Beechie, T. J., G. Pess, E. Beamer, G. Lucchetti, and R.E. Bilby.

2003

Role of watershed assessments in recovery planning for salmon, pp 194-225. In: Restoration of Puget Sound Rivers (eds.) D. R. Montgomery, S. B. Bolton, D. B. Booth, and L. Wall.

University of Washington Press. Seattle and London.

Puget Sound, salmon, riverine, recovery, abundance, watershed, assessment, historic

Part of a larger body of work, this chapter discussed the role of watershed assessments in salmon (Oncorhynchus spp.) recovery planning. The importance of identifying and clearly defining goals and objectives related to assessment needs were described, as a means to limit expense and effort during the restoration-planning phase. Two roles watershed assessments may play in recovery planning of ESA-listed Puget Sound salmon were proposed. First, these assessments ?can be used to estimate changes in habitat conditions and smolt production capacity from the time prior to non-Native American settlement to the present day? and secondly, ?identify causes (human and natural) of habitat change or loss, and identify needed habitat protection and restoration actions.? A conceptual framework for watershed assessments was discussed, and two important questions relevant to salmon recovery planning were identified for which watershed assessments can help to answer. The first question pertained to historic and present-day habitat abundance ?for watersheds containing one or more genetically distinct salmon populations? and the second question pertained to the causes of habitat degradation.

The two roles watershed assessments play in salmon recovery planning and examples of application were discussed at length. Three steps were identified for the first role of estimating historic and current habitat and fish production potential. These were identifying habitat types, estimating historic and present-day habitat abundance and linking fish production and habitat. Two examples of application were provided for juvenile coho salmon (Oncorhynchus kisutch), one each in the Skagit River basin and the Stillaguamish River basin. The second role, assessing causes of habitat change, was discussed and several landscape processes requiring assessment were identified. These included hydrology, sediment supply, riparian functions, channel-floodplain interactions, isolated habitat, and water quality. Examples of application were provided for sediment supply, riparian function and habitat isolated and blocked for fish access. The use of assessment results was then described.

It was concluded ?assessments of the historic and current condition of a watershed can greatly improve our efforts to plan, implement, and monitor habitat restoration for the recovery of Pacific salmon.? Systematic inventories of a variety of data should be conducted throughout a watershed. Data gaps and sources of uncertainty were addressed.

Beechie, T.J., and S. Bolton.

1999

An approach for restoring salmonid habitat-forming processes in Pacific Northwest watersheds.

Fisheries 24(4):6-15.

Processes, watershed, habitat, scale, restoration, salmonid

A restoration approach centered on identifying habitat degradation and restoring watershed processes versus individual habitat characteristics was presented. Diagnosing and treating the causes of habitat degradation instead of the effects of degradation was stressed. The strategy of process-based restoration "focuses on understanding changes to habitat-forming processes and identifies locations where specific restoration actions are needed to restore such processes." By restoring processes that shape salmonid habitat, it was noted that an array of habitat conditions will be expressed where local salmonid stocks are adapted.

A process-oriented restoration goal was presented, as were locally defined restoration priorities. Next, implementation of this approach was discussed and included five steps and strategies (estimate historical rates of habitat-forming processes; estimate current rates of habitat-forming processes - address changes in rates due to land use; identify restoration risks; estimate effectiveness of restoration tasks with respect to local biological objectives and; prioritize restoration tasks) and examples of methods or data. Finally, two examples (sediment supply, stream temperature) of this approach were illustrated.

Borde, A. B., R. M Thom, S. Rumrill, and L.M. Miller.

2003

Geospatial habitat change analysis in Pacific Northwest coastal estuaries

Estuaries 26 (4B):1104-1116.

Pacific Northwest, historical, estuary, marsh, eelgrass, habitat, stressor

Historical information and recent geospatial information was used to assess changes in potential estuarine habitat, specifically unvegetated flats and eelgrass, in Washington (Grays Harbor, Willapa Bay) and Oregon (Coos Bay). Principal factors suspected of contributing to changes in tidal habitat were discussed. Historical and present-day data sources included navigation charts, hydrographic surveys, wetland inventories and published descriptions. Data layers for shoreline location, bathymetry and wetlands were created and digitized, and then geospatially analyzed using GIS. An accurate and quantitative assessment of habitat changes was the goal of this study.

