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Title: Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat, Physical Sciences Component, Progress Report.

Abstract

Long-term changes and fluctuations in river flow, water properties, tides, and sediment transport in the Columbia River and its estuary have had a profound effect on Columbia River salmonids and their habitat. Understanding the river-flow, temperature, tidal, and sediment-supply regimes of the Lower Columbia River (LCR) and how they interact with habitat is, therefore, critical to development of system management and restoration strategies. It is also useful to separate management and climate impacts on hydrologic properties and habitat. This contract, part of a larger project led by the National Oceanic and Atmospheric Administration (NOAA), consists of three work elements, one with five tasks. The first work element relates to reconstruction of historic conditions in a broad sense. The second and third elements consist, respectively, of participation in project-wide integration efforts, and reporting. This report focuses on the five tasks within the historic reconstruction work element. It in part satisfies the reporting requirement, and it forms the basis for our participation in the project integration effort. The first task consists of several topics related to historic changes in river stage and tide. Within this task, the chart datum levels of 14 historic bathymetric surveys completed before definition of Columbia River Datummore » (CRD) were related to CRD, to enable analysis of these surveys by other project scientists. We have also modeled tidal datums and properties (lower low water or LLW, higher high water or HHW, mean water level or MWL, and greater diurnal tidal range or GDTR) as a function of river flow and tidal range at Astoria. These calculations have been carried for 10 year intervals (1940-date) for 21 stations, though most stations have data for only a few time intervals. Longer-term analyses involve the records at Astoria (1925-date) and Vancouver (1902-date). Water levels for any given river flow have decreased substantially (0.3-1.8 m, depending on river flow and tidal range), and tidal ranges have increased considerably (by a factor of 1.5 to 4 for most river-flow levels) since the 1900-1940 period at most stations, with the largest percentage changes occurring at upriver stations. These changes have been caused by a combination of changes in channel roughness, shape and alignment, changes in coastal tides, and (possibly) bed degradation. Tides are growing throughout the Northeast Pacific, and Astoria (Tongue Pt) has one of the most rapid rates of increase in tidal range in the entire Eastern Pacific, about 0.3m per century. More than half of this change appears to result from changes within the system, the rest from larger scale changes in coastal tides. Regression models of HHW have been used to estimate daily shallow water habitat (SWHA) available in a {approx}25 mile long reach of the system from Eagle Cliff to Kalama for 1925-2004 under four different scenarios (the four possible combinations of diked/undiked and observed flow/ virgin flow). More than 70% of the habitat in this reach has been lost (modern conditions vs. virgin flow with not dikes). In contrast, however, to the reach between Skamokawa and Beaver, selective dike removal (instead of a combination of dike removal and flow restoration) would suffice to increase spring SWHA. The second task consists of reconstruction of the hydrologic cycle before 1878, based on historic documents and inversion of tidal data collected before the onset of the historic flow record in 1878. We have a complete list of freshet times and peak flows for 1858-1877, and scattered freshet information for 1841-1857. Based on tidal data, we have reconstructed the annual flow cycles for 1870 and 1871; other time periods between 1854 and 1867 are under analysis. The three remaining tasks relate to post-1878 hydrologic conditions (flows, sediment supply and water temperature), and separation of the human and climate influences thereon. Estimated ob-served (sometimes routed), adjusted (corrected for reservoir manipulation) and virgin (corrected also for irrigation diversion) flows for 1878-2004 have been compiled for the Columbia River at The Dalles and Beaver, and for the Willamette River at Portland. Sediment transports for the ob-served, adjusted and virgin flows have been calculated for 1878-2004 for the Columbia River at Vancouver and Beaver, for the Willamette River at Portland, and for other west-side tributaries seaward of Vancouver. For Vancouver and Portland, it has been possible to estimate sand trans-port (including gravel), fine sediment transport and total load. Only total load can be estimated at Beaver, and only fine sediment transport can be determined for the west-side tributaries, except for the post-1980 period influenced by the 1980 eruption of Mt St. Helens. Changes in flows and sediment transport due to flow regulation, irrigation diversion, and climate have been estimated.« less

Authors:
 [1]
+ Show Author Affiliations
  1. Portland State University
Publication Date:
Research Org.:
Bonneville Power Administration (BPA), Portland, OR (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
965263
Report Number(s):
P112804
R&D Project: 2003-010-00; TRN: US200920%%531
DOE Contract Number:
38924
Resource Type:
Technical Report
Resource Relation:
Related Information: document submitted July 2009
Country of Publication:
United States
Language:
English
Subject:
13 HYDRO ENERGY; ALIGNMENT; CLIMATES; COLUMBIA RIVER; FLUCTUATIONS; HABITAT; IRRIGATION; JUVENILES; PROGRESS REPORT; REPORTING REQUIREMENTS; ROUGHNESS; SALMON; SAND; SEDIMENTS; TRANSPORT; US NOAA

