• Projects
  • Columbia River Estuary Tidal Habitats


Northwest Fisheries Science Center (NWFSC) Fish Ecology FE - Estuarine and Ocean Ecology


Columbia River Estuary
Columbia River Estuary Tidal Habitats
The goal of the tidal-fluvial estuary study is to determine the estuary's contribution to the spatial structure and life history diversity of Columbia River salmon stocks and the implications for estuary restoration. The study targets salmon use of tidal-fresh habitats in the estuary from Rkm 75 to Bonneville Dam, and addresses four primary objectives:

1. Characterize the temporal and spatial distribution of Chinook salmon genetic stock groups throughout the estuary (March 2010 - March 2012).

2. Determine stock-specific habitat use, life histories, and performance of juvenile salmon in key habitat complexes to fill data gaps in the tidal fluvial reaches of the estuary (2012-2016).

3. Monitor juvenile salmon life histories and their contributions to adult returns in selected estuary tributaries, including tributary examples where tidal habitats have been restored (2012-2018).

4. Evaluate estuary restoration needs for recovery of all salmon ESUs and account for projected effects of climate change through application of a salmon life-cycle model (2011-1015).

The study, funded by the U.S. Army Corps of Engineers, involves a large team of researchers organized by NOAA Fisheries, including researchers from the Oregon Health and Sciences University, University of Washington, and Washington Department of Fish and Wildlife. The study addresses critical uncertainties identified in the research, monitoring, and evaluation (RME) program for the Federal Columbia River Estuary Program (FCREP). The Estuary Program is intended to conserve and restore the estuary ecosystem to improve the performance of listed salmonid populations. Products from the tidal-fluvial study will include:

1. Descriptions of stock-specific temporal and spatial distributions of Chinook salmon throughout the estuary.

2. Estimates of variations in Chinook salmon stock composition and stock-specific growth, food habits, consumption rates, and bioenergetic efficiencies within selected tidal-fluvial habitats.

3. Estimated contributions of estuarine life histories among returning adult Chinook salmon from selected populations throughout the Columbia River Basin.

4. A hydrological model quantifying the dynamics of rearing habitat opportunities for juvenile salmon at estuary reach and habitat scales.

5. Improved life-cycle models to account for the estuarine life histories of juvenile salmon and estimating the potential effectiveness of estuary restoration actions on the recovery and viability of selected salmon stocks. These results will directly address information needs to support estuary actions specified in the Federal Columbia River Power System (FCRPS) Biological Opinion for the Columbia River. The tidal-fluvial estuary study is part of an ongoing estuary research program initiated in 2002. The current study expands upon earlier research conducted in the lower 100 km of the estuary from 2002 to 2008. Although all objectives will be addressed by 2018 to correspond with a review of progress implementing the FCRPS Biological Opinion, some sampling activities may extend beyond this date to allow brood-year reconstruction of estuary contributions to adult returns in selected streams (Objective 3).

Research Themes

Habitats to support sustainable fisheries and recovered populations
Healthy oceans, coastal waters, and riverine habitats provide the foundation for aquatic resources used by a diversity of species and society. Protecting marine, estuarine and freshwater ecosystems that support these species relies on science to link habitat condition/processes and the biological effects of restoration actions. The NWFSC provides the habitat science behind many management actions taken by NOAA Fisheries and other natural resource agencies to protect and recover aquatic ecosystems and living marine resources. The NWFSC also maintains a longstanding focus on toxic chemical contaminants, as a foundation for regional and national research on pollution threats to fisheries and protected resources.
Recovery and rebuilding of marine and coastal species
The Pacific Northwest is home to several iconic endangered species, including Pacific salmon and killer whales, and several rockfish species. Mandates such as the Endangered Species Act, MagnusonStevens Act, and the Marine Mammal Protection Act, grant NOAA Fisheries the authority to manage the recovery of depleted species and stocks. The NWFSC contributes to species recovery through research, monitoring and analysis, providing NOAA managers and regional stakeholders the tools and information they need to craft effective regulations and develop sustainable plans for recovery.

