National Park Service 

U.S. Department of the Interior 

Natural Resources Program Center 

Assessment of Coastal Water Resources and 

Watershed Conditions at Lewis and Clark National 

Historical Park, Oregon and Washington

Natural Resource Report NPS/NRPC/WRD/NRTR—2007/055 
ON THE COVER 

Upper left, Fort Clatsop, NPS Photograph 

Upper right, Cape Disappointment, Photograph by Kristen Keteles 

Center left, Ecola, NPS Photograph 

Lower left, Corps at Ecola, NPS Photograph 

Lower right, Young’s Bay, Photograph by Kristen Keteles 
Assessment of Coastal Water Resources and 

Watershed Conditions at Lewis and Clark 

National Historical Park, Oregon and Washington

Natural Resource Report NPS/NRPC/WRD/NRTR—2007/055 

Dr. Terrie Klinger 

School of Marine Affairs 

University of Washington 

Seattle, WA 98105-6715 

Rachel M. Gregg 

School of Marine Affairs 

University of Washington 

Seattle, WA 98105-6715 

Jessi Kershner 

School of Marine Affairs 

University of Washington 

Seattle, WA 98105-6715 

Jill Coyle 

School of Marine Affairs 

University of Washington 

Seattle, WA 98105-6715 

Dr. David Fluharty 

School of Marine Affairs 

University of Washington 

Seattle, WA 98105-6715 

This report was prepared under Task Order J9W88040014 of the Pacific Northwest Cooperative 

Ecosystems Studies Unit (agreement CA9088A0008) 

September 2007 

U.S. Department of the Interior 

National Park Service 

Natural Resources Program Center 

Fort Collins, CO 

i 
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or recommendation for use by the National Park Service. 

Printed copies of reports in these series may be produced in a limited quantity and they are only 

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internet, or by sending a request to the address on the back cover. 

Please cite this publication as: 

Klinger, T., R.M. Gregg, J. Kershner, J. Coyle, and D. Fluharty. 2007. Assessment of Coastal 

Water Resources and Watershed Conditions at Lewis and Clark National Historical Park, Oregon 

and Washington. Natural Resource Technical Report NPS/NRPC/WRD/NRTR—2007/055. 

National Park Service, Fort Collins, CO. 

NPS D-80, September 2007 

ii 
 

iii
Table of Contents 

List of Acronyms and Abbreviations vii 

Executive Summary viii

 

A. Park and Regional Description 1 

A.1. Background 1 

A.1.a. Setting 1 

A.1.b. Site History 3 

A.1.c. Human Utilization 5 

A.2. Hydrology 6 

A.2.a. Oceanographic Setting 6 

A.2.b. Hydrologic Setting 8 

A.3. Aquatic Habitats and Biological Resources 12 

A.3.a. Aquatic Habitats 12 

A.3.b. Biological Resources 20 

B. Water Resources Assessment 21

B.1. Water Quality 21 

B.1.a. Data Sources 21 

B.1.b. Water Quality 21 

B.1.c. Data Gaps and Information Inconsistencies 31 

B.2. Water Quality Degradation 31 

B.3. Sources of Pollutants 34 

C. Other Areas of Concern 40 

C.1. Harmful Algal Blooms 40 

C.2. Non-native and Invasive Species 40 

C.3. Harvest and Collection of Organisms 42 

C.4. Water Withdrawals 42 

C.5. Hydropower and Salmon Recovery 44 

C.6. Habitat Modification 45 

C.7. Oil and Fuel Spills 48 

C.8. Land-based and Water-based Recreation 50 

C.9. Tsunami Hazards 51 

C.10. Climate Change 51 

D. Recommendations 55

D.1. Condition Overview 55 

D.2. Recommendations 65 

D.2.a. Context and General Recommendations 65 

D.2.b. Specific Recommendations 68 

Literature Cited 69

Appendix A. Water Quality Standards 79

iv 
List of Figures 

Figure 1. The Lower Columbia River Estuary 1 

Figure 2. LEWI park sites 2

Figure 3. Surface salinity, Columbia River Plume 8 

Figure 4. Youngs Bay Watershed 11 

Figure 5. Youngs Bay Subwatersheds 12 

Figure 6. NWI coverage in region of LEWI 14 

Figure 7. Land cover types within the Cape Disappointment site 15 

Figure 8. Land cover types within the Station Camp site 16 

Figure 9. Land cover types within the Dismal Nitch site 17 

Figure 10. Land cover types within the Fort Clatsop National Memorial site 18 

Figure 11. Land cover types within the Sunset Beach site 19

Figure 12. CORIE sampling locations 23 

Figure 13. Water Resource Inventory Areas 24 and 25 25 

Figure 14. Summary of land use adjacent to streams in the Oregon region of LCRE 38 

Figure 15. Accumulation of non-indigenous species over time 41 

Figure 16. LCRANS collections by taxonomic group and origin 42 

Figure 17. Water withdrawals in the Youngs Bay watershed 43 

Figure 18. Dikes and wetlands in Youngs Bay watershed 45 

Figure 19. Columbia River Basin dams 46 

Figure 20. North and South jetties at Columbia River Mouth 47 

v 
List of Tables 

Table i. Summary of coastal water resource conditions in LEWI xi 

Table ii. Specific Recommendations xii 

Table 1. Water quality degradation within the Youngs Bay watershed 24 

Table 2. Category 5 and 4a 303(d) listings for the Columbia River (Water Medium) 26 

Table 3. Category 5 303(d) listings for the Columbia River (Tissue Medium) 26 

Table 4. BEACH bacterial monitoring results for Cape Disappointment State Park, 

2004-2006 27 

Table 5. Watershed issues by land use category 35 

Table 6. Industrial discharges in the vicinity of Fort Clatsop National Memorial 

and the LCRE 36

Table 7. Entities and facilities with permits to discharge into Youngs Bay 

Watershed 37

Table 8. Land use summary in the LCRE 38 

Table 9. Spills in the LCRE region 2005-2007 49 

Table 10. Observed and projected impacts of climate change in major climate and 

hydrologic indicators 52 

Table 11. Potential management implications associated with projected climate 

change impacts on water resources in the Pacific Northwest 54 

Table 12. Condition of water resources in and around LEWI 56 

Table 13. Condition of water resources in the Lower Columbia River Estuary 57 

Table 14. Condition of water resources in the Youngs Bay Watershed 59 

Table 15. Condition of water resources in freshwater wetlands, lakes, and streams 61 

Table 16. Condition of water resources in outer coastal areas 63 

Table 17. Specific Recommendations 68

vi 
Acknowledgments 

We wish to acknowledge and thank the many people that have assisted us in preparing this 

report. Within the National Park Service, Kristen Keteles, Cliff McCreedy, and Mark Flora have 

been very helpful in guiding this work. Scott Stonum, Chip Jenkins, and others at LEWI have 

helped us acquire site-specific information. Craig Dalby and Roger Hoffman have generously 

provided assistance with GIS aspects of the project. Numerous others have provided helpful 

information and data; we thank them all.

vii 
Acronyms & Abbreviations 

ACOE Army Corps of Engineers 

ASP Amnesic Shellfish Poisoning 

BEACH Beach Environmental Assessment Community and Health Program

BEACON Beach Advisory and Closing Online Notification Program

CIG Climate Impacts Group 

CRK Columbia Riverkeeper 

CRP Columbia River Plume 

DA Domoic Acid 

DAP Domoic Acid Poisoning 

DG Data Gap 

EPA Environmental Protection Agency 

GIS Geographic Information System

HAB Harmful Algal Bloom

HUC Hydrologic Unit Code 

LCRANS Lower Columbia River Aquatic Nonindigenous Species Survey 

LCRE Lower Columbia River Estuary 

LCREP Lower Columbia River Estuary Partnership 

LEWI Lewis and Clark National Historic Park 

NOAA National Oceanic and Atmospheric Administration 

NPS National Park Service 

NRDC National Resources Defense Council 

ODA Oregon Department of Agriculture 

ODEQ Oregon Department of Environmental Quality 

ODFW Oregon Department of Fish and Wildlife 

OHS Oregon Historical Society 

OWQI Oregon Water Quality Index 

PNW Pacific Northwest 

PSP Paralytic Shellfish Poisoning 

STORET Environmental Protection Agency’s STOrage and RETrieval database for water 

quality, biological, and physical data sets contributed by state environmental 

agencies, EPA and other federal agencies, universities, private citizens, and others. 

TMDL Total Maximum Daily Loads 

USGS U.S. Geological Survey 

UW University of Washington 

WDOE Washington Department of Ecology 

WDFW Washington Department of Fish and Wildlife 

WDNR Washington Department of Natural Resources 

WRD Water Resources Division 

WRIA Water Resources Inventory Area 

viii 
Executive Summary 

The purpose of this report is to provide a better understanding of the coastal water resources and 

watershed conditions of Lewis and Clark National Historical Park (LEWI). To accomplish this 

task we review the existing literature and summarize what is known about the current condition 

of the coastal water resources of the park and the degree to which they may be affected by 

natural and anthropogenic factors. As a result, this report provides both a status report on water 

resource conditions as well as an assessment of the present state of knowledge pertaining to 

environmental indicators and stressors. We further identify information gaps, topics where data 

are sparse and inadequate to fully assess resource condition, and make recommendations to fill 

information gaps necessary to support resource management. While the focus of this effort is on 

coastal resources, watershed conditions and surface and groundwater in the adjacent watersheds 

are also considered to a limited extent. 

The current condition of the water-related coastal resources within LEWI is based upon an 

assessment of common ecological indicators and stressors including water quality (e.g., 

nutrients, dissolved oxygen, fecal bacteria, metals and toxic contaminants), land use (e.g., timber 

practices, coastal development), habitat modification (e.g. coastal erosion), recreational use (e.g., 

fishing, shellfish harvesting, collection of marine organisms), and other concerns such as the 

introduction of non-native and invasive species, harmful algal blooms, and oil and fuel spills. 

We begin by describing the coastlines that characterize LEWI, which is situated within the 

Lower Columbia River Estuary (LCRE) region where it discharges into the Pacific Ocean. The 

park is comprised of twelve sites that are located on both sides of the Columbia River in 

Washington and Oregon. Originally established as Fort Clatsop National Memorial in 1958, 

LEWI was expanded in 2004 to include multiple sites that account for approximately 3,200 acres 

spread over forty miles of coastline. LEWI was established to commemorate the Lewis and Clark 

Expedition of the early 1800s. This assessment focuses on those units within the context of the 

LCRE, as well as the Lewis and Clark River, a tributary of the Columbia River; coastal sites 

within LEWI that lie outside the estuary are not focused on in this report. 

We review the site history and human utilization of the region in Section A. Prior to European 

contact in 1792, the Chinook peoples occupied much of the region. The Lewis and Clark 

Expedition party wintered over at Fort Clatsop from 1805-1806. European settlement of 

Washington and Oregon increased around 1846, following the signing of a boundary treaty with 

Great Britain (Lavender 1956). The primary emphasis in resource management for the park has 

been on reforestation in order to restore the dense forest canopy and thickets described by Lewis 

and Clark in their journals. 

The coastal region that influences LEWI is part of an eastern boundary current system. The 

Columbia River empties into the Pacific Ocean in an oceanographic region dominated by 

prevailing currents including the California Current, flowing southward; the Davidson Current, 

flowing northward in the winter; and the California Undercurrent, flowing northward at 

intermediate depth. These currents can create complex eddy fields, as well as upwelling and 

downwelling patterns. In addition, topographic features such as submarine canyons influence 

circulation; among these is Astoria Canyon, located offshore of the mouth of the Columbia 

ix 
River. The most conspicuous oceanographic feature in the region is the Columbia River Plume 

(CRP). It reaches as far south as 38°N and as far north as 49°N, and varies in strength and 

directionality both annually and seasonally as the result of changes in wind, rain, and snowmelt 

(Thomas and Weatherbee 2006). The tidal plume generates significant mixing and downwelling, 

bringing nutrients into the water column and increasing primary productivity. 

LEWI is situated in the Lower Columbia/Youngs Bay and the Necanicum Subbasins. Water 

resources in the region include lakes, ponds, seeps, seasonal streams, small upland streams, and 

several rivers. Youngs Bay and Baker Bay are prominent features of the lower estuary. Youngs 

Bay is located on the south side of the river, between Astoria and Warrenton, Oregon. The bay is 

fed by four rivers: the Lewis and Clark, Youngs, Klaskanine, and Wallooskee (Walluski). Baker 

Bay, on the north side of the river, is fed by the Chinook River; this water body has been 

significantly altered by anthropogenic activities, which have reduced wave and current energy. 

Aquatic habitats within LEWI generally are comprised of soft sediments, although substantial 

variation in sediment type and grain size occurs across locations. Tidal flats, epibenthic 

communities, and channel bottom habitat dominate the estuary’s entrance. These aquatic habitats 

support a variety of wildlife, including marine and freshwater fish species, birds, and mammals, 

and are influenced by both natural processes and human activities, especially by the extensive 

hydropower system in place on the river. 