Factors suspected of affecting salt marshes were listed, among them diking, filling, eutrophication, grazing and agricultural activities, exotic species (Spartina alterniflora and Zostera japonica in particular), chemical pollution, and rising sea levels. Factors affecting seagrasses were also listed, among them reduced water clarity, mechanical damage, sea level rise, and toxic chemicals. Estuarine habitat loss in Grays Harbor, Willapa Bay and the Columbia River from 1870-1983 was reported from previous studies? results.

Results from the historical change assessment indicated that for the areas compared, tidal flats decreased for all three estuaries (22% for Grays Harbor and Willapa Bay), tidal wetland areas declined for the estuaries where comparative data existed (Willapa Bay, Coos Bay), and potential eelgrass habitat increased in two of the three estuaries (Grays Harbor, Willapa Bay) but decreased somewhat in Coos Bay. Potential sources of errors were noted. Substantial changes were noted at the mouths of Grays Harbor and Willapa Bay. Physical alterations such as diking, filling, armoring and dredging (filled material converting flats to marsh and upland conversion) were reported as reasons for the change in habitat. Potential factors for the loss of flats in Grays Harbor and Willapa Bay were noted (e.g., reduced sediment input from the Columbia River due to reduced flows, water withdrawal, dredging, jetty construction). Possible indirect causative agents were also discussed (forest practices, climate and oceanographic processes), as were the role of introduced species and sea level rise. An assessment such as this provides valuable insight and critical information for managers planning restoration actions.

Bortelson, G.C., M.J. Chrzastowski, and A. K. Helgerson.

1980

Historical changes of shoreline and wetland at eleven major deltas in the Puget Sound region, Washington.

Atlas HA-617, Department of Interior, U.S. Geological Survey.

Puget Sound, historical condition, map accuracy, river deltas, wetlands, shoreline modification

The earliest available and authoritative historical maps depicting the condition of Puget Sound shorelines and wetlands were compared to present-day topographic maps for eleven delta regions. Considerable effort was taken to transfer historical data to present-day maps. Factors affecting accuracy were noted, and included the land grid, analytical and interpretive limitations, delineation of shoreline and wetlands, low-water line, map symbols, judgment of compilers, data transfer, map stability, optical transfer and tracing.

Comparison of historical maps between 1855 and 1900 (80 to 125 years prior to the 1980 published date of this paper) to modern topographic maps provided documentation of shoreline alteration, wetland gain or loss and change in delta land use. A general discussion of the principles and processes - natural and human caused- affecting delta shorelines as a means of evaluating change was presented. These included progradation and sediment supply, recession, shifting of stream channels, human-induced shoreline modifications and development on the deltas. It was stressed that only overall changes in shoreline condition could be distinguished since information was evaluated from only two periods in time (i.e., based on historical maps and present-day maps).

Based on comparisons of historic and present-day maps, the loss of subaerial wetlands and intertidal areas for the 11 deltas were presented. A majority of the 11 deltas showed a loss of subaerial wetlands, of which three deltas (Lummi, Snohomish and Puyallup) exhibited a significant loss totaling 5km2 or more. Diking was identified as the primary causative agent. The Nooksack and Stillaguamish deltas exhibited a slight increase in subaerial wetland area. For intertidal areas, data were available for eight of the 11 deltas. The Lummi, Skokomish and Dungeness deltas showed relatively minor loss of intertidal area, whereas the Duwamish and Puyallup deltas exhibited nearly a complete loss of intertidal area. Extensive dredge and fill operations were identified as the primary causative agent.

Bottom, D. L., C. A. Simenstad, A. M. Baptista, D. A. Jay, J. Burke, K. K. Jones, E. Casillas, and M. H. Schiewe.

2001

Salmon at River?s end: The role of the estuary in the decline and recovery of Columbia River Salmon.

Report by National Marine Fisheries Service, Seattle, Washington.

