2028).


Metric Completed Originally

Funding Details

No Funding data has been entered for this project.

Project Map


Pt Adams CMOP station    

  • Worksite Identifier: Pt Adams CMOP station
  • Start Date: 04/01/2024
  • End Date: 06/30/2028
Area Description

No Area Description data was found for this worksite.

Location Information

  • Basin:
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: Oregon
  • Recovery Domain: Lower Columbia River
  • Latitude: 46.1997
  • Longitude: -123.94


  • Mid-Columbia River Spring-run Chinook Salmon ESU
  • Upper Columbia River Summer- and Fall-run Chinook Salmon ESU
  • Deschutes River Summer/Fall-run Chinook Salmon ESU
  • Lower Columbia River Coho Salmon ESU
  • Columbia River Chum Salmon ESU
  • Upper Columbia River Steelhead DPS
  • Snake River Basin Steelhead DPS
  • Lower Columbia River Steelhead DPS
  • Middle Columbia River Steelhead DPS
  • Okanogan River Sockeye Salmon ESU
  • Upper Columbia River Spring-run Chinook Salmon ESU
  • Snake River Spring/Summer-run Chinook Salmon ESU
  • Snake River Fall Chinook Salmon ESU
  • Snake River Fall Chinook Salmon ESU
  • Lower Columbia River Chinook Salmon ESU




  • B.0 Salmonid Restoration Planning and AssessmentsY (Y/N)
    •      . . B.0.a Planning And Assessment Funding .00
    •      . . B.0.b.1 Area Encompassed
    •      . . B.2 Salmonid Habitat Assessment / InventoryY (Y/N)
      •      . . . . B.2.a Habitat Assessment Funding
      •      . . . . B.2.d Habitat surveysY (Y/N)
        •      . . . . . . B.2.d.1 Type of habitat survey/assessment (LOV)
        •      . . . . . . B.2.d.2 Amount of habitat assessed
        •      . . . . . . B.2.d.3 Amount of habitat assessed that needed restoration