With respect to water quality, it is apparent that there is a lack of consistent sampling and 

analysis over time in the region of LEWI. We reviewed existing data for bacterial contamination, 

contaminants, and marine biotoxins/harmful algal blooms. Regional water quality appears to be 

generally acceptable; however, some water quality standards have been exceeded in some places 

at some times. Toxics appear to be of the most concern in the region, especially pesticides (DDE 

and DDT), PCBs, dioxin/furans, radionuclides, PAHs, and metals (aluminium, iron, copper, lead, 

etc.). These contaminants have been found in both fish tissue and sediments. 

Sources of pollution in the LCRE and the Lewis and Clark River include non-point and point 

sources such as municipal and industrial wastewater discharges, stormwater runoff, timber 

harvesting, agricultural activities, landfill operations, sand and gravel pit activities, recreational 

use, marine watercraft traffic, and atmospheric deposition (NPS WRD 2000). Each of these 

sources has the potential to degrade water quality. For example, discharges from paper and pulp 

mills located along the Columbia River have been blamed for high levels of dioxins, found in 

both sediment and tissue samples. High water temperatures are believed to be caused by 

discharges from mills, dams, and industrial and municipal facilities. 

Other areas of concern include harmful algal blooms, non-native and invasive species, harvest 

and collection of organisms, water withdrawals, hydropower activities, habitat modification, oil 

and fuel spills, recreation, tsunami hazards, and climate change. 

Harmful algal blooms (HABs) are known to occur off the Oregon-Washington coast and are 

often produced by phytoplankton that can cause paralytic shellfish poisoning or domoic acid 

poisoning. The potential health impacts of HABs in commercially- and recreationally-harvested 

shellfish have motivated monitoring and research activities. 

x 
Non-native and invasive species are established in the LCRE. At least 81 organisms have been 

introduced into the region since the mid-1800s, the majority of which are fish, aquatic plants, and 

crustaceans. Over the past ten years, a new invertebrate species has been discovered about every 

five months. This likely reflects increasing rates of introduction, coupled with higher rates of 

reporting. Ballast water is believed to be the primary vector responsible for these introductions. 

The largest water withdrawals in the vicinity of LEWI are for municipal, domestic, and 

agricultural uses. It is estimated that these withdrawals have reduced flows within the Columbia 

River, affecting both timing and magnitude. Flow has also been affected by hydropower activity 

within the region. More than 400 dams exist within the Columbia River Basin, comprising one of 

the largest hydropower systems in the country. These dams have restricted fish passage, reduced 

river flow levels, and destroyed fish habitat, especially for anadromous fish. 

Aquatic habitats in the region have been modified by dike and jetty construction as well as by 

dredging. Dikes were constructed in Youngs Bay and the Lewis and Clark River between 1917 

and 1939, and jetty construction in the region began as early as the 1800s near the mouth of the 

Columbia River. These activities have reduced wave action and currents throughout the estuary. 

Dredging is regularly used to maintain the Columbia River’s navigability. For example, the 

Columbia River Channel Improvement Project will deepen the river by 43 feet in order to 

increase access by larger container ships. There is concern that such intensive dredging will 

resuspend contaminants buried in bottom sediments thereby increasing the chances for exposure 

to fish and other wildlife. 

Oil and fuel spills pose a chronic low-level threat to LEWI, as do seismic events that could 

generate tsunamis or landslides. Climate change is projected to intensify present stresses within 

the ecosystem through sea level rise, increased storm frequency and intensity, increased rates of 

erosion, and increased stream and river flow, all of which could impact biological communities 

and ecosystem function. 

We summarize the condition of water resources in and around LEWI in Table i. 

xi 
Table i. Condition of water resources in and around LEWI. 

Legend: 

EP= 

existing 

problem

PP= 

potential 

problem 

IP= 

intermittent 

problem

OK= 

no 

detectable 

problem

ID= 

insufficient 

data to 

evaluate 

Stressor/ 

Environmental 

Indicator 

Lower 

Columbia 

River 

Estuary 

Youngs 

Bay 

Watershed

Wetlands, 

Lakes, 

Streams 

Outer Coastal 

Waters 

WATER QUALITY 

INDICATOR 

 Nutrients ID EP ID OK

 Dissolved Oxygen EP EP ID ID

 Fecal Bacteria EP EP ID OK

Toxic Compounds EP EP ID OK

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

IP IP EP OK

 Stormwater 

Runoff 

IP IP EP OK

 Agricultural 

Runoff 

IP IP EP OK

HABITAT

MODIFICATION 

Upland Habitat 

Modification 

EP EP EP OK

 Shoreline/Aquatic 

Habitat 

Modification 

EP EP EP EP

 Erosion EP EP EP EP 

RECREATIONAL 

USAGE 

Harvest/Collection 

of Organisms 

OK OK OK OK

OTHER 

STRESSORS/ 

INDICATORS 

Non-Native 

Invasive Species 

EP EP EP OK

Harmful Algal 

Blooms

ID ID ID ID

Fuel / Oil Spills PP PP OK PP 

xii 
Based on our review and assessment of water resource condition and threats in coastal areas of 

LEWI, we offer the following specific recommendations. More general recommendations are 

offered in Section D.2.a. 

Table ii. Specific Recommendations 

• Maintain and expand the current water quality monitoring program to include new park 

sites. 

• Integrate the water quality monitoring program with regional programs (e.g., LCREP 

monitoring program). 

• Determine feasibility of restoring aquatic habitats within LEWI to the approximate 

conditions encountered by Lewis and Clark; prioritize habitats by feasibility, and modify 

management goals for aquatic habitats deemed not feasible for restoration.

• Where feasible, partner with local groups and tribes to restore degraded freshwater and 

estuarine habitats, especially those that provide essential fish habitat. 

• Develop a plan for managing non-indigenous marine, estuarine, and freshwater species. 

• Work with other agencies and entities to reduce the impacts of hydropower and land use 

on water resources within LEWI. 

• Encourage NACP to update the Oil Spill Geographic Response Plans for the Lower 

Columbia River Estuary and outer coastal regions. Consider whether the definition of 

sensitive areas under existing Oil Spill Contingency Plan rules could be expanded to 

include sensitive areas within LEWI. 

• Measure stormwater runoff and manage to reduce impacts to estuarine environments. 

• Measure the amounts of toxins and contaminants introduced to coastal streams and rivers 

and to beach areas by surface water flow from primary and secondary roadways and 

parking areas. Determine whether toxins and contaminants from roadway sources impair 

water resources in LEWI.

• Plan for impacts due to climate change, including impacts to restoration sites. 

xiii 
A. Park and Regional Description

The physical, biological, and cultural attributes of terrestrial and aquatic habitats within Lewis 

and Clark National Historical Park (LEWI) are described in excellent detail by Wetherbee and 

Hall (2006), and we guide the reader to that source for an overview of terrestrial and aquatic 

resources and habitats within and around the park. Here we focus more narrowly on attributes of 

water resources within and adjacent to LEWI. 

 

A.1. Background 

This section provides an overview of the location of LEWI, describes its general features, 

reviews the history of the site, and covers human uses of the area through time. 

A.1.a Setting 

The Columbia River forms the boundary between the states of Oregon and Washington, both of 

which are located in the Pacific Northwest region of the United States (Figure 1). 

Figure 1. The Lower Columbia River Estuary (www.columbiaestuary.org).

1 
LEWI straddles the banks of the Lower Columbia River Estuary (LCRE) as it discharges into the 

Pacific Ocean and includes several disjunct sites located on the outer coast (Figure 2). 

Figure 2. Park sites within LEWI. Source: Map created by authors. 

Originally established as Fort Clatsop National Memorial on 125 acres in 1958, LEWI was 

expanded in 2004 to approximately 3,200 acres extending across 40 miles of the coast. LEWI is 

2 
made up of 12 units under national or state administration. The units are significant sites as 

recorded during the December 1805 to March 1806 winter encampment of the Lewis and Clark 

Expedition. They include Fort Clatsop National Memorial, Dismal Nitch, Station Camp, Netul 

Landing, Salt Works, Cape Disappointment, Fort Columbia, Fort Stevens, Sunset Beach, Ecola, 

the Fort to Sea Trail (from Fort Clatsop National Memorial out to Sunset Beach), and the 

memorial to Thomas Jefferson (Cannon 1995). 

Fort Clatsop National Memorial was established “for the purpose of commemorating the 

culmination, and the winter encampment, of the Lewis and Clark Expedition following its 

successful crossing of the North American Continent” (PL 85-435, 72 Stat. 153). Fort Clatsop 

National Memorial was the first U.S. military post west of the Rocky Mountains, although the 

expeditionary party only occupied it for a little over three months. The work done by the party in 

collecting and reporting flora and fauna contributed to an early understanding of the natural 

resources of the United States. The depiction of the Chinook peoples as recorded in the 

expedition’s reports is considered to be among the best-documented post-contact views of daily 

life and culture among these tribes (Cannon 1995). 

In addition to the obvious historic importance of LEWI, the various units contain a variety of 

ecosystems ranging from soft sediment intertidal areas in the estuary, extensive sandy shorelines 

and dunes, rocky headlands, temperate rainforests, riparian zones, and swamps, as well as rural 

land used for farming, dairying, and grazing (NPS 2006a). This water resources assessment 

focuses on the National Park units within the context of the LCRE, as well as the Lewis and 

Clark River, a tributary of the Columbia. The inventory includes freshwater springs, streams, 

marshes and ponds, brackish water sloughs, salt marshes, and intertidal areas. Some of these 

freshwater features are ephemeral, appearing during the wet fall, winter, and spring seasons, but 

disappearing in the dry summer. 

Geologically, LEWI is within the Columbia embayment of the Coast Range Province. This area 

is characterized by Cenozoic era sediment strata capped by Eocene and Oligocene basaltic lavas 

that are exceptionally thick (McKee 1972). The surface geology that is currently visible consists 

of Tertiary marine and non-marine sediments and basalts from the Miocene (NPS 2006a). 

Alteration of the estuary by dredging, diking, and jetty construction has changed the form of the 

estuary and affected sediment transport. No minerals of economic importance have been located 

although clay, sand, and gravel do exist in commercial quantities. The combination of deep 

sediments and thick basalt cap rock has induced several rounds of petroleum and natural gas 

exploratory drilling with only partially successful results (McKee 1972). 

The combination of landforms, hydrology, and vegetation creates habitats for a diversity of 

resident species of mammals, birds, fish, amphibians, and reptiles as well as migrating species 

(NPS 2006a). 

A.1.b. Site History 

This section is abstracted from the Fort Clatsop Administrative History (Cannon 1995) except 

where otherwise noted. 

3 
Chinook peoples occupied many sites on the coast and in the Columbia River estuary prior to the 

first recorded European contact in 1792 with explorers and traders on ships. The Lewis and Clark 

Expedition party wintered-over at Fort Clatsop from 1805-1806. The next settlement attempt 

came from the Pacific Fur Company, which established Fort Astor in 1811. 

Fort Clatsop 

Fur traders and other visitors curious about the Lewis and Clark Expedition sought out the site of 

the abandoned Fort Clatsop. They reported that as late as 1821, remains of the original walls of 

the encampment could be found. Two houses occupied by Clatsop tribe members were also 

found. European settlement of Washington and Oregon increased following the signing of a 

boundary treaty with Great Britain in 1846 (Lavender 1956). Claims were staked on the Fort 

Clatsop site and it was transferred into private ownership in 1850. As the property passed 

through various hands, the original forests were cleared. Over time and with changes in land use, 

the exact location of the Fort Clatsop site became subject to speculation. Various efforts were 

made to relocate the site around 1900, the most serious being that by the Oregon Historical 

Society (OHS) which purchased three acres determined to be the most likely site. In 1912, the 

OHS installed a bronze marker at the site. The society acquired two more acres in 1928 that 

included the spring thought most likely to be the source of water for Fort Clatsop. Controversy 

still surrounded the exact location of Fort Clatsop, however, so the OHS asked the National Park 

Service (NPS) to perform an archeological survey of the area; this survey was completed in 

1948. A replica of Fort Clatsop was constructed in 1955 through the actions of a state, civic, and 

private collaboration to commemorate the 150th anniversary of the Lewis and Clark encampment. 

Calls for national recognition of Fort Clatsop began as early as 1906 when Congress was 

petitioned to purchase the site and to construct a commemorative monument. The NPS reviewed 

the site in collaboration with the Oregon State Parks Board in 1935 and made the determination 

that it should be a state park. The question arose again in 1937 and the same result was attained. 

More requests were made to Congress until 1955 when a bill to reexamine the question of Fort 

Clatsop’s national significance was passed. The resulting report recommended designation as a 

“Memorial” and not a “Monument” because a monument designation required physical features 

to remain. In 1958, Congress designated the Fort Clatsop National Memorial. Concerns still were 

expressed regarding whether or not this was the exact location of the site, that the designation 

removed property from tax rolls, and that the designation did not recognize the Lewis and Clark 

sites on the Washington side of the river at Dismal Nitch, Station Camp, and Fort Canby (now 

Cape Disappointment). 

Salt Works and Netul Landing 

Efforts were made to locate the Salt Works site where salt was distilled for the expedition party. 