Columbia River, estuary, Pacific salmon, population, survival, stressor, life history, predator, historic

They discuss the decline in Columbia River salmon populations in the context of industrial development of the estuary and salmon harvest. Approximately 65% of the lower estuary (downstream from Jones Beach) had been diked or filled by the middle 1900s, while the remaining habitat has been degraded by other human activities. They provide a conceptual framework for evaluating estuarine habitat conditions based on geographic complexity. They discuss how changes in the hydrologic conditions of the river basin have influenced the estuarine habitat by suppression of winter and spring freshet flows that together with diking and filling have eliminated interactions between the lower river and its floodplain. Estuarine habitat opportunity or availability to young salmon is discussed as a change that influences juvenile rearing. ?Suitable habitat? is defined as physical conditions that have water depths of 0.1 to 1 m deep and velocities lower than 0.3 m/sec. Modeling indicates historic estuarine conditions may have provided more ?suitable habitat? conditions throughout a range of flows than current conditions. They found the food web in the existing estuary has changed from historic conditions. Existing conditions have a microdetrital food web supporting a largely pelagic food base, whereas the historic conditions likely supported a macrodetrital bsed food web. The introduction of non-indigenous fishes and piscivorous avian predators has influenced juvenile salmon survival in the estuary. They concluded the population structure and life-history diversity of subyearling Chinook (Oncorhynchus tshawytscha) have been simplified influencing timing and growth of juveniles passing through the estuary. Young Chinook now enter the estuary by at least two weeks later than with historic conditions, and are dominated by hatchery reared fish.

Bottom, D.L.

1997

To till the water: a history of ideas in fisheries conservation, pp 569- 597. In D. J. Stouder, P.A. Bisson, and R. J. Naiman (eds.) Pacific salmon and their ecosystems.

Chapman and Hall, New York.

Fisheries conservation, historic, ecosystem management, hatchery

Part of a larger body of work, this chapter described the early history of ideas in fisheries management and what these may teach scientists and resource managers about ecosystem management. Early ideas pertaining to fisheries management were shaped by social and ecological changes consistent with that period (e.g., westward expansion, economic progress across America). Early technologies for propagating fish in hatcheries and resulting conservation movements were discussed. The culturing of fish provided a source of income to many and a means to increase food supply to an increasing population. The economic potential of artificial propagation was touted by many, and spawned the creation of state fish commissions and passage of laws. The influence of agricultural goals in early fishery management (fish culture) was described at length (utilitarian ideals, ?waste? reduction [egg survival in wild compared to hatchery], predator control, removal of ?trash fish,? production levels). ?The same ideas and tools that the fisheries profession developed to produce an agricultural commodity may not be very useful if we now wish to promote the health and integrity of complex natural-cultural systems.? Ecosystem management in place of conservation ?implies a continuing search for an analytical solution to a value-based problem. A more important role for fisheries than ecosystem management will be to foster a better understanding and appreciation of human ecosystem dependence.?

Burger, C.V., R.L. Wilmot, and D.B. Wangaard.

1985

Comparison of spawning areas and times for two runs of chinook salmon (Oncorhynchus tshawytscha) in the Kenai River, Alaska

Canadian Journal of Fisheries and Aquatic Sciences 42:693-700.

Alaska, Chinook salmon, migration, timing, distribution, spawning

Spawning characteristics (location, timing) of Chinook salmon (Oncorhynchus tshawytscha) in Kenai River, Alaska were studied to determine the presence of two distinct Chinook runs. Factors determining the spawn timing and distribution of Chinook salmon in this system were hypothesized. Over a four-year period (1979-1982), 188 Chinook were captured by gill net in the lower 20 km of the Kenai River. Radio telemetry was used to track the fish to their spawning areas and to determine spawning times. Behavioral effects to fish from radio tagging were not observed. The development of criteria for determining spawning areas and times was discussed.

These study results, combined with unpublished sport harvest data from the Alaska Department of Game and Fish, revealed ?strong evidence? of two distinct runs and discrete spawning stocks of Chinook salmon within the Kenai River system. An early-run entered the Kenai River in May and June and spawned in Kenai River tributaries (primarily two tributaries, located in the lower Kenai system) during mid-July. A late-run entered the river from late June through August and spawned in the mainstem Kenai River in late August. The radio tagging data ?suggested a tendency for spawning to occur progressively later as distance from Cook Inlet increased.? The influence of lakes and water temperatures were considered. Lakes influenced tributary drainages where peak spawning takes place during August. Conversely, lakes were not present in tributary systems when peak spawning occurred in July. An increase in fall and winter water temperatures downstream from lakes may have been due to the presence of lakes, ?enabling successful reproduction for later spawning fish within these tributaries.? The late spawning stock may exist because of two large lakes within the mainstem. Finally, ?if run timing is genetically controlled, and if the various components of the two runs are isolated stocks that have adapted to predictable stream temperatures, there are implications for stock transplantation programs and for any activities of man that alter stream temperatures.?