Research Foci

Characterize relationships between habitat and ecosystem processes, climate variation, and the viability of organisms
Developing effective conservation and restoration strategies for species or populations requires a clear understanding of how ecosystem processes and climate change will influence the viability of organisms in the future. Key research needs include (1) evaluating the vulnerability of organisms and ecosystems to climate change and human impacts (e.g., fishing, pollution, land use), and (2) devising adaptation strategies that will help achieve conservation goals despite climate change and increasing human pressures. Understanding how climate change or trends in human impacts might influence organisms is based on an understanding of linkages between ecosystem processes, habitat conditions, and abundance, survival or demographics of organisms. This necessitates modeling influences of ecosystem processes on habitats and species, or developing models to examine influences of human pressures on population or ecosystem dynamics. With this foundation, vulnerability assessments can focus on understanding how interactions between climate change and human impacts influence vulnerability of species or populations. Adaptation strategies require knowledge of current conservation needs, predictions of how those needs might change as a result of climate change or future human impacts, and assessments of the robustness of alternative conservation strategies or techniques to climate trends.
Characterize the population biology of species, and develop and improve methods for predicting the status of populations
To evaluate species status and recovery, it is necessary to understand key aspects of the population biology of the species in question. This includes basic information on abundance, age structure, recruitment, spatial distribution, life history and how the species interacts with its ecosystem. For some recovering species, including most overfished groundfish stocks, many ESA-listed Pacific salmon stocks, and high profile species such as Southern Resident killer whales, this basic information is often reasonably well understood. For other recovering species, such as Pacific eulachon and some ESA-listed rockfish species, even basic information (e.g. stock abundance) is unknown. Even for well-studied species, key information on survival rates for critical life stages and how the environment affects these vital rates is lacking. Without basic information on species dynamics, achieving other goals such as quantifying relationships between human activities and species recovery or even knowing if species recovery goals are being met will not be successful. The NWFSC, in partnership with regional stakeholders, including states, tribes and industry, is conducting research to collect and monitor critical demographic information for recovering species.
Describe the relationships between human activities and species recovery, rebuilding and sustainability
Human activities play a major role in determining the status of species and stocks. Rebuilding and recovery therefore need to address how these activities affect their status. At the NWFSC, biophysical modeling is used to link specific human activities such as land use and pollution to habitat conditions, and then to link these conditions and other activities to particular life stages. These models can be used to quantitatively assess how human activities influence species abundance, productivity, distribution and diversity. Not surprisingly, altering human activities in some way is often necessary for species or stock recovery and rebuilding. It is therefore important to understand the socio-economic effects of alternative management structures. Gathering data on their economic costs and social impacts helps identify actions that are cost-effective. These actions will need to be resilient to potential changes in climate throughout the region. Research on how humans react to management strategies helps policy makers avoid those that lead to unintended consequences that can hinder rather than help recovery.
Develop effective and efficient habitat restoration and conservation techniques
Maintaining and re-establishing viability and sustainability of living marine resources requires conservation and rehabilitation or restoration of habitats upon which species depend. Common habitat restoration approaches and tech-niques often presume that habitats are static features of the environment, and that creation of stable habitats is a desirable restoration strategy. However, riverine, nearshore, and marine habitats are created and sustained by dynamic landscape, climatic, and oceanographic processes and biota are adapted to changing habitats that are within the range of natural variability. Hence, current restoration strategies often have limited success, in part because they fail to recognize larger scale processes that drive habitat change, and in part because they fail to recognize intrinsic habitat potential of individual restoration sites. The main goals of this research focus are to: improve understanding of how large-scale processes create diverse and dynamic habitats that support marine and anadromous species, better understand how human activities alter habitat-forming processes and habitats, develop new restoration techniques that are compatible with sustainable habitat-forming processes, and understand the variety of actions needed to adequately conserve intact critical habitats. In addition, NWFSC’s research will improve understanding of how new and existing habitat restoration and protection techniques affect fish and habitat at multiple scales (i.e., reach, watershed, Evolutionarily Significant Unit).
Develop methods to use physiological, biological and behavioral information to predict population-level processes
Understanding the biological processes occurring within organisms is a powerful way of understanding how environmental changes affect those organisms. Genetics, developmental, physiological and behavioral studies all provide important information for effective species recovery and rebuilding. Integrating this information into models is vital to predict how populations will respond to natural or human perturbations, and to assess the constraints to stock rebuilding efforts. For example, data on thermal tolerance and physiological responses to temperature can be used to explore changes caused by shifts in climate on reproductive behavior and productivity, viability, movement, habitat selection, and population dynamics. Similarly, data on contaminants that impact physiological processes (immune system, growth, development, reproduction, and general health) are critical in determining how these compounds affect population dynamics. Data on biological responses of organisms to ocean acidification are useful for understanding how acidification may affect individual development and survival. The NWFSC collects such information for several species that are of concern, targets of fisheries or otherwise important for overall ecosystem function. NWFSC scientists will continue to expand current efforts and develop methods to incorporate physiological, biological and behavioral data into population models in order to predict population-level processes from these individual level data.


Chinook salmon
species of interest
Columbia River
Columbia River
related to fish habitat (terrestrial or marine)
juvenile salmonid
early life stages of salmonids
life history
research focus


Genetic Identification of Chinook Salmon in the Columbia River Estuary: Stock-specific Distributions of Juveniles in Shallow Tidal Freshwater Habitats
David J. Teel, Daniel L. Bottom, Susan A. Hinton, David R. Kuligowski, George T. McCabe, Regan McNatt, G. Curtis Roegner, Lia A. Stamatiou & Charles A. Simenstad (2014) Genetic Identification of Chinook Salmon in the Columbia River Estuary: Stock-Specific Distributions of Juveniles in Shallow Tidal Freshwater Habitats, North American Journal of Fisheries Management, 34:3, 621-641, DOI: 10.1080/02755947.2014.901258
Genetic stock distribution
Genetic stock group ID for juvenile Chinook Salmon collected from 3 habitats each from 6 tidal-fluvial estuary reaches
Residency and movement of juvenile Chinook salmon at multiple scales in a tidal marsh of the Columbia River Estuary
Regan A McNatt, Susan, A Hinton, Daniel L. Bottom


Family Salmonidae


Curtis Roegner
Daniel Bottom
Internal Collaborator
David Kuligowski
David Teel
Internal Collaborator
Regan McNatt
Principal Investigator
Susan Hinton