This site proved easy to locate based on the oral and family histories of Clatsop elders. The OHS 

marked the site with permission of the property owner, and in 1910 the owner donated the site to 

the people of Oregon. In 1978 the Salt Works site was added to Fort Clatsop National Memorial 

after repeated efforts to introduce and pass such legislation in Congress. Archaeological digs to 

locate traces of the Chinook longhouses were unsuccessful. 

There had been long-term interest in locating the route of the trail taken by the Lewis and Clark 

Expedition party from Fort Clatsop across the Coast Range to the Salt Works site (Hussey 1958). 

4 
In 2002, Congress authorized the NPS to enter into a land exchange with Crown Zellerback 

Timber Company for lands it owned along the proposed route. The lands contained a trail (now 

know as Netul Landing) from Fort Clatsop to Salt Works (P.L. No. 107-221). In 2006, the trail 

was dedicated with the successful additions of other lands. 

Dismal Nitch, Station Camp, Cape Disappointment, Fort Columbia, and Fort Stevens 

As the bicentennial of the Lewis and Clark Expedition approached in 2003, interest grew in 

recognizing and protecting other significant areas used by the party. In 2002, Congress 

authorized the NPS to study the expansion of Fort Clatsop National Memorial (PL 107-122 116 

Stat. 1333). The study was completed in 2003 with the preferred alternative to include Dismal 

Nitch (Megler’s Rest), Station Camp, Fort Canby (now Cape Disappointment), and Fort 

Columbia in Washington with Fort Clatsop National Memorial (NPS 2003). Congress accepted 

these recommendations in 2004 with the passage of the Lewis and Clark National Historical Park 

Designation Act (PL 108-387 118 Stat. 2234). 

Fort Stevens is a Civil War era fortification that is now an Oregon State Park. Fort Columbia and 

Fort Canby (now Cape Disappointment) were former military sites designed to defend the mouth 

of the Columbia River from 1896 to 1947. They were later surplused to Washington as state 

parks. Station Camp is the former site of an important Chinook tribal trading center that had been 

acquired by Washington for a park commemorating the site and its importance for trade

development. The Megler Rest Area (Dismal Nitch) is owned and operated by the Washington 

Department of Transportation (NPS 2006b). Since LEWI’s designation in 2004, the NPS has 

been engaged in negotiations with property owners, the Washington State Parks and Recreation 

Commission, and the Washington State Department of Transportation on how best to secure and 

interpret these sites. In addition, the NPS is seeking to obtain conservation easements on several 

privately held lands adjacent to some sites for long-term resource and scenic protection.

Resource management plans have been produced since 1973, most recently in 1995. The primary 

objectives for management include 1) re-creation of native plant communities where ecologically

feasible; 2) re-creation of traditional animal populations where ecologically feasible; 3)

measuring the impact of humans on the environment; and 4) monitoring the impact of humans on 

the environment. The major resource management emphasis has been on reforestation of the site 

to regain the dense forest canopy and thickets that Lewis and Clark described in their journals. 

Thousands of trees have been planted to revegetate the sites, and as a result, current visitors now 

see a much different environment than those who visited in 1958. 

A.1.c. Human Utilization 

The name Chinook has been applied to four groups of native peoples occupying the Lower 

Columbia River (the Chinooks, Wahkiakums, Clatsops, and Cathlamets) who were among the 

first tribes encountered by European traders arriving by sea and later by fur traders and early 

settlers to the region (Ruby and Brown 1976). The Chinooks on the north side of the estuary and 

the Clatsops on the south are the native groups most closely associated with LEWI. These 

peoples were renowned for their canoe carving abilities and for the extensive trade networks that 

they maintained up and down the Columbia River for thousands of years prior to European 

contact. Coastal and river mouth areas were sites of fairly dense settlements by Chinooks. 

5 
Disease, however, had greatly diminished their numbers by the time Lewis and Clark arrived. 

While they were known for hunting game, as well as for gathering local berries, fruits, and roots, 

their real competitive advantage was in utilization and preservation of fish and shellfish. It is 

generally considered that much of the Lower Columbia habitat and areas around the estuary were 

densely covered with evergreen forests; however, reinterpretation of some historic accounts may 

indicate that the Chinooks had a sophisticated and selective use of fire as a tool for creating 

forest clearing to increase productivity of deer and elk for hunting and gathering (Botkin 2004). 

The immediate objective of European contact was to obtain furs from Indian hunters. Primary 

occupation was along the rivers and in sheltered harbors. Settlement of the boundary with 

Canada sharply increased interest in settlement in Washington and Oregon. The first claim for 

the area containing Fort Clatsop was made in 1849 but it was not settled until 1850. In 1852, a 

timber mill was built on the site of the Lewis and Clark Expedition canoe landing and the 

surround area was logged between 1852 and 1854; this lumber was sent to market in San 

Francisco. The extensive land clearing permitted the establishment of orchards, small gardens, 

and land for animal grazing. The canoe landing on the Lewis and Clark River proved to be a 

useful site for operations of the U.S. Revenue Service in the early 1860s and served the needs of 

the Oregon Steam and Navigation Company with regular steamship service between Portland 

and Fort Clatsop during the summertime. Around 1900, other transportation routes and a railroad 

supplanted steam navigation. Clay of suitable quality for pottery was available on the Fort 

Clatsop site and extraction occurred between 1887 until about 1920 (Cannon 1995). 

The activity on the Fort Clatsop site was indicative of the settlement of the estuary region. Small 

farms and orchards were hewn from the forests, and fishing developed in ports such as Ilwaco, 

WA, and Astoria, OR, especially for salmon. The estuary lowland environments were rapidly 

transformed into cultural landscapes. In the present day, these farms and grazing areas are 

becoming uneconomical and are being subdivided for use as retirement and recreation property. 

Some larger dairy farms have developed and much of the landscape is reverting to intensively 

managed forests. Coastal and historic tourism is increasing, especially as a result of interest in 

the Lewis and Clark Bicentennial. Salmon fishing has vastly diminished as a part of the economy 

due to downturns in the abundance of Columbia River salmon (e.g. Cone 1995; Taylor 1999; 

Blumm 2002). In addition, the Columbia River serves as a major international shipping route. 

A.2. Hydrology 

A.2.a. Oceanographic Setting 

Hickey and Banas (2003) describe major large scale oceanographic features of the Pacific 

Northwest, including the Pacific Coast and estuary region. The Columbia River empties into the 

Pacific Ocean in an oceanographic region that is dominated by features associated with the North 

Pacific Gyre, a circular flow formed by the California, Alaska, and Davidson currents. These 

currents can vary significantly on interannual, seasonal, and multi-day timescales, creating 

complex eddy fields, as well as upwelling and downwelling patterns. 

The California Current is a south-flowing offshore current apparent from the surface to 500 

meters depth. It is balanced in part by the north-flowing California Undercurrent, which is 

6 
narrower and faster, and generally occurs at intermediate depths, between 100 and 400 meters. 

Both the California Current and Undercurrent are generally stronger in summer than in winter. 

The Davidson Current also flows north, but is primarily a fall/winter feature. Topographic 

features such as submarine canyons also influence circulation. Turbidity currents have formed a 

major submarine canyon (Astoria Canyon) offshore of the mouth of the Columbia. 

Winds along the coast are the primary determinants of surface flow. In the winter, winds are 

primarily from the south, generating onshore currents that lead to downwelling along the coast. 

In the spring (April or May), winds begin to shift north, and by summer, the predominant coastal 

winds blow from the north. This leads to offshore flow and strong upwelling from depths of 

around 200 meters close to the coast. Upwelling contributes to higher productivity and cooler 

water along the coastal margin (Hickey and Banas 2003). The conversion from winter to summer 

conditions is known as the Spring Transition. Sea level may drop 10 centimeters or more along 

much of the coast during this transition, and currents can reverse within just a few days (Strub et

al. 1987). 

Columbia River Plume 

The current and eddy patterns are further complicated by the significant and seasonal flow of the 

Columbia River. Where the river flows into the Pacific Ocean, it forms the Columbia River 

Plume (CRP), a coherent tongue of low salinity water. The CRP is a dominant and dynamic 

feature in regional oceanography, reaching as far south as 38°N and as far north as 49°N, and 

seaward as far as 600 kilometers (Barnes et al. 1972; Thomas and Weatherbee 2006). 

The CRP varies in strength and directionality from year to year and season to season, primarily 

as a result of differences in wind, rain, and snowmelt (Thomas and Weatherbee 2006). Mean 

surface speeds are 12 cm/sec in summer and 17 cm/sec in winter. Flow is much slower along the 

bottom, averaging 1-2 kilometers/day. Although a common view of the CRP is that it flows north 

in winter and south in summer, following seasonal wind patterns, Hickey et al. (2005) suggest 

that such a view is misleading. They found that the CRP is often bidirectional and that even with 

strong southward summer winds, plume water may travel as much as 150 kilometers north of the 

river mouth. Further, they found that plume water was commonly present over the Washington 

shelf during the summer months. The CRP can respond within hours to changes in wind speed 

and direction, and the southward branch can disappear completely with strong downwelling 

winds (Hickey et al. 1998, 2005; Figure 3 below). 

7 
Figure 3. Changes in surface salinity over a one-week period in July 2004. On the left, weak 

winds cause a bidirectional plume. The center graph shows that during strong downwelling 

periods, the plume extends north. The right graph shows that with upwelling, the plume moves 

far offshore. The salinity ranges from <20 psu (blue) to ~32 psu (red) (Banas and MacCready 

2007). 

During the summer, the CRP tends to be farther offshore than in winter. The plume core 

generally flows perpendicular to shore for tens of kilometers, and may extend up to 50 or 60 

kilometers off the coast. In winter, the core is rarely more than 30 kilometers from the coast. The 

CRP itself may extend as far as 800 kilometers southwest of the river mouth in summer (Barnes 

et al. 1972), and may flow into the California Current (Thomas and Weatherbee 2006). The CRP 

has variable thickness, and is between five and 15 meters in depth if offshore, thicker (10-40 

meters) if it hugs the coast (Hickey et al. 1998). 

The discharge rate of the Columbia River typically varies between 2,500 cubic meters/sec in late 

summer and 17,000 cubic meters/sec in spring. During times of maximum river flow, the 

discharge rate can be as high as 30,000 cubic meters/sec (Hickey and Banas 2003), and can 

extend to depths of 40 meters during times of heavy river flow (Barnes et al. 1972). The mixing 

of shelf water by and into the plume can resuspend bottom sediment, bringing iron and other 

nutrients up into the water column and therefore increasing primary productivity. The tidal 

plume front generates significant mixing and downwelling, and can generate transitory bottom

currents as fast as one meter/sec, down to 65 meters. The leading edge of the CRP also generates 

high-energy internal waves that may contribute to mixing as well (Nash and Moum 2005). 

A.2.b. Hydrologic Setting 

LEWI exists within a temperate coastal setting characterized by mild, wet winters and dry 

summers. In Astoria, OR, the average annual air temperature from 1971-2000 was 51°F, with 

average monthly mean temperatures ranging between 60.8°F in July and 42.4°F in January. The 

maximum and minimum temperatures recorded during the same period were 96°F and 6°F. The 

average annual precipitation in Astoria from 1971-2000 was 67.13 inches while in Seaside (on 

the Oregon coast), it was 75.74 inches. In both locations, July and August were the driest 

8 
months, averaging less than two inches of rain, while November and December were the wettest

months, averaging close to 10.5 inches each in Astoria and 11.3 inches each in Seaside. 

The Columbia River dominates the hydrologic environment in which LEWI is situated. It is the 

second-largest river in the conterminous United States, crossing two major mountain ranges and 

draining a basin of approximately 665,000 square kilometers (Thomas and Weatherbee 2006). 

The drainage basin is divided into two primary subbasins. The upper basin lies east of the 

Cascades, and the lower coastal basin lies west of the Cascades. Flow through the upper basin 

historically was controlled by snowmelt, while flow through the lower basin was controlled by 

rainfall. 

Flow in the Columbia River is manipulated by dams. Bonneville Dam, completed in 1938, is one 

of 18 dams on the Columbia and Snake Rivers. Its location now defines the upstream boundary 

of the Lower Columbia River. Below Bonneville Dam, the Columbia River extends 146 miles to 

the mouth. Currently, river flow in the Lower Columbia is regulated largely by releases from

Bonneville Dam and by inputs from the Willamette River. This river is the largest tributary 

entering the lower river; like the Columbia, the Willamette is also heavily dammed. While the 

coastal basin represents just eight percent of the total drainage areas of the Columbia River, it 

drains approximately 46,000 square kilometers of the watershed (Systma et al. 2004) and 

contributes 24% of the total river flow (Simenstad et al. 1984a). 

Flows in the Lower Columbia average 273,000 cubic feet per second (cfs) at the river mouth, 

with peak flows occurring during winter storm events (LCRE Subbasin Summary 2002). 

Discharge varies seasonally according to runoff, snowmelt, and hydropower demands. Spring 

freshets once were a source of flooding along the lower river, but dams now regulate freshets. 

Discharges in May and June have been reduced by more than 50% since impoundment for water 

storage, hydropower generation, and irrigation diversion in the middle and upper basins (Systma 

et al. 2004). Late summer and fall flows now are higher and slower than prior to damming, and 

water temperatures are warmer by a few degrees (LCRE Subbasin Summary 2002). 