Carl, L. M., and M. C. Healy.

1984

Differences in enzyme frequency and body morphology among three juvenile life history types of Chinook salmon (Oncorhynchus tshawytscha) in the Nanaimo River, British Columbia.

Canadian Journal of Fisheries and Aquatic Sciences 41:1070-1077.

British Columbia, juvenile Chinook salmon, life history, timing, morphology, residence time, genetics, smolt

There are three life-history types of Chinook, one of which migrates directly to the estuary for rearing upon emergence from the gravel. The second migrates to the estuary following about two months of stream rearing. The third type migrates as smolts after one year of stream rearing. Both genetic information and body characteristics indicate these life-history types are genetically isolated subpopulations.

Collins, B.D., and D.R. Montgomery.

2001

Importance of archival and process studies to characterizing pre-settlement riverine geomorphic processes and habitat in the Puget lowland.

Pages 227-243 In Geomorphic Processes and Riverine Habitat J. M. Dorava, D.R. Montgomery, B. B. Palcsak, F.A. Fitzpatrick (eds.).Water Science and Application Volume 4.

Puget Sound, salmonid, landscape, riverine, estuarine, historic, habitat, process-based, riparian vegetation, restoration

Archival investigations and present-day field studies were applications used in a continuing study of primarily the Nisqually, Snohomish, Stillaguamish and Skagit Rivers in the Puget Lowland. Understanding the process dynamics that shaped the historic landscape and habitat, and the development of ?quantitative, process-based, and river-specific templates for river and habitat restoration?? were goals of the study. The relationship between and complementary nature of archival studies and field studies was described. Primary archival sources of data included General Land Office surveys from about 1850-1880 and surveys by the U.S. Coast and Geodetic Survey depicting coastlines and coastal rivers. Additional sources of archival data were listed.

The historic abundance and distribution of riverine habitats in lowland floodplains and deltas were described primarily from archival sources for the four rivers. River pattern and floodplain interaction, floodplain habitats, in-channel wood, and wood and pools were described from archival sources and current field studies. Graphics and aerial photographs were presented for the lowland river and deltas, illustrating change in the landscape over time. The importance of wood to channels, floodplains and pools was described. Thus, ?a true program of river restoration therefore must emphasize restoring floodplain forests, the river?s lateral erosion, and wood jams.?

A greater emphasis on restoration of lowland habitats in watershed planning was argued for as a means of providing refugia for salmonids (i.e., ?because of their historic quantitative importance?) as well as being ?buffered from upstream watershed disturbances.? Furthermore, ?the importance of undertaking historic analysis early in restoration and conservation planning? was argued for.

Collins, B.D., D.R. Montgomery, and A.J. Sheikh.

2003

Reconstructing the historical riverine landscape of the Puget Lowland, pp. 79-128. In Restoration of Puget Sound Rivers (eds.) D. R. Montgomery, S. B. Bolton, D. B. Booth, and L. Wall

University of Washington Press. Seattle and London.

Puget Sound, riverine, historic, landscape, process-based, riparian vegetation, restoration, lowland forest, wood

Part of a larger body of work, this chapter described the use of archival studies and field investigations in the reconstruction of the historical riverine landscape of the eastern Puget Lowland. The geological characteristics and forces responsible for shaping the region were discussed. The reliability of historic reconstructions was discussed, and depends on the methods used. The relationship between and complementary nature of archival studies and field studies was described. Archival sources can assist in forming hypotheses about processes and features formerly operating throughout a historical landscape. Field investigations can produce specific process models, providing the basis for designing and applying effective management and restoration/conservation efforts. Together, archival studies and field investigations ?can adequately characterize the changes occurring on decadal and more frequent time scales.? An emerging technique for mapping historical river landscapes and habitats was discussed. Historical information is combined with geographic information system (GIS) and remote sensing imagery.

Archival sources of data were described in some detail. Between 1850 and 1890 the General Land Office surveyed Puget Lowlands and produced maps and field notes, considered ?a fundamental resource? because of the spatial coverage and characterization of the riverine landscape prior to Euro-American settlement. The field notes contained information about natural vegetation and presence of land and water features, including major changes and measurements of distance and size. Additional archival data sources such as early U.S. Coast and Geodetic Survey charts of coastlines and coastal rivers and U.S. Army Engineer annual reports were also discussed. Current mapping techniques were also described. The benefits of map interpretations of the historical landscape were touted (e.g., stripping away the accumulated stressors to ?gain a new view of river and floodplain morphology? as well as variations in response to glacial activity).