Citation Formats

Jay, David A. Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat, Physical Sciences Component, Progress Report.. United States: N. p., 2009. Web. doi:10.2172/965263.
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Jay, David A. Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat, Physical Sciences Component, Progress Report.. United States. doi:10.2172/965263.
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Jay, David A. Mon . "Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat, Physical Sciences Component, Progress Report.". United States. doi:10.2172/965263. https://www.osti.gov/servlets/purl/965263.
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@article{osti_965263,
title = {Historic Habitat Opportunities and Food-Web Linkages of Juvenile Salmon in the Columbia River Estuary and Their Implications for Managing River Flows and Restoring Estuarine Habitat, Physical Sciences Component, Progress Report.},
author = {Jay, David A.},
abstractNote = {Long-term changes and fluctuations in river flow, water properties, tides, and sediment transport in the Columbia River and its estuary have had a profound effect on Columbia River salmonids and their habitat. Understanding the river-flow, temperature, tidal, and sediment-supply regimes of the Lower Columbia River (LCR) and how they interact with habitat is, therefore, critical to development of system management and restoration strategies. It is also useful to separate management and climate impacts on hydrologic properties and habitat. This contract, part of a larger project led by the National Oceanic and Atmospheric Administration (NOAA), consists of three work elements, one with five tasks. The first work element relates to reconstruction of historic conditions in a broad sense. The second and third elements consist, respectively, of participation in project-wide integration efforts, and reporting. This report focuses on the five tasks within the historic reconstruction work element. It in part satisfies the reporting requirement, and it forms the basis for our participation in the project integration effort. The first task consists of several topics related to historic changes in river stage and tide. Within this task, the chart datum levels of 14 historic bathymetric surveys completed before definition of Columbia River Datum (CRD) were related to CRD, to enable analysis of these surveys by other project scientists. We have also modeled tidal datums and properties (lower low water or LLW, higher high water or HHW, mean water level or MWL, and greater diurnal tidal range or GDTR) as a function of river flow and tidal range at Astoria. These calculations have been carried for 10 year intervals (1940-date) for 21 stations, though most stations have data for only a few time intervals. Longer-term analyses involve the records at Astoria (1925-date) and Vancouver (1902-date). Water levels for any given river flow have decreased substantially (0.3-1.8 m, depending on river flow and tidal range), and tidal ranges have increased considerably (by a factor of 1.5 to 4 for most river-flow levels) since the 1900-1940 period at most stations, with the largest percentage changes occurring at upriver stations. These changes have been caused by a combination of changes in channel roughness, shape and alignment, changes in coastal tides, and (possibly) bed degradation. Tides are growing throughout the Northeast Pacific, and Astoria (Tongue Pt) has one of the most rapid rates of increase in tidal range in the entire Eastern Pacific, about 0.3m per century. More than half of this change appears to result from changes within the system, the rest from larger scale changes in coastal tides. Regression models of HHW have been used to estimate daily shallow water habitat (SWHA) available in a {approx}25 mile long reach of the system from Eagle Cliff to Kalama for 1925-2004 under four different scenarios (the four possible combinations of diked/undiked and observed flow/ virgin flow). More than 70% of the habitat in this reach has been lost (modern conditions vs. virgin flow with not dikes). In contrast, however, to the reach between Skamokawa and Beaver, selective dike removal (instead of a combination of dike removal and flow restoration) would suffice to increase spring SWHA. The second task consists of reconstruction of the hydrologic cycle before 1878, based on historic documents and inversion of tidal data collected before the onset of the historic flow record in 1878. We have a complete list of freshet times and peak flows for 1858-1877, and scattered freshet information for 1841-1857. Based on tidal data, we have reconstructed the annual flow cycles for 1870 and 1871; other time periods between 1854 and 1867 are under analysis. The three remaining tasks relate to post-1878 hydrologic conditions (flows, sediment supply and water temperature), and separation of the human and climate influences thereon. Estimated ob-served (sometimes routed), adjusted (corrected for reservoir manipulation) and virgin (corrected also for irrigation diversion) flows for 1878-2004 have been compiled for the Columbia River at The Dalles and Beaver, and for the Willamette River at Portland. Sediment transports for the ob-served, adjusted and virgin flows have been calculated for 1878-2004 for the Columbia River at Vancouver and Beaver, for the Willamette River at Portland, and for other west-side tributaries seaward of Vancouver. For Vancouver and Portland, it has been possible to estimate sand trans-port (including gravel), fine sediment transport and total load. Only total load can be estimated at Beaver, and only fine sediment transport can be determined for the west-side tributaries, except for the post-1980 period influenced by the 1980 eruption of Mt St. Helens. Changes in flows and sediment transport due to flow regulation, irrigation diversion, and climate have been estimated.},