Columbia River Estuary

The estuary comprises tidally influenced portions of the Lower Columbia River from river mile 

34 to the seaward edge of the CRP (LCRE Subbasin Summary 2002). Sites within LEWI are 

located along the LCRE and its tributaries, or in coastal areas influenced by the CRP. 

Consequently, hydrological characteristics of the LCRE profoundly influence aquatic areas 

within LEWI. 

The LCRE is a river-dominated drowned river valley estuary. It is partitioned into three distinct

sections based on the degree of mixing of salty and fresh water: the fluvial, or freshwater, portion 

from Bonneville Dam downstream to the maximum upstream extent of saltwater intrusion 

(approximately river mile 34); the brackish region, where salinity varies as a function of river 

flow and tidal energy, from river mile 19 to river mile 34; and the marine region, which is 

heavily influenced by coastal processes, from the mouth to river mile 19. The LCRE contains 

main, distributary, and dendritic tidal channels, as well as shoals, wetlands, and mudflats. Nearly 

71% of the LCRE is less than six meters deep relative to mean lower low water (MLLW). The 

estuary contains four large, shallow bays (Grays, Baker, Youngs, and Cathlamet), two of which 

9 
(Baker and Youngs) are in the vicinity of LEWI. Silt and clay sediments predominate in 

peripheral bays, while sandy sediments dominate elsewhere (Bottom et al. 2001, and references 

therein). At the river mouth, the estuary is about five miles wide. 

Mixing in the estuary results from tidal action, wind, turbulent flow, and velocity shear between 

the salt wedge and freshwater outflow. Maximum tidal range is around three meters in the 

estuary (Thomas and Weatherbee 2006). When river flow is high, the effluent salinity is around 

20 parts per thousand (ppt); when flow is low, effluent salinity is about 28-30 ppt. 

Watersheds 

The U.S. Geological Survey (USGS) delineates watersheds using a nationwide system based on 

surface hydrologic features. This system divides the country into 21 regions, 222 subregions, 352 

accounting units, and 2,262 cataloging units. A hierarchical hydrologic unit code (HUC) 

consisting of two digits for each level in the hydrologic unit system is used to identify any 

hydrologic area. The six digit accounting units and the eight digit cataloging units are generally 

referred to as basin and subbasin, respectively. HUC is defined as the Federal Information 

Processing Standard (FIPS) and generally serves as the backbone for the country’s hydrologic 

delineation. 

The parks that comprise LEWI fall into the Lower Columbia/Youngs Bay Subbasin (HUC 

17080006, in the Lower Columbia Basin) and the Necanicum Subbasin (HUC 17100201, in the 

Northern Oregon Coastal Basin). Water resources in this area include lakes, ponds, seeps, 

seasonal streams, small upland streams, and several rivers. In the region covered by this report, 

two major rivers drain into the Columbia from the south (the Lewis and Clark and Youngs 

Rivers), and one from the north (the Chinook River). 

Youngs Bay 

Youngs Bay, on the south side of the river, is two miles wide where it meets the Columbia River 

between Astoria and Warrenton (Figure 4), and has been the subject of much research; therefore 

much of the information in this assessment focuses on this region. 

10 
Figure 4. Youngs Bay Watershed (Bischoff et al. 2000) 

The area was historically one of the most biologically diverse regions of the estuary (NCWA 

2007). The relatively shallow entrance limits the volume of salt water entering the bay. The 

Youngs Bay watershed consists of more than 250 miles of streams and rivers. The bay itself is 

fed primarily by four rivers: the Lewis and Clark River (21 miles long), Youngs River (17 miles 

long), Klaskanine River (16 miles long), and Wallooskee (Walluski) River (6 miles long), which 

in combination drain approximately 184 square miles of the watershed (Figure 5). All four rivers 

originate in the Coast Range. Although elevations within the watershed range from sea level to 

3,284 feet, the bay itself is characterized by a broad floodplain, much of which has been 

converted to pasture. 

11 
Figure 5. Youngs Bay Subwatersheds (Bischoff et al. 2000). 

Baker Bay

Baker Bay, on the north side of the river between River Miles 3 and 9, is fed by the salmonbearing Chinook River. Most of the Chinook River Watershed, with an area of 13.6 square miles, 

has an elevation of less than 200 feet, although the highest point is 1,400 feet. Prior to dredging 

and jetty construction, the bay was a high-energy environment, but anthropogenic alterations, 

combined with the migration of mid-channel islands deeper into the bay, have significantly 

reduced incoming wave and current energy. 

A.3. Aquatic Habitats and Biological Resources 

Physical and biological attributes of individual park sites are described by Wetherbee and Hall 

(2006). Here we expand their characterization by focusing on aquatic habitats in a regional 

context. 

A.3.a. Aquatic Habitats 

The LCRE is generally a soft-substrate environment, although sediment grain size is strongly 

affected by location. In Baker, Trestle, and Youngs Bays, sediment tends to be poorly sorted, 

ranging from fine sand to coarse silt. Sediment size in estuarine channels tends to be medium12 
fine sand (Simenstad et al. 1984b). Within the estuary, six basic habitat types can be 

distinguished based on location and biological community: water column, demersal slope, high 

marsh and swamp, low marsh, tidal flats, channel bottom, and epibenthic layer. Tidal flats, 

epibenthic communities, and channel bottom habitat dominate the entrance to the estuary. Baker, 

Trestle, and Youngs Bays contain all but the channel bottom habitat. 

Aquatic habitats in the LCRE are influenced by dynamic interactions between fluvial and 

oceanographic processes, which in turn are modulated by climate and human activities (LCREP 

2004 Supp). Human activities in particular have altered natural processes and habitat conditions; 

chief among these has been the construction and operation of the Columbia River hydropower 

system. This system along with irrigation withdrawals have resulted in changing both the timing 

and magnitude of Columbia River flows; in addition maximum flows have been reduced over 

time, which when combined with diking and dredging activities, has essentially “eliminated 

overbank flows” in the river (LCREP 2004 Supp). The disappearance of these flows is important 

because they historically “created a variety of habitats of value to focal species by connecting the 

river with its floodplain, increasing channel complexity through the deposition of large woody 

debris, and transporting crucial riverine sediment to the estuary” (LCREP 2004 Supp). Species 

especially affected include juvenile salmonids such as Chum and fall Chinook, bald eagles, and 

Columbia white-tailed deer. 

The construction of dams has also affected sediment transport and salinity distribution in the 

estuary. The reduction of spring freshet flow and the construction of reservoirs that trap upstream

sediment supply also affect sediment transport (LCREP 2004 Supp). The consequences include 

the alteration of estuarine habitat, disturbance of turbidity patterns, and a decrease in the amount 

of sediment that the river can “flush” from its system (LCREP 2004 Supp). Flow has also 

affected salinity distributions, particularly the “location, size, shape, and salinity gradients of the 

estuary turbidity maximum zone...[which] can affect seasonal species distributions and the 

structure of entire fish, epibenthic, and benthic invertebrate prey species assemblages throughout 

the estuary” (LCREP 2004 Supp). 

Land Cover Types 

Land cover types within LEWI as designated by the National Wetlands Inventory (NWI) 

are shown in Figures 6-11. Because the regional NWI coverage is incomplete, reliable acreages 

are not available by land cover type, but relative proportions of each land cover type can be 

discerned from the figures. 

13 
Figure 6. NWI coverage in region of LEWI. Map created by authors from NWI data. 

14 
Figure 7. Land cover types within the Cape Disappointment site. Map created by authors from

NWI data. 

15 
Figure 8. Land cover types within the Station Camp site. Map created by authors from NWI data. 

16 
Figure 9. Land cover types within the Dismal Nitch site. Map created by authors from NWI data. 

17 
Figure 10. Land cover types within the Fort Clatsop National Memorial site. Map created by 

authors from NWI data. 

18 
Figure 11. Land cover types within the Sunset Beach site. Map created by authors from NWI 

data. 

19 
A.3.b. Biological Resources 

The following section provides a sampling of some of the wildlife species found throughout the 

LCRE and within reach of LEWI’s boundaries. 

Fish 

The LCRE supports a variety of freshwater and marine fish and invertebrate species, and serves 

as an important habitat for feeding and breeding. Taxa of economic importance include oysters, 

clams, mussels, Dungeness crab, sturgeon, and salmon. Salmon especially benefit from this 

estuarine habitat in various life stages. Chum, Coho, and Chinook salmon are the focal species in 

the region. Overall, anadromous fish populations are estimated to be at about 10 percent or less 

of their historic run size; in order to compensate, hatchery programs have become prevalent on 

the river and now make up about 75 percent of all fish returning to the LCRE (LCREP Subbasin 

Plan 2002). Critical habitat has been established for Snake River sockeye, spring/summer 

Chinook, and fall Chinook salmon (WSPRC and COC, LLC 2005). Salmon have been the 

subject of numerous studies and assessments in order to determine life history, habitat needs, and 

vulnerabilities. In general, Pacific salmon and steelhead generally exhibit similar characteristics:

“Adult fish migrate upstream into freshwater rivers to spawn. After hatching, juveniles spend a 

period of time ranging from days to up to 18 months (depending on species and stock) rearing in 

fresh water before emigrating downstream to the ocean where they live for 1 to 6 years before 

maturing and returning to fresh water to spawn, thus completing the life cycle. All Pacific 

salmon die after spawning, though some repeat spawning occurs among steelhead. After 

emigrating to marine waters, juveniles of all species utilize nearshore areas for rearing and 

foraging prior to entering the open ocean” (WSPRC and COC, LLC 2005). 

Birds 

Approximately 175 species of birds use the LCRE habitat, including gulls, terns, blue herons, 

bald eagles, peregrine falcons, hawks, ospreys, owls, marbled murrelets, and brown pelicans 

(LCREP Subbasin Plan 2002). The region is important for migratory birds and in the winter, 

populations can reach peaks of around 200,000 birds. 

Mammals

A variety of marine mammals use the LCRE including Northern and California sea lions. Harbor 

seals use the jetties and other parts of the lower estuary as haul-out areas. Offshore mammals 

include northern fur seals, elephant seals, killer whales, gray whales, and harbor porpoise; some

of these are occasionally observed in the estuary itself. In addition to these marine species, other 

mammals in the LCRE include nutria, beavers, muskrats, raccoons, voles, shrews, moles, 

coyotes, skunks, bats, black bear, black-tailed deer, Roosevelt elks, and Columbia white-tailed 

deer (LCRE Subbasin 2002). 

20 
B. Water Resources Assessment 

B.1. Water Quality 

We reviewed multiple sources of water quality data for the LCRE region, including information 

collected by federal and state agencies, non-profit environmental groups, and citizen science 

groups. We also utilized previous water quality assessments, including the NPS’s Fort Clatsop 

National Memorial Water Resources Scoping Report (1994), the Water Resources Division’s 

Baseline Water Quality Data Inventory and Analysis for Fort Clatsop National Memorial (2000), 

and the Youngs Bay Watershed Assessment (2000), as references. 

B.1.a. Data Sources 

The water quality data discussed in this report were extracted from number of sources, including: 

• Washington State Department of Health (WDOH) 

• Washington State Department of Ecology (WDOE) 

• The Environmental Protection Agency’s STOrage and RETrieval database 

(STORET) 

• National Park Service’s Water Resources Division (NPS WRD) 

• The Beach Environmental Assessment, Communication and Health (BEACH) 

Program, jointly administered by WDOH and WDOE 

• The EPA’s Beach Advisory and Closing Online Notification (BEACON) 

Program

• The Surfrider Foundation’s Blue Water Task Force (BWTF) and Rashguard.org 

• The Oregon Department of Environmental Quality (ODEQ) 

• The Lower Columbia River Estuary Partnership (LCREP); and 

• Natural Resources Defense Council (NRDC)’s report Testing the Waters: a 

Guide to Water Quality at Vacation Beaches.

B.1.b. Water Quality 

In August 2000, the National Park Service’s Water Resources Division (NPS WRD) completed a 

baseline water quality data inventory and analysis report for Fort Clatsop National Memorial 

(NPS WRD 2000). This was an effort to retrieve, format and describe existing data on surface 

water quality (both marine and freshwater) collected by various agencies and housed in the EPA 

national databases, including STORET, River Reach File (RF3), Industrial Facilities Discharge 

(IFD), Drinking Water Supplies (DRINKS), Water Gages (GAGES), and Water Impoundments 

(DAMS). The data, covering the years 1901-1998, were then assessed against published EPA 

water-quality criteria and instantaneous concentration values selected by NPS WRD to identify 

potential water quality problems within the study area. Eleven parameters exceeded water quality 

criteria at least once. Dissolved oxygen, pH, and copper exceeded the criteria for both freshwater 

and marine aquatic life. In addition, chloride exceeded the criteria for freshwater aquatic life, and 

zinc exceeded the criteria for marine life (NPS WRD 2000). The EPA drinking water criteria 

were not met with respect to chloride, sulfate, and beryllium (NPS WRD 2000). Total coliform,

fecal coliform, E. coli, and turbidity “exceeded the WRD screening limits for freshwater and 

marine bathing, and aquatic life, respectively” (NPS WRD 2000). The report determined that 

21 
human activities have caused the greatest impact on surrounding surface waters, and identified 

potential contaminant sources as “municipal and industrial wastewater discharges; stormwater 

runoff; timber harvesting; agricultural activities; landfill operations; sand and gravel pit 

activities; recreational use; marine watercraft traffic, and atmospheric deposition” (NPS WRD 

2000). These potential sources are discussed throughout this assessment, especially in Section C. 