The influence of Pleistocene glaciation on river patterns of several Puget Lowland rivers was discussed and graphics were presented. A meandering channel characterizes the Snoqualmie River whereas the lower Nisqually River exhibits a branching and multiple channel pattern (anastomosing). Both rivers have responded differently to glacial activity and are associated with different river dynamics and landforms. The meandering Snoqualmie River channel and oxbows have changed little since the earliest mapping some 130 years ago. The most extensive changes have occurred in the valley wetlands and loss of valley floor forests. Over the same period the Nisqually River exhibited frequent channel shifts or course changes, with wood jams as a critical component to maintaining the anastomosing character of the lower Nisqually River. Patches of mature forests on the floodplain of the Nisqually River still exist and contributed to the ?channel-switching dynamic? of this system. Reconstruction analysis of the Stillaguamish River showed this system was once similar to the Nisqually River (anastomosing pattern).

The historical forest, amount of wood and the geomorphic and ecological importance of wood in the Puget Lowland were examined. Much of the dense river bottom forests in Puget Sound have been eradicated. Historically, ?the riverine forest was heavily weighted towards hardwoods.? Tree species, sizes and locations recorded in historical field notes were reported. Field notes from 1885 reported dense concentrations of wood in rivers. Field data were collected in 1998, and the potential effects of in-stream wood removal in the late 1800?s from the Snohomish, Stillaguamish and Nisqually Rivers were investigated. The lower Snohomish and Stillaguamish River systems have been dramatically altered. The Nisqually River contained approximately 8 times more wood per channel width than the Snohomish and 21 times more wood than the Stillaguamish, most of the difference ?accounted for by the abundance of wood in jams in the Nisqually River.? A decrease in the recruitment of wood from historic levels and the absence of ?long, large-diameter pieces with rootballs? were cited as reasons for the lack of wood jams in the two rivers. The U.S. Army Engineer records pertaining to ?snagging? wood from river channels provided quantitative numbers: 150,000 snags removed from five rivers between 1880 and 1980, with 30,000 snags removed from just the Skagit River between 1898 and 1908. Finally, the geomorphic and ecological importance of wood was described. Factors such as river dynamics, water and sediment distribution, flooding patterns, maintenance of multiple channels, islands and sloughs, and pool formation and function were addressed.

GIS maps of the ?nature and distribution of habitats? in the historic riverine environment are being created for Puget Sound, available at this time for the North Sound region. Prior to extensive modification of the landscape by settlers, the large floodplain wetlands and extensive estuarine marshes ?accounted for nearly two-thirds (62%) of the valley bottom? of the Snohomish River. The Nooksack mainstem exhibited a similar distribution of habitats, historically. A ?simpler channel pattern? now exists for the upper Nooksack mainstem and the Skykomish River, due in part to levees and isolating meanders. Historically, estuarine wetlands were extensive in the Skagit-Samish delta, consuming an area more than twice that of the Nooksack, Stillaguamish and Snohomish deltas, combined. Diking and draining of wetlands has reduced the area. These differences ?demonstrate the important role of archival sources in characterizing the abundance and variation of aquatic habitats.?

The use of historical information in restoration, rehabilitation and conservation planning was discussed. The utility of historical analysis relative to restoration needs, identifying primary elements, issue and opportunities, planning riverine reforestation and wood reintroduction, and conservation planning were discussed in detail. Historical analyses ?can reveal opportunities and constraints, which in turn may dictate the choice of restoration versus rehabilitation.? Identification of the historically dominant processes should occur at the initial planning stage for restoration of a river. This action identifies ?the appropriate conceptual models of riverine function and restoration.? Description of the types and distribution of riverine habitats ?associated with these processes then makes it possible to set restoration or rehabilitation targets.? The ?regional differences in channel morphologies, processes, suites of valley-bottom landforms, and forests, combined with different land-use histories, have important implications for the rationale, approach, and land area needed in restoring lowland river and forest ecosystems.? Insights gained from this Puget Sound Lowland study are likely to be applicable to regions outside the Puget Lowland.