doi = {10.2172/965263},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Aug 03 00:00:00 EDT 2009},
month = {Mon Aug 03 00:00:00 EDT 2009}
}
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DOI:  10.2172/965263
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  • ; ;
    In 2002 with support from the U.S. Army Corps of Engineers (USACE), an interagency research team began investigating salmon life histories and habitat use in the lower Columbia River estuary to fill significant data gaps about the estuary's potential role in salmon decline and recovery . The Bonneville Power Administration (BPA) provided additional funding in 2004 to reconstruct historical changes in estuarine habitat opportunities and food web linkages of Columbia River salmon (Onchorhynchus spp.). Together these studies constitute the estuary's first comprehensive investigation of shallow-water habitats, including selected emergent, forested, and scrub-shrub wetlands. Among other findings, this research documented themore » importance of wetlands as nursery areas for juvenile salmon; quantified historical changes in the amounts and distributions of diverse habitat types in the lower estuary; documented estuarine residence times, ranging from weeks to months for many juvenile Chinook salmon (O. tshawytscha); and provided new evidence that contemporary salmonid food webs are supported disproportionately by wetland-derived prey resources. The results of these lower-estuary investigations also raised many new questions about habitat functions, historical habitat distributions, and salmon life histories in other areas of the Columbia River estuary that have not been adequately investigated. For example, quantitative estimates of historical habitat changes are available only for the lower 75 km of the estuary, although tidal influence extends 217 km upriver to Bonneville Dam. Because the otolith techniques used to reconstruct salmon life histories rely on detection of a chemical signature (strontium) for salt water, the estuarine residency information we have collected to date applies only to the lower 30 or 35 km of the estuary, where fish first encounter ocean water. We lack information about salmon habitat use, life histories, and growth within the long tidal-fresh reaches of the main-stem river and many tidally-influenced estuary tributaries. Finally, our surveys to date characterize wetland habitats within island complexes distributed in the main channel of the lower estuary. Yet some of the most significant wetland losses have occurred along the estuary's periphery, including shoreline areas and tributary junctions. These habitats may or may not function similarly as the island complexes that we have surveyed to date. In 2007 we initiated a second phase of the BPA estuary study (Phase II) to address specific uncertainties about salmon in tidal-fresh and tributary habitats of the Columbia River estuary. This report summarizes 2007 and 2008 Phase II results and addresses three principal research questions: (1) What was the historic distribution of estuarine and floodplain habitats from Astoria to Bonneville Dam? (2) Do individual patterns of estuarine residency and growth of juvenile Chinook salmon vary among wetland habitat types along the estuarine tidal gradient? (3) Are salmon rearing opportunities and life histories in the restoring wetland landscape of lower Grays River similar to those documented for island complexes of the main-stem estuary? Phase II extended our analysis of historical habitat distribution in the estuary above Rkm 75 to near Bonneville Dam. For this analysis we digitized the original nineteenth-century topographic (T-sheets) and hydrographic (H-sheets) survey maps for the entire estuary. Although all T-sheets (Rkm 0 to Rkm 206) were converted to GIS in 2005 with support for the USACE estuary project, final reconstruction of historical habitats throughout the estuary requires completion of the remaining H-sheet GIS maps above Rkm 75 and their integration with the T-sheets. This report summarizes progress to date on compiling the upper estuary H-sheets above Rkm 75. For the USACE estuary project, we analyzed otoliths from Chinook salmon collected near the estuary mouth in 2003-05 to estimate variability in estuary residence times among juvenile out migrants. In Phase II we expanded these analyses to compare growth and residency among individuals collected in tidal-fresh water wetlands of the lower main-stem estuary. Although no known otolith structural or chemical indicators currently exist to define entry into tidal fresh environments, our previous analyses indicate that otolith barium concentrations frequently increase before individuals encounter salt water. Here we evaluate whether otolith barium levels may provide a valid indicator of tidal fresh water entry by Columbia River Chinook salmon. We also examine otolith growth increments to quantify and compare recent (i.e., the previous 30 d) growth rates among individuals sampled in different wetland habitats along the estuarine tidal gradient.« less