In August 1996, water quality surveys were undertaken by the NPS for the Lewis and Clark 

River near Fort Clatsop National Memorial. Fecal coliform levels were low, and “river sediment 

analysis indicated that mean concentrations of several metals (arsenic, beryllium, nickel, and 

zinc) exceed typical levels in soils, perhaps due to anthropogenic sources. Although no sediment, 

semi-volatile organic compounds, pesticides, or polychlorinated biphenyls (PCBs) were detected, 

toxicity equivalency concentrations suggest a source of dioxin/furans upriver from [Fort Clatsop 

National Memorial]” (Fort Clatsop National Memorial 2001 in NPS 2002). 

The Lower Columbia River Estuary Partnership (LCREP) maintains a Water Quality Monitoring 

Program, which is supplemented with information about other water quality programs 

maintained by the group’s Monitoring Partners. LCREP worked with the U.S. Geological Survey 

(USGS) throughout 2004 and 2005 to collect data for sites along both the Columbia and 

Willamette Rivers. In the Lower Columbia River, data were collected near Point Adams, OR 

(LCREP 2006a; Morace 2006). Morace (2006) found that none of the aquatic life or human 

health benchmarks based on EPA water quality standards were exceeded at either the Columbia 

or Willamette River sampling sites. However, no standards have been established for many of

compounds measured in the study, so interpretation of some of the data is difficult. In a spatial 

comparison, concentrations of trace elements in the Columbia River near Point Adams were 

elevated compared to concentrations further upstream. 

CORIE is a continuous environmental observation and monitoring program maintained by the 

Oregon Graduate Institute for the Columbia River. Its purpose is to “characterize and predict 

complex circulation and mixing processes in a system encompassing the lower river, the estuary 

and the near-ocean....[and is] designed to provide objective insights on the spatial and temporal 

variability of the Lower Columbia River.” Eight stations within the CORIE program are of 

relevance to LEWI (Figure 12), including Astoria Meglar Bridge South Channel (am169), 

Astoria Meglar Bridge North Channel (am012), Tansy Point (tansy), Fort Stevens Wharf 

(red26), Desdemona Sands light (dsdma), Lower Sand Island light (sandi), Chinook River 

(chnke), and Jetty A (jetta) (CORIE 2006). 

22 
Figure 12. CORIE sampling locations (CORIE 2006). 

The CORIE program collects data on environmental parameters (i.e., temperature, salinity, and 

conductivity) at sites throughout the upper and lower reaches of the river. The majority of the 

sites of relevance to LEWI either are historical stations or are sites for which no current data are 

available. The exceptions are Tansy Point and Fort Stevens Wharf, which have reported normal 

values for both temperature and salinity. 

In August 2000, Bischoff et al. released the Youngs Bay Watershed Assessment (incorporating 

data from 1965 to 1999 inclusive), which contains information on Youngs Bay, the Lewis and 

Clark River, and the Lower Columbia River ecosystem. The assessment used the Oregon Water 

Quality Index (OWQI), which evaluates measurements of certain water quality parameters (i.e., 

temperature, dissolved oxygen, pH, fecal coliform) by “a single index value that ranges from 10 

(the worst) to 100 (the best).” Based on these criteria, the authors rated the Youngs Bay 

watershed as “Excellent” with an index value of 92. The Lewis and Clark River at Stavebolt 

Lane (RM 7.6) is rated “Fair” with a value of 81, and the Klaskanine River at Youngs River 

Loop Road (RM 1.3) is rated “Very Poor” with a value of 59 (Bischoff et al. 2000). Water 

quality with respect to individual parameters is presented in Table 1, adapted from Bischoff et al. 

(2000). Throughout the entire watershed, nutrients and bacteria were found to be moderately 

degraded. At both Youngs Bay Mouth and the Lower Lewis and Clark River, temperature was 

found to be degraded. No data were available for toxics in any subwatershed, and no data exist 

for dissolved oxygen, nutrients, turbidity, or bacteria in the Lower Lewis and Clark River. 

23 
Table 1. Water quality within the Youngs Bay watershed (adapted from Bischoff et al. 2000; see 

text for explanation of individual rankings)

Subwatershed Temperature DO pH Nutrients Turbidity Bacteria Toxics

Lower Lewis & Clark River No data No data No data No data No data 

Klaskanine River No data

Upper Lewis & Clark River No data

Upper Youngs River No data

Youngs Bay East No data

Youngs Bay Mouth No data

Youngs Bay West No data

Red = Degraded 

Yellow = Moderately Degraded 

Green = Not Degraded

The Lewis and Clark River near Fort Clatsop National Memorial has been occasionally 

monitored by ODEQ since 1969 “at two locations upstream (one-half mile upstream of Peterson 

Slough and at Stavebolt Lane) and one location downstream (old Highway 101 bridge) of [Fort 

Clatsop National Memorial].” In general, the data suggest that “water quality within the Lewis 

and Clark River is usually good and within state standards” (NPS WRD 1994). 

Section 303(d) Water Quality Assessment 

In order to meet the requirements of Section 303(d) of the Clean Water Act, states are required to 

submit water quality assessment reports to the EPA. Water bodies are divided into five 

classification categories, ranging from 1 (water meets tested standards) to 5 (standards violated). 

Category 4A waters are those “where the data show that a characteristic use is impaired by a 

pollutant, but a TMDL [Total Maximum Daily Load] addressing that impairment has already 

been developed and approved” by the EPA (WDOE 2006f). Category 5 waters are those “from

which at least one characteristic or designated use is impaired, as evidenced by failure to attain 

the applicable water quality standard for one or more pollutants” (WDOE 2006f). 

Washington State 303(d) 

The LCRE borders two Water Resource Inventory Areas (WRIAs) in Southwest Washington, 

WRIA 24 (Willapa Basin) and WRIA 25 (Grays-Elochoman Basin; WDOE 2006c) (Figure 13). 

WRIA 24 consists of almost 814,900 acres, and has sixty-seven known Category 5 water bodies. 

WRIA 25 encompasses nearly 323,097 acres, and has thirty-six known Category 5 water bodies. 

24 
Figure 13. Water Resource Inventory Areas 24 (Willapa Basin) and 25 (Grays-Elochoman 

Basin). Source: Map created by authors. 

The 2004 Category 5 listings for fresh water bodies in WRIA 24 include exceedances of both 

fecal coliform (water samples) and total PCBs (mussel tissue samples) in the Columbia River 

(WDOE 2006d). The 2004 Category 5 listings for fresh water bodies in WRIA 25 include a 

25 
number of temperature exceedances in the Columbia River. Some have attributed temperature 

exceedances to pulp mill operations throughout the LCRE and its tributaries, but a two year 

(2002 and 2004) study conducted by Parametrix (and contracted by the Northwest Pulp and 

Paper Association), concluded that “temperatures higher than the 20°C numeric criteria are a 

natural condition [in the region]...[and] mills [do] not have a measurable effect on temperatures” 

(WDOE 2006e). 

Category 4A and 5 listings within the Columbia River region of WRIAs 24 and 25 are 

summarized in Tables 2 and 3 (after WDOE 2006f). 

Table 2. Category 5 and 4A 303(d) Listings for the Columbia River (Water Medium) 

Category WRIA Parameter

5 24 Fecal Coliform

5 25 Fecal Coliform

5 25 Temperature

5 25 Temperature

5 25 Temperature

4A 24 Dioxin

4A 25 Dioxin

4A 25 Dioxin

4A 25 Dioxin

4A 25 Total Dissolved Gas 

Table 3. Category 5 303(d) Listings for the Columbia River (Tissue Medium) 

Category WRIA Parameter

5 24 Total PCBs

5 25 4,4'-DDE

5 25 Dieldrin

5 25 Total PCBs 

5 25 Total PCBs 

5 25 Total PCBs 

Oregon State 303(d) 

The 2004 303(d) listings within the Lower Columbia watershed in Oregon include Bear Creek 

(4A, temperature), Gnat Creek (4A, temperature), Klaskanine River (5, fecal coliform), Skipanon 

River (5, dissolved oxygen), Youngs River (4A, temperature), and Lewis and Clark River (5, 

fecal coliform and temperature) (ODEQ 2006a). In all, about 0.359 mi/mi

2

 of streams of the 

Lower Lewis and Clark River are included on the 303(d) list (Pacific Watersheds 2006). 

Other Sources 

Other water quality information sources examined include the USGS program, the National 

Stream Water Quality Network (NASQAN), and Columbia Riverkeeper’s (CRK) citizen-based 

group. NASQAN has collected data at Beaver Army Terminal on the Columbia River from

26 
1996-2003; the site is located near Quincy, OR, which is about 40 miles east of Astoria (USGS 

2006). CRK monitors for conductivity, pH, dissolved oxygen, and temperature west of Portland 

(CRK 2006a). Both of these regions are outside of LEWI and therefore not within the scope of 

this assessment. 

Bacterial Contamination 

The Washington Beach Environmental Assessment, Communication and Health (BEACH) 

program was developed in response to the BEACH Act of 2000. This legislation “required states 

with coastal recreational waters to adopt new or revised water quality standards by April 2004 

for pathogens and for pathogen indicators for which the EPA has published criteria under the 

Clean Water Act” (NRDC 2006). The program is jointly administered by WDOE and WDOH, 

and monitors high risk beaches for enterococci, bacteria considered to be indicators of water 

quality. The criteria for acceptable enterococcus levels were established by the EPA in 1986 and 

have not been changed officially since then. Possible public health action (such as posting 

warning signs or closing beaches) is recommended if Enterococcus levels exceed the EPA 

criteria of “104 colonies of Enterococcus bacteria per 100 milliliters of water for a sample event 

or a geomean of 35 colonies of Enterococcus per 100 milliliters of water for a five-week time 

period” (BEACH 2006a). 

Of all of the sites of relevance to LEWI in Pacific County, WA (i.e., Cape Disappointment, 

Ilwaco Marina, Chinook County Park, Fort Columbia Historical State Park, Lewis and Clark 

Campsite State Park), only Cape Disappointment is monitored by BEACH (BEACH 2006b). 

There were no recorded exceedances in bacterial levels from 2004-2006 (Table 4). 

27 
Table 4. BEACH bacterial monitoring results for Cape Disappointment State Park, 2004 – 2006 

(BEACH 2006c) 

Cape Disappointment State Park 

Date # of Enterococcus colonies/ 100mL H20 

8/29/06 <10 

8/22/06 <10 

8/15/06 <10 

8/8/2006 <10 

8/1/2006 <10 

7/25/2006 <10 

7/18/2006 19

7/11/2006 <10 

7/3/2006 no samples 

6/27/2006 <10 

6/20/2006 13

6/13/2006 <10 

6/6/2006 16

5/30/2006 no samples 

5/23/2006 <10 

9/21/2005 <10 

9/13/2005 <10 

8/30/2005 <10 

8/8/2005 <10 

8/3/2005 <10 

7/26/2005 <10 

7/19/2005 <10 

7/12/2005 <10 

7/5/2005 <10 

6/28/2005 <10 

6/21/2005 <10 

6/14/2005 <10 

6/8/2005 <10 

5/31/2005 <10 

10/5/2004 <10 

9/27/2004 <10 

9/14/2004 <10 

9/7/2004 <10 

8/31/2004 <10 

The same information is displayed for the public on the Earth911 Beach Water Quality website 

with results by location updated on a Google map (Earth911 2006). 

In May 2006 WDOE solicited public comment regarding prioritization of beaches to be 

monitored weekly for bacteria; there was sufficient state funding to test about 65 out of the 900 

or more beaches throughout the entire state, including those located near LCRE and LEWI 

(WDOE 2006a). Public opinion is one of over 60 parameters that are used to determine which 

28 
beaches are chosen for testing; others include usage and potential fecal contamination sources. 

The BEACH program released a proposed list of beaches to be monitored; of relevance to the 

LCRE is Cape Disappointment State Park (WDOE 2006a). 

The Surfrider Foundation, in collaboration with Rashguard.org, also tracks and posts water 

quality information on their website (Surfrider 2006a). Cape Disappointment State Park is 

monitored and is listed as “OK,” although the last test date was May 19, 2006. Longitudinal 

water quality data for the park is not listed; instead, daily updates on indications of water 

pollution are posted (i.e., from polluted runoff in the coastal zone after a rainfall event, sewage 

spills, or other acute incidents). For example, a polluted runoff warning was posted for Cape 

Disappointment on August 23, 2006 because of light rain in the region; the warning stated that 

“higher than normal amounts of polluted runoff in beach waters near river mouths, lagoon 

openings, storm drain outlets and the like” could be expected (Surfrider 2006a). 

Surfrider’s Oregon chapter also sponsors water quality testing. The testing is organized through 

the Blue Water Task Force program (Surfrider BWTF 2006b). Tests are conducted by volunteers 

who are trained in Colilert and Enterolert methodology, but who are not necessarily water quality 

professionals. Through this program, tests are performed for the presence of E. coli and 

Enterococcus sp. Thirty-six beaches along the Oregon coastal strip are monitored, but none are 

within the LCRE. Both Fort Stevens and Seaside, OR, located directly outside of the estuary, 

were found to have low levels of bacteria in 2004. 

Contaminants

Among the toxics of concern in the Lower Columbia are pesticides (DDE and DDT), PCBs, 

dioxin/furans, radionuclides, semi-volatiles, PAHs, and metals (Rosetta and Borys 1996 in

ODEQ 2000). LCREP worked with the USGS throughout 2004 and 2005 to collect information 

on water quality data, including contaminants, for sites along both the Columbia and Willamette 

Rivers. Findings include: 

• Concentrations of arsenic, chromium, copper, and lead were present, although at 

levels below concern with regard to aquatic-life toxicity. 

• Of the 173 pesticides and degradation products analyzed, 14 compounds 

were detected in the Columbia River. 

• The known endocrine disruptor, bisphenol A, was detected in both the 

Columbia and Willamette Rivers. 

• Acetaminophen (analgesic) and diphenhydramine (antihistamine) were 

detected in the Columbia River. 

• The antibiotics anhydroerythromycin and trimethoprim were detected at 

most sites during low-flow conditions, but at only one site during high-flow 

conditions. 

• No organochlorine compounds or PAHs were detected at any of the sites 

during seasonal samplings of suspended sediment. 

• Quantifiable concentrations of the 11 PBDE congeners were detected on 

suspended sediment near Point Adams. 

• 102 PCB congeners were detected at some time on suspended sediment at 

the sites, usually in trace amounts (Morace 2006). 

29 
Johnson et al. (2007) sampled tissues and stomach contents of Chinook and coho salmon from

the estuary. The contaminants found included PCBs, PAHs, and DDTs, although additional 

organochlorine pesticides (such as chlordanes, lindane, hexachlorobenzene, dieldrin, aldrin, and 

mirex) were also detected in lower concentrations. Concentrations of DDTs were especially high 

in juvenile Chinook salmon from the Lower Columbia River and within the range that could 

potentially affect fish health and survival (Johnson et al. 2007). DDTs and PCBs have been 

identified as the possible cause of decline of white sturgeon populations in the Columbia River; 

these contaminants have been found in high levels in the livers, sex organs, and muscle tissue 

(Feist et al. 2005). 

Metal contamination has occurred throughout the Columbia River Basin, and some studies have 

indicated that sources upstream of the Bonneville Dam are the cause. Metals that “exceeded 

federal and state allowable limits in the water column testing included aluminum, iron, copper, 

lead, selenium, and silver...[also] fish tissue testing showed the presence of barium, cadmium,

chromium, copper, lead, mercury, and zinc” (CRK 2006b). Some estimates from “governmental 

sources indicate that a possible 281,600 pounds of mercury were dumped into the Columbia 

from the 1940s to the 1980s” (CRK 2006b). 

Concentrations of contaminants “are found throughout the estuary, sometimes near cities and 

other times in bays and shallows where low-velocity flows allow suspended contaminants to 

settle. Salmon and steelhead are affected by contaminants through short-term exposure to lethal 

substances or through longer exposures to chemicals that accumulate over time and magnify 

through the food chain” (LCREP Module 2006). It is believed that stream-type juvenile 

salmonids are typically more affected by the short term exposure to pesticides and dissolved 

metals, while ocean-type juveniles are more susceptible to DDT and PCBs, which can 

bioaccumulate “during longer estuarine residence times” (Fresh et al. 2005 in LCREP 2006 

Module). 

Contaminants can enter the water through surface water runoff and erosion. In the LCRE, PCBs, 

PAHs, dioxins, and metals have been found in sediments, with the highest concentrations 

primarily in the Portland, OR and Longview, WA area (Leary 2005). 

Marine Biotoxins/Harmful Algal Blooms 

WDOH manages a general biotoxin monitoring program in which state, tribal, county, and local 

agencies, as well as commercial shellfish ventures and federal agencies, collect samples from

various bivalve species. Samples are analyzed for the presence of paralytic shellfish poison 

(PSP) and domoic acid (DA). When the level of PSP in a single sample of a particular shellfish 

species exceeds the U.S. Food and Drug Administration (FDA) action level of 80 micrograms of 

PSP toxin in 100 grams of shellfish tissue, WDOH closes commercial and recreational harvest 

areas for that species. DA closure levels were reassessed by WDOH in September 2000 and 

established at 20 ppm in sample tissue. Closed areas are reopened only when continued 

monitoring assures a return to safe conditions (Determan 2003). 

Molluscan shellfish tissue samples taken from shellfish growing areas and recreational 

harvesting areas are monitored for marine biotoxins, specifically saxitoxins (algal compounds 

responsible for PSP) and DA (WDOH 2006a). Near Cape Disappointment and Fort Canby State 

30 
Park, there are marine biotoxin/pollution closures as of March 2007, and the area is closed for 

clams, geoduck, scallops, mussels, oysters, snails and other invertebrates (WDOH 2006b). 

B.1.c. Data Gaps and Information Inconsistencies 

Our research has revealed a number of data gaps and information inconsistencies regarding water 

quality monitoring and data collection in the LCRE region, as illustrated by the following: 

• WDOE conducts water quality monitoring on an annual or rotating basis 

at locations throughout Washington’s waters. However, the only locations 

monitored are in Puget Sound, Grays Harbor, and Willapa Bay. Therefore, 

no WDOE data are available that describe conditions within or adjacent to 

LCRE (WDOE 2006g). 

• The EPA program BEACON (Beach Advisory and Closing On-line 

Notification) program provides a public database concerning the status of 

state beaches. Each beach contains information regarding contact 

information, monitoring and notification information, general beach 

characteristics, advisories and closings, and location data (BEACON 

2006). The website shows that no water quality or advisory data has been 

made available for Pacific County, WA beaches along the Lower 

Columbia River. Clatsop County, OR beaches monitored through the 

BEACON program are located only along the Pacific coast and not near 

LEWI boundaries. 

• According to Testing the Waters: A Guide to Water Quality at Vacation 

Beaches, a report published by the Natural Resources Defense Council in 

July 2005, Washington State “regularly monitors less than half of [its] 

beaches.” The report does note that Cape Disappointment State Park was 

monitored once a week in 2005 for a total of 53 samples, yielding no 

exceedances (NRDC 2006). In Oregon, no beaches near LCRE are 

monitored (NRDC 2006). 

• While WDOE does have a Marine Sediment Monitoring Program, all of 

the current sampling locations are within Puget Sound, and none are 

located near the LCRE region (WDOE 2006b). 

B.2. Water Quality Degradation 

WDOE’s 303(d) water quality assessment for 2004 includes WRIAs 24 and 25. In WRIA 24 

(Willapa), approximately sixty-seven Category 5 water bodies are known. The Columbia River is 

listed for exceedances of both fecal coliform and total PCBs (WDOE 2006d). In WRIA 25 

(Grays-Elochoman), approximately thirty-six known Category 5 water bodies are known. The 

Columbia River is listed for numerous temperature exceedances. There is debate over whether 

these high temperatures are related to pulp mill operations upstream, or are part of the natural 

conditions of the ecosystem (WDOE 2006e). 

31 
In Oregon, 303(d) listings in 2004 included Bear Creek, Gnat Creek, Klaskanine River, Lewis 

and Clark River, Skipanon River, and Youngs River (ODEQ 2006a). Approximately 0.359 

mi/mi

2

 of streams of the Lower Lewis and Clark River are included on the 303(d) list (Pacific 

Watersheds 2006). 

Of the beaches monitored through the BEACH program, only Cape Disappointment State Park is 

of relevance to the LCRE. There were no recorded bacterial exceedances from 2004 to 2006 at 

this location (BEACH 2006b and 2006c). These results are supported by the Surfrider 

Foundation’s monitoring program. 

The WDOH biotoxin monitoring program monitors levels of PSP and DA in shellfish tissue 

samples. Areas near Cape Disappointment State Park were closed as of March 2007 for clams, 

geoduck, scallops, mussels, oysters, snails, and other invertebrates (WDOH 2006b). 

In 1994, NPS WRD published the Fort Clatsop National Memorial Water Resources Scoping 

Report, which addressed some past, present, and future water quality influences on and concerns 

for the memorial and surrounding areas, including the Lewis and Clark River. The report 

determined that the majority of water quality influences and concerns were “low-level chronic” 

and were the result of land-use activities such as logging and agriculture (NPS WRD 1994). 

Other concerns for water quality in the region were identified as dumps and landfills, farming 

and dairies, timber harvest and transport, dredging, dikes and levees, and NPS operational 

activities. These concerns for the pre-expansion region of the memorial are discussed as follows: 

• Unauthorized dumps and landfills: “may have a localized effect on the surface and 

groundwater resources of the Memorial. Specifically, illegal public dumping in a small 

ravine to the west of the Memorial is suspected of leaking waste oil (and other possible 

contaminants) into at least one small perennial stream that enters the Memorial. Other 

more distant landfills could also be affecting the water quality of tributary streams to the 

Lewis and Clark River.” 

• Farming and dairies along the Lewis and Clark River: The pesticides and fertilizers 

used in farming and agricultural operations could enter the aquatic environment. Also, 

“dairy operations concentrate livestock, and their waste may also degrade water quality.” 

• Timber harvest and transport: Timber activities have been identified as a possible 

source of the alteration of flow and degradation of water quality of the Lewis and Clark 

River. Other potential problems from harvesting include erosion, sedimentation, 

increased water temperatures, and nutrient loading, all of which could have “profound 

effects on the diversity and dynamics of the natural flora and fauna of the river system.” 

In addition, “log booming and log transport on the Lewis & Clark River is the primary 

means of moving timber to market...as organic debris (primarily bark) decompose from 

this activity, several water quality parameters may be affected [including] dissolved 

oxygen concentration, biological oxygen demand (increased due to bark decomposition), 

chemical oxygen demand (increased due to soluble organic chemicals leaching from 

logs), and turbidity. Extensive bottom deposits of bark also are suspected to create a 

physical barrier to the development of a healthy community of benthic organisms.”

32 
• Dredging of the Lewis and Clark River in order to facilitate timber transport “can have a 

pronounced short term effect on several water quality constituents such as turbidity, as 

well as a protracted influence on the benthic fauna.” The dredged material is then placed 

outside of Fort Clatsop National Memorial boundaries.

• Dikes and levees on the Lewis and Clark River, common throughout the tributaries of 

the Columbia River estuary, “were constructed to provide additional farmland within the 

floodplain, to prevent flooding in settled areas, and as an aid to navigation for boat and 

commercial traffic...[but] draining and filling has destroyed or greatly altered over 70 

percent of the estuarine and riverine wetlands that once occurred within the lowlands 

along the Lewis and Clark River (Blanchard 1977).” The remaining wetlands have 

changed due to alterations in water flows and salinity concentrations. In addition, 

“flooding potential has increased in recent years because of extensive logging over much 

of the watershed.” 

• National Park Service operations, including the construction and maintenance of the 

visitor center and parking lots, have caused “the alteration of the natural channel in two 

locations which resulted in the elimination or modification of pristine wetlands. In 

addition, the parking lot and visitor center roof now drain into this stream, potentially 

degrading its overall water quality...[and] wastewater systems now in use within the 

Memorial consist of three separate septic tank/leachfield systems which service the 

headquarters/visitor center complex and two residences. Wastewater from these systems 

leaches into the near surface groundwater and may contaminate springs and surface 

waters within the Memorial.” 

The Youngs Bay Watershed Assessment (Bischoff et al. 2000) concluded that dredging has a 

long history in Youngs Bay and along the Lewis and Clark River, mainly in order to “maintain 

navigability for the Port of Astoria.” These activities have “led to losses in aquatic habitats” 

(Bischoff et al. 2000). In addition, diking has occurred extensively throughout the watershed, 

“extending throughout the south portion of the bay along the entire stretch of the Lewis and 

Clark River as well as the Youngs River” (Bischoff et al. 2000). Diking and draining were 

identified as having the largest impact on the watershed. These activities were primarily 

undertaken in order to improve agriculture; however, “disconnecting the floodplain from the 

rivers has resulted in the loss of flood attenuation that is naturally provided by the floodplains 

ability to store and impede peak flows which can result in the downcutting of channels and 

increased flow velocities” (Bischoff et al. 2000). The effects of habitat modification are 

discussed further in Section C.6. 

33 
B.3. Sources of Pollutants 

Potential sources of pollution in the LCRE include non-point and point sources such as 

municipal and industrial wastewater discharges, stormwater runoff, timber harvesting, 

agricultural activities, landfill operations, sand and gravel pit activities, recreational use, marine 

watercraft traffic, and atmospheric deposition (NPS WRD 2000). All of these sources have the 

potential to degrade water quality. Bischoff et al. (2000) summarized typical watershed issues 

such as habitat-related and water quality effects by major land uses; their findings are 

represented in Table 5. 