  • This work focuses on the numerical modeling of Columbia River estuarine circulation and associated modeling-supported analyses conducted as an integral part of a multi-disciplinary and multi-institutional effort led by NOAA's Northwest Fisheries Science Center. The overall effort is aimed at: (1) retrospective analyses to reconstruct historic bathymetric features and assess effects of climate and river flow on the extent and distribution of shallow water, wetland and tidal-floodplain habitats; (2) computer simulations using a 3-dimensional numerical model to evaluate the sensitivity of salmon rearing opportunities to various historical modifications affecting the estuary (including channel changes, flow regulation, and diking of tidalmore » wetlands and floodplains); (3) observational studies of present and historic food web sources supporting selected life histories of juvenile salmon as determined by stable isotope, microchemistry, and parasitology techniques; and (4) experimental studies in Grays River in collaboration with Columbia River Estuary Study Taskforce (CREST) and the Columbia Land Trust (CLT) to assess effects of multiple tidal wetland restoration projects on various life histories of juvenile salmon and to compare responses to observed habitat-use patterns in the mainstem estuary. From the above observations, experiments, and additional modeling simulations, the effort will also (5) examine effects of alternative flow-management and habitat-restoration scenarios on habitat opportunity and the estuary's productive capacity for juvenile salmon. The underlying modeling system is part of the SATURN1coastal-margin observatory [1]. SATURN relies on 3D numerical models [2, 3] to systematically simulate and understand baroclinic circulation in the Columbia River estuary-plume-shelf system [4-7] (Fig. 1). Multi-year simulation databases of circulation are produced as an integral part of SATURN, and have multiple applications in understanding estuary/plume variability, the role of the estuary and plume on salmon survival, and functional changes in the estuary-plume system in response to climate and human activities.« less

  • ; ;
    From 2002 through 2006 we investigated historical and contemporary variations in juvenile Chinook salmon Oncorhynchus tshawytscha life histories, habitat associations, and food webs in the lower Columbia River estuary (mouth to rkm 101). At near-shore beach-seining sites in the estuary, Chinook salmon occurred during all months of the year, increasing in abundance from January through late spring or early summer and declining rapidly after July. Recently emerged fry dispersed throughout the estuary in early spring, and fry migrants were abundant in the estuary until April or May each year. Each spring, mean salmon size increased from the tidal freshwater zonemore » to the estuary mouth; this trend may reflect estuarine growth and continued entry of smaller individuals from upriver. Most juvenile Chinook salmon in the mainstem estuary fed actively on adult insects and epibenthic amphipods Americorophium spp. Estimated growth rates of juvenile Chinook salmon derived from otolith analysis averaged 0.5 mm d-1, comparable to rates reported for juvenile salmon Oncorhynchus spp. in other Northwest estuaries. Estuarine salmon collections were composed of representatives from a diversity of evolutionarily significant units (ESUs) from the lower and upper Columbia Basin. Genetic stock groups in the estuary exhibited distinct seasonal and temporal abundance patterns, including a consistent peak in the Spring Creek Fall Chinook group in May, followed by a peak in the Western Cascades Fall Chinook group in July. The structure of acanthocephalan parasite assemblages in juvenile Chinook salmon from the tidal freshwater zone exhibited a consistent transition in June. This may have reflected changes in stock composition and associated habitat use and feeding histories. From March through July, subyearling Chinook salmon were among the most abundant species in all wetland habitat types (emergent, forested, and scrub/shrub) surveyed in the lower 100 km of the estuary. Salmon densities within wetland habitats fell to low levels by July, similar to the pattern observed at mainstem beach-seining sites and coincident with high water temperatures that approached or exceeded 19 C by mid-summer. Wetland habitats were used primarily by small subyearling Chinook salmon, with the smallest size ranges (i.e., rarely exceeding 70 mm by the end of the wetland rearing season) at scrub/shrub forested sites above rkm 50. Wetland sites of all types were utilized by a diversity of genetic stock groups, including less abundant groups such as Interior Summer/Fall Chinook.« less