34 
Table 5. Watershed issues by land use category (modified from Bischoff et al. 2000) 

Land Use Category Habitat-Related Effects Water Quality Effects 

Forestry Channel modification

Pool quantity and quality

Large wood abundance 

Shade and canopy

Substrate quality

Flow alteration 

Passage barriers 

Temperature 

Turbidity 

Fine sediments 

Pesticides and herbicides 

Crop-land grazing Channel modification 

Pool quantity and quality

Large wood abundance 

Shade and canopy

Substrate quality

Flow alteration 

Temperature 

Dissolved oxygen 

Turbidity 

Fine sediments 

Suspended sediments 

Nutrients, bacteria 

Pesticides and herbicides 

Feedlots and dairies Channel modification Suspended sediments

Nutrients 

Bacteria

Pesticides and herbicides 

Urban areas Channel modification 

Pool quantity and quality

Large wood abundance 

Shade and canopy

Substrate quality

Flow alteration 

Temperature 

Dissolved Oxygen 

Turbidity 

Suspended Sediments 

Fine Sediments 

Nutrients 

Organic and inorganic toxics 

Bacteria

Mining Channel modification

Pool quantity and quality

Substrate quality

Turbidity 

Suspended sediments 

Fine sediments 

Nutrients 

Organic and inorganic toxics 

Dams and irrigation works Channel modification 

Pool quantity and quality

Substrate quality

Flow alteration 

Passage barriers 

Temperature 

Dissolved oxygen 

Fine sediments 

Road networks Channel modification 

Pool quantity and quality

Substrate quality

Flow alteration 

Passage barriers 

Turbidity 

Suspended sediments 

Fine sediments 

35 
Columbia Riverkeeper (CRK) has identified a number of problems that face the river and 

surrounding ecosystem (CRK 2006b). Paper and pulp mills along the river have been blamed for 

high levels of dioxins, which have been found in sediment and tissue samples. High water 

temperatures are believed to be caused by mills, dams, and industrial and municipal discharges. 

Industrial facilities discharges occur in the vicinity of Fort Clatsop National Memorial (NPS 

WRD 2000), as summarized in Table 6. 

 

Table 6. Industrial discharges in the vicinity of Fort Clatsop National Memorial and the LCRE 

(adapted from NPS WRD 2000). 

Facility Name City Receiving Water 

New England Fish Co Warrenton Warrenton Skipanon Ch 

American Can Co Astoria Columbia R.

Astoria Seafood Co Astoria Columbia R.

Clatsop Co School Dist. Astoria 

Ocean Foods of Astoria Astoria Columbia R 

Barbey Packing Corp. Astoria Columbia R 

Astoria Dock Co. Astoria 

Astoria Fish Factors Inc. Edmonds Columbia R 

Barbey Packing Corp. Astoria Columbia R 

Port of Astoria Astoria 

Alaska Packers Assn. Hammond Astoria Tr to Columbia R 

City of Warrenton Warrenton Columbia R 

Sundown Sanitary Dist Astoria Youngs R 

Union Oil Co Astoria 

Bumble Bee Seafoods Astoria Columbia R 

Pacific Hake Fisheries Astoria Columbia R 

Warrenton Deep Sea, Inc. Warrenton Skipanon Ch

Pacific Fabricators Inc. Warrenton Skipanon R 

Port of Astoria Astoria 

Bumble Bee Seafoods Astoria LW Columbia R 

36 
A number of entities and facilities within the Youngs Bay watershed have discharge permits 

(Table 7). 

Table 7. Entities and facilities with permits to discharge into the Youngs Bay watershed (ODEQ 

2000) (adapted from Bischoff et al. 2000). 

Facility Name Stream 

Adamonis, Charles Youngs River 

Astoria, City of Youngs River 

Astoria, City of Youngs Bay

Brugh, George D. Youngs River 

Chadsey, Betty A. and others DBA John Day River 

Clatsop Economic Development Council Youngs Bay

Clatsop Transfer and Disposal Co. Youngs River 

Junes, Warren Lewis and Clark River 

Meiners, Darwin L. Lewis and Clark River 

Morisee, Steve Youngs Bay

Northwest Ready Mix, Inc. Youngs River 

Nygaard, David – DBA Klaskanine River 

Port of Astoria Youngs Bay

Schock, Donald Duane Lewis and Clark River 

Svensen, Tom John Day River 

Thompson, Barbara L. Lewis and Clark River 

Three D Corp Youngs River 

US Coast Guard Youngs Bay

Weber, Terry Lewis and Clark River 

The ODEQ Nonpoint Pollution Plan notes that the Youngs Bay watershed has a number of 

dissolved oxygen problems, and that toxics are of concern in the Lower Columbia region’s rivers 

and tributaries (ODEQ 2000). According to the plan, “87 stream miles in agriculture and 

rangeland areas are water quality limited. Agriculture and rangeland use is adjacent to 

approximately 19 percent of the total stream miles. Approximately 59 percent of the water 

quality limited water bodies that are adjacent to agricultural land use are contained in the Hood 

watershed. This watershed coincidentally also contains 59 percent of the agricultural lands in the 

Oregon portion of the combined Southwest Washington and Lower Columbia River ESUs” 

(ODEQ 2000). Regional land use is summarized in Table 8 and Figure 14. 

37 
Table 8. Land use summary in the LCRE (Tetra Tech 1992, Task 2) 

Forest Agriculture Urban Other Total

Oregon 

Clatsop 454,803 25,821 14,719 19,857 515,200

Columbia 288,000 73,949 23,000 54,731 439,680

Multnomah 142,498 35,011 74,016 19,195 270,720

Washington 

Clark 226,969 94,646 43,699 36,030 401,344

Cowlitz 583,024 37,612 36,816 74,644 732,096

Pacific 530,000 34,870 720 15,510 581,100

Skamania 1,044,016 6,726 2,235 17,295 1,070,272

Wahkiakum 146,346 14,616 1,280 4,606 166,848

TOTAL 3,415,656 323,251 196,485 241,868 4,177,260

81.8% 7.7% 4.7% 5.8% 100%

Figure 14. Summary of land use adjacent to streams in Oregon region of LCRE (ODEQ 2000) 

38 
The largest cities near the LCRE are Vancouver, WA and Portland, OR. Smaller cities include 

Longview, WA and Astoria, OR, making the area below Bonneville Dam “the most urbanized 

section of the river” (LCREP 2006 Module). Sewage treatment plants in Portland, OR and 

Vancouver, WA were identified as the “largest sources of effluent” to the LCRE by Fresh et al.

(2004), and Portland Harbor, OR was listed as a Superfund site in December 2000 due to 

contaminated river sediments (ODEQ 2006c). 

39 
C. Other Areas of Concern 

In this section we examine other potential threats to water resources within and near the LCRE. 

The list is not exhaustive but is intended to reflect the nature and range of threats that are known 

to occur or are anticipated in the region. The concerns listed in subsections C.1 – C.10 differ in 

their characteristic scales, level of risk, likelihood of occurrence, natural range of variation, and 

reversibility. They are not equally amenable to local or regional management. 

C.1. Harmful Algal Blooms 

Harmful algal blooms (HABs) are a potential threat to water quality along the OregonWashington coast. HABs are known to cause deaths of both wild and farmed fish and shellfish, 

illness or death in other marine animals and birds, human illness or death “from toxic seafood or 

from toxin exposure through inhalation or water contact...and alteration of marine habitats and 

trophic structure” (Anderson et al., 2002). HABs in the vicinity of the Oregon-Washington coast 

are most likely to be produced by phytoplankton species that can cause paralytic shellfish 

poisoning (PSP) or amnesic shellfish poisoning (ASP), also known as domoic acid poisoning 

(DAP). The alert levels for domoic acid and PSP are 2 ppm and 80 μg/100 g, respectively. 

Trainer (2002) found the high domoic acid levels (~308 ppm) in razor clams at Clatsop Spit in 

October 1998; the “highest PSP level (>4367 μg/100 g) was measured in mussels from the south 

jetty of the Columbia River in late September 1992.” 

The Oregon Department of Fish and Wildlife (ODFW), Oregon Department of Agriculture 

(ODA), NOAA, and the National Ocean Service initiated a project in 2005 in order to document 

and monitor phytoplankton blooms off the coast of Oregon (ODFW 2006). Currently, ODA 

conducts testing (bi-monthly in winter, weekly in summer) of commercial and recreational 

shellfish species, including mussels, bay clams, crab, oysters and razor clams (ODA 2006). In 

July 2006 DA levels in razor clams located on Clatsop Beach (from South Jetty to Tillamook 

Head) were elevated, but have since declined. The highest levels were recorded the week of July 

24 at 31 ppm. One month later, DA levels measured 27 ppm in razor clams. The elevated levels 

coincided with a seasonal “summer conservation closure,” which runs annually from July 15 to 

September 30 (ODA 2006). 

C.2. Non-indigenous and Invasive Species 

From the 1880s to the 1970s a new introduced species was found in the lower Columbia River 

about every five years. Over the past ten years, a new invertebrate species has been discovered 

about every five months (Figure 15). 

40 
Figure 15. Accumulation of non-indigenous species by year of discovery (Sytsma et al. 2004). 

This apparent increase in the appearance of non-native species likely reflects both an increase in 

the frequency of introductions and an increase in detection and reporting. The majority of 

introduced species originate from North America. Ballast water is believed to be the primary 

vector responsible for the introduction of nonindigenous invertebrates in the region (Sytsma et 

al. 2004). 

One of the most recent aquatic nonnative species found in the lower Columbia River is 

Pseudodiaptomus inopinus, an invasive Asian copepod that became established in abundance in 

the estuary between 1980 and 1990 (Cordell et al. 1992). The species was more recently 

discovered in the Youngs River. The occurrence of P. inopinus appears to be related to 

temperature and salinity: the species reportedly prefers warmer water temperatures (19.3 ± 

1.5oC) and lower salinities (less than 5 psu – practical salinity units; Cordell and Morrison 1996). 

Very little is known of the biology and ecology of P. inopinus in the invaded habitat; however, 

its ability to proliferate in high temperature/low salinity environments may have substantial 

implications as global climate change modifies estuarine environments. 

The Lower Columbia River Aquatic Nonindigenous Species Survey (LCRANS) was initiated to 

provide comprehensive information about the nonindigenous species present in the region and 

was intended to provide a baseline for evaluating the rate of introduced species. The project 

included a literature review (2001-2002) and field surveys (2002-2003). From the literature 

review, it was determined that at least 81 new organisms had been introduced into the lower 

Columbia River since the mid 1800s. The majority of these species were fish, aquatic plants, and 

crustacea. Over the course of the field survey, 134 stations were sampled and 269 aquatic species 

were reported. Of these, 54 species (21%) were introduced, 92 species (34%) were native, and 

123 species (45%) were cryptogenic, or of unknown origin. Eight of the 54 introduced species 

reported were new records for the lower Columbia River. The number of species categorized by 

minor taxonomic group is shown in Figure 16. The project report is comprehensive and includes 

an annotated list of native and non-native species (Sytsma et al. 2004). 

41 
 Figure 16. LCRANS field survey species collections by taxonomic group and origin (Sytsma et 

al. 2004). 

Specific examples of non-indigenous plant species that have been found in the LCRE include 

purple loosestrife, Eurasian milfoil, parrot feather, and Brazilian elodea. Introduced plants can 

out-compete native species, contribute to unhealthy water quality, and “create dense 

monospecific stands that represent poor habitat for native species (Northwest Power and 

Conservation Council 2004). In turn, these new plant communities may alter insect and detritus 

production in and around vegetated wetlands” (LCREP 2006 Module). 

C.3. Harvest and Collection of Organisms 

LEWI regulations state that “approaching, feeding, hunting or removing wildlife from the park is 

illegal” [and] a state fishing license is required for fishing within the Lewis and Clark River 

(NPS 2006). Beyond park boundaries, fishing is permitted in the LCRE and is regulated by the 

Washington and Oregon Departments of Fish and Wildlife. Although several runs of salmonids 

are listed as threatened or endangered under the ESA, the sources of these declines are likely 

attributable to factors other than direct removal within park boundaries. 

C.4. Water Withdrawals 

In the LCRE, a permit is generally required for water withdrawals from surface and groundwater 

sources. The primary water source for Warrenton, OR is the Lewis and Clark River, and the 

largest withdrawals are “for municipal and domestic uses, representing 97 percent of the total” 

(Bischoff et al. 2000; Figure 17 below). Water withdrawals are known to “affect both the 

magnitude and timing of flows entering the estuary and plume” (LCREP 2006 Module). 

Withdrawals are often the result of irrigation practices; these withdrawals as well as other water 

42 
uses are “estimated to have reduced flows of the Columbia River by 7 percent since the latter 

part of the nineteenth century” (Jay and Kukulka 2002 in LCREP 2006 Module). Surface water 

withdrawals for irrigation purposes account for about 96 percent of total water used, while the 

remaining four percent are used by municipal sources (National Research Council 2004 in 

LCREP 2006 Module). Groundwater withdrawals for irrigation purposes account for about 75 

percent of total water used, while other uses are responsible for the remaining 25 percent 

(National Research Council 2004 in LCREP 2006 Module). Approximately 2,155 acres of land 

are used during the irrigation season (May 1-September 30, annually) (Tetra Tech 1992). 