  • ; ;
    This project analyzes in greater detail the coded-wire-tag (CWT) returns of Priest Rapids Hatchery fall chinook for the years 1976--1989 initially begun by Hilborn et al. (1993a). These additional analyses were prompted by suggestions made by peer reviews of the initial draft report. The initial draft and the peer review comments are included in this final report (Appendices A and B). The statistical analyses paired Priest Rapids stock with potential downriver reference stocks to isolate in-river survival rates. Thirty-three potential reference stocks were initially examined for similar ocean recovery rates; the five stocks with the most similar recovery patterns (i.e.,more » Bonneville Brights, Cowlitz, Gray's River, Tanner Creek, and Washougal) to the Priest Rapids stock were used in the subsequent analysis of in-river survival. Three alternate forms of multiple regression models were used to investigate the relationship between predicted in-river survival and ambient conditions. Analyses were conducted with and without attempts to adjust for smolt transportation at McNary Dam. Independent variables examined in the analysis included river flows, temperature, turbidity, and spill along with the total biomass of hatchery releases in the Columbia-Snake River Basin.« less

  • ;
    Developing an understanding of the distribution and changes in estuarine and tidal floodplain ecosystems is critical to the management of biological resources in the lower Columbia River. Columbia River plants, fish, and wildlife require specific physicochemical and ecological conditions to sustain their populations. As habitats are degraded or lost, this capability is altered, often irretrievably; those species that cannot adapt are lost from the ecosystem. The Lower Columbia River Estuary Partnership (Estuary Partnership) completed a comprehensive ecosystem protection and enhancement plan for the lower Columbia River and estuary in 1999 (Jerrick, 1999). The plan identified habitat loss and modification asmore » a critical threat to the integrity of the lower Columbia River ecosystem and called for a habitat inventory as a key first step in its long term restoration efforts. In 2000, the Estuary Partnership initiated a multiphase project to produce a spatial data set describing the current location and distribution of estuarine and tidal freshwater habitat cover types along the lower Columbia River from the river mouth to the Bonneville Dam using a consistent methodology and data sources (Fig. 1). The first phase of the project was the development of a broadbrush description of the estuarine and tidal freshwater habitat cover classes for the entire study area ({approx}146 river miles) using Landsat 7 ETM+ satellite imagery. Phase II of the project entailed analysis of the classified satellite imagery from Phase I. Analysis of change in landcover and a summary of the spatial relationships between cover types are part of Phase II. Phase III of the project included the classification of the high resolution hyperspectral imagery collected in 2000 and 2001 for key focal areas within the larger study area. Finally, Phase IV consists of this final report that presents results from refining the Landsat ETM+ classification and provides recommendations for future actions. Previous studies (Thomas, 1980; Thomas, 1983; Graves et al., 1995; NOAA, 1997; Allen, 1999) produced similar landcover data sets; however, most of these studies used multiple and varied data sources and differed from one another in methodologies. Currently, no single data set has been produced using a consistent methodology and uniform scale data, which describes current estuarine and tidal freshwater floodplain cover types from the Columbia's mouth to the Bonneville Dam (Fig. 1). Results from this study will be used by the Estuary Partnership and its cooperators to: (1) develop indicators of 'habitat health' for target species and populations, and biological integrity at the community and ecosystem scales; (2) develop definitions of 'important salmonid habitat'; (3) identify and evaluate potential wetland conservation and restoration sites; (4) track non-indigenous and invasive species; and (5) develop an understanding of how estuarine and floodplain habitats have changed over the past 200 years. This study focused on estuarine and tidal freshwater floodplain habitat cover types, which are important to native species, particularly juvenile salmonids. Results from this study are meant to provide support for the multiple efforts currently underway to recover 12 species of Columbia River salmonids identified as endangered or threatened under the Endangered Species Act. Spatial scale was an important consideration in this study. Our goal was to create a geographic information system (GIS) coverage depicting habitat cover types for the entire 146 river miles of the study area and the associated floodplain, at a spatial resolution sufficient to resolve important estuarine and floodplain features, wherever possible. Thus, in addition to the small scale (30 m pixel size) satellite imagery covering the study area described in this report, we also acquired high spatial resolution imagery ({approx}1.5 m pixel size) for key portions of the study area using a Compact Airborne Spectrographic Imager (CASI). Compared to the rather coarse, low spectral resolution of the satellite imagery, the CASI imagery provides the spectral resolution (19 CASI bands vs. 7 ETM+ Bands) necessary to discriminate between spectrally similar vegetation types and thus provided a greater ability to resolve habitat features important to species such as salmonids. Unfortunately, image acquisition costs and logistics (time and poor weather) prevented complete coverage of the study area at a 1.5 m spatial scale. However, in 2000/01 CASI imagery was collected for several key focal areas including the Chinook watershed, the area around the Astoria Airport mitigation site, Russian Island, Tenasillahe Island, Sauvie Island, Scappose Bay lowlands, Lord and Walker Islands and much of the shoreline. This report presents the classification methodology and initial results from the satellite image classification.« less