Figure 17. Water withdrawals in the Youngs Bay watershed (Bischoff et al. 2000). 

43 
C.5. Hydropower and Salmon Recovery 

Several federal and non-federal hydropower dam projects exist along the Columbia River (UW

CBR 2006). Over 400 dams are located in the Columbia River Basin, including two large federal 

dams, Bonneville and Grand Coulee. The purpose of these dams is to create “large reservoirs that 

provide flood control and water for vast irrigation systems on the Columbia Plateau.” The Army

Corps of Engineers (ACOE) and Bureau of Reclamation (USBR) cooperatively operate the 31 

federal hydropower dams on the Columbia and Snake Rivers that make up the Federal Columbia 

River Power System (FCRPS). Environmental degradation of the river has been attributed to 

these dams, especially with regard to declines in anadromous fish (by limiting fish passage), 

decreasing stream flow levels, and destruction of vital fish habitat (NWR 2006; WDOE 2006h). 

Dams also can cause increased predation of fish in reservoirs (WDOE 2006h). 

Pacific salmon stocks have declined substantially since the impoundment of the Snake and 

Columbia rivers by hydropower dams. Hydropower dams have subjected smolts to delays in 

migration, injuries and stress associated with dam passage (Kareiva & Marvier 2000), and 

increased predation by avian predators (Schreck et al. 2006). Wilson (2003) reported delayed 

mortality of juvenile salmon as the result of passage through dams. Salmon spawning and rearing 

habitat has been reduced by 55% due to the installment of hydroelectric and irrigation diversion 

dams without providing for fish passage (Bottom et al. 2005). Wetlands and floodplain habitats 

have been eliminated through diking activities, resulting in a reduction of the salmon-rearing 

capacity of the LCRE (Bottom et al. 2005). 

These activities and their resultant impacts have led to the listing of twelve Columbia River fish 

species as either endangered or threatened under the Endangered Species Act. One additional 

species currently is proposed for listing under the ESA. These include the following (LCREP 

2006b): 

Endangered 

Snake River Sockeye Salmon ESU (Evolutionarily Significant Unit) 

Upper Columbia River Chinook Salmon Spring-run ESU 

Upper Columbia River Steelhead ESU

Threatened 

Snake River Chinook Salmon Spring/Summer-run ESU 

Snake River Chinook Salmon Fall-run ESU 

Lower Columbia River Chinook Salmon ESU 

Upper Willamette River Chinook Salmon ESU 

Columbia River Chum Salmon ESU 

Snake River Basin Steelhead ESU 

Lower Columbia River Steelhead ESU 

Upper Willamette River Steelhead ESU 

Middle Columbia River Steelhead ESU 

Proposed 

Lower Columbia River Coho Salmon ESU 

Hatchery programs have been used throughout the region to supplement fish populations. 

However, hatcheries can contribute to the decline of wild salmon through the spread of disease 

44 
and through increased competition for food and habitat in streams and in the ocean. They can 

also interbreed with wild fish, resulting in a loss of genetic diversity (WDOE 2001). 

C.6. Habitat Modification 

Habitat modification to the LCRE has occurred through the construction of dikes, dams and 

jetties, dredging activities, and resulting erosion of the banks and river mouth. Many portions of 

the Youngs Bay watershed have been extensively diked (Figure 18). Most of these dikes were 

installed between 1917 and 1939 and extend along both the Lewis and Clark and Youngs rivers 

(Bischoff et al. 2000). These structures have caused a 10-12% reduction in the estuary’s tidal 

prism (NOAA Fisheries 2006). 

Figure 18. Dikes and wetlands in Youngs Bay Watershed (Bischoff et al. 2000).

These alterations have reduced the availability of estuarine habitat to salmonids. In particular 

“access to and use of floodplain habitats by ocean-type ESUs (salmonids that typically rear for a 

shorter time in tributaries and a longer time in the estuary) have been severely compromised 

through alterations in the presence and availability of these critical habitats” (LCREP 2006 

Module). 

45 
In addition to diking activities, the construction of dams along the Columbia and Snake Rivers 

(Figure 19) has “significantly restrict[ed] new sand from reaching the ocean” (LCREP 2006 

Module). 

Figure 19. Columbia River Basin dams (www.ecy.wa.gov). 

The sediment load in the Columbia River has been reduced by an estimated 24-50% percent 

from the 1800s. Without sand from the Columbia delta, the coastal shorelines are in the early 

stages of a long-term erosion phase (WDOE 2001). Erosion along the southwest coast of 

Washington is affected by jetties, dams, sediment supply, geologic events such as earthquakes, 

wave action, and weather events like El Niño (WDOE 2006i). The jetties have caused beaches to 

grow and “possibly erode,” and Columbia dams have “reduced the sand supply to coastal 

beaches by two thirds” (WDOE 2006i). 

In the late 1800s, jetties were constructed on both sides of the mouth of the Columbia River 

(Figure 20). 

46 
Figure 20. North and South Jetties at Columbia River Mouth (www.ecy.wa.gov). 

The jetties are intended to help accelerate the flow of the river, help maintain the depth and 

orientation of the navigation channel, and provide protection for ships (both commercial and 

recreational) entering and leaving the estuary (ACOE 2006a). Portions of the North and South 

Jetty have become weakened due to wave action, causing concern that the jetties could breach 

should a large storm event occur along the outer coast. This would allow sand “to be transported 

and deposited directly into the navigation channel,” which would consequently impact both 

commercial and recreational activities (ACOE 2006a). Some repairs were completed on the 

North Jetty in 2005, and repairs on the South Jetty are expected to be completed by October 

2007. 

Jetty construction and dredging have changed the dynamic nature of the estuary entrance in the 

areas of Clatsop Spit and Trestle Bay. These activities have limited wave action and the marine 

supply of sediment and have caused the export sand and gravel out of the estuary at a rate three 

times higher than that at which they enter the estuary (NOAA Fisheries 2006). These activities 

have also altered currents and wave action in Baker Bay. Mid-channel islands have migrated 

toward the interior of Baker Bay and as a result, tidal marsh habitat has recently begun to 

develop in some areas. However, much of the historical tidal marsh and tidal swamp habitat has 

been lost because of dike construction in the floodplain (NOAA Fisheries 2006). 

Dredging has historically occurred throughout the Youngs Bay watershed in order to maintain 

navigability for the Port of Astoria and the Lewis and Clark River. These alterations have led to 

loss of aquatic habitat (Bischoff et al. 2000). Despite concerns over habitat modifications, some

major projects are underway in the LCRE. One is the Columbia River Channel Improvement 

Project, a collaborative effort between the ACOE and six lower river ports in Oregon and 

Washington. The overall plan is to deepen the 40-foot channel by three feet in order to improve 

navigation and the condition of the estuary through various environmental restoration projects 

(ACOE 2006a). The first phase of the project was completed in February 2006 and the dredged 

material was deposited at an upland site in Vancouver, WA. This project will allow for increased 

access to the river by larger container ships and will likely result in increased domestic and 

47 
international commerce. A White House press release from August 13, 2004 stressed the 

potential environmental benefits of the project: 

• Migrating juvenile and adult salmon will be helped by tidegate retrofits with fish 

slides installed along the lower Columbia River, at Grizzly Slough, Tide Creek, and 

Hall Creek in Oregon, and at Burris Creek and Deep River, Washington; 

• Juvenile salmon rearing will be helped by connecting channels constructed at the 

upstream end of Walker-Lord and Hump-Fisher Islands to improve juvenile salmonid 

access to their embayment-rearing habitats; 

• Juvenile salmon rearing will be helped by the dredging of Bachelor Slough to 

improve flow and water quality and restoration of rearing habitat in shallow 

water/flats and riparian forest habitat; 

• Restoration and maintenance of native tidal marsh will be helped by implementation 

of an integrated pest management plan for purple loosestrife control between 

Columbia River miles 18 and 52; 

• Migrating juvenile and adult salmon will be helped by implementation of a 3-phase 

effort to improve water circulation and fisheries ingress and egress at Tenasillahe

Island, Columbian white-tailed deer translocation will establish a secure and viable 

deer population at Cottonwood-Howard Island, and tidal marsh habitat will be 

restored at Tenasillahe Island via breaching the encircling dike; and 

• Waterfowl and wading birds will be helped by the restoration of wetland habitat at 

Shillapoo Lake. 

Despite these potential positive impacts, other studies have shown that dredging activities can 

resuspend contaminants trapped in bottom sediments. Seelye et al. (1982) “demonstrated the 

potential for uptake of DDE and PCBs by fish as a result of dredging” while Steidl et al. (1991) 

“suggested that the source of DDE and PCBs in ospreys from Delaware Bay was from bottom

sediments and dredging activities” (in Anthony et al. 1993). 

C.7. Oil and Fuel Spills

Heavy shipping traffic on the Columbia River renders it vulnerable to oil and fuel spill. The 

lower estuary region is at additional risk due to the hazards of navigating the lower river and 

river mouth, and because tides and currents within the lower estuary will cause rapid spread once 

a spill occurs. In 2005, transport of total domestic tonnage of all commodities exceeded 17 

million tons, of which petroleum and petroleum products accounted for more than 6 million tons 

(USACE Waterborne Commerce Statistics Center 2005). 

Oil spill response in the Columbia River System is addressed by the Northwest Area 

Contingency Plan (NACP 2007). Committee members include Coast Guard Sector Seattle, Coast 

Guard Sector Portland, Environmental Protection Agency Region Ten, WDOE, ODEQ, Idaho 

Bureau of Homeland Security, Other federal agencies, Other state agencies, Local government 

agencies, Tribes, Non-governmental organizations, Industry, and Response Contractors. The US 

Department of Interior is represented by the Regional Environmental Officer in Portland, OR. 

The NACP was most recently updated in July 2007. According to that document, Geographic 

Response Plans (GRPs) exist for many areas within the Columbia River system. Up-to-date 

GRPs provide a means of improving response in the event of a spill, especially with regard to 

48 
sensitive areas and those containing wildlife. The Lower Columbia GRP is maintained by 

WDOE; its status and date of most recent update are unclear.

Recent oil spills in this region have been small but frequent; the cumulative impacts of these 

spills could degrade water quality and aquatic habitats in the LCRE region. Table 9 shows spills 

that were reported between October 2005 and June 2007 (ACOE 2006b): 

Table 9. Spills in the LCRE Region 2005-2007 (ACOE 2006b) 

Date Location and Source (if available) Amount of Spill 

October 25, 2005 John Day Dam - Navigation Lock Less than 3 gallons 

November 8, 2005 The Dalles Dam - Spillway Bay 23 Less than 1 pint 

February 14, 2006 Lookout Point Dam About 15 gallons 

February 22, 2006 Bonneville Less than 1 cup 

March 27, 2006 Lookout Point - Tailrace Less than 1 cup 

May 10, 2006 The Dalles Lock and Dam - Main Unit 9 

scroll case 

Less than 50 gallons 

May 30, 2006 The Dalles Lock and Dam - Main Unit 

18 governor oil pump 

Less than 1 pint 

June 29, 2006 The Dalles Lock and Dam - Unknown 

source 

Less than 1 pint 

July 11, 2006 The Dalles Lock and Dam - Oil/Water 

separator 

Less than 1 quart 

July 19, 2006 The Dalles Lock and Dam - Oil/Water 

separator 

Less than 1 gallon 

July 28, 2006 Mouth of the Columbia River South Jetty 

- Komatsu 1250 excavator 

Less than 10 gallons on jetty 

August 8, 2006 The Dalles Lock and Dam - Tailrace Less than 1 gallon 

August 17, 2006 The Dalles Lock and Dam - A pilot 

pressure line blew in the governor 

cabinet of Main Unit 17 

Less than 1 gallon made its 

way to the floor drain 

August 25, 2006 Mouth of the Columbia River South Jetty 

- Komatsu 1250 excavator 

Less than 10 gallons on jetty 

September 14, 2006 Dexter Dam - from drainage sump in 

powerhouse 

Less than 1 gallon 

October 30, 2006 The Dalles Lock and Dam Main Unit 15 

blade seals 

Less than 1 gallon discharged 

November 3, 2006 Dredge Essayons – Columbia River Mile 

82, between St. Helens and Kalama, 

Oregon, Columbia County 

11 gallons bow thruster light 

gear oil, Texaco Meopa 68 

November 25, 2006 Dredge Yaquina - from forepeak tank in 

river at 8010 NW Saint Helens Road, 

Portland, OR. 

About 1 ounce 

December 5, 2006 The Dalles Lock and Dam – Main Unit 

14 

Less than 1 gallon 

December 11, 2006 John Day Lock and Dam – Navigation 

Lock – drainage pump #4 

1 quart of Mobil EAL 244H 

49 
December 12, 2006 John Day Lock and Dam – Navigation 

Lock – drainage pump #3 

1 quart of Mobil EAL 244H 

December 18, 2006 The Dalles Lock and Dam – Tailrace – 

de-water drainage sump

Sheen 

February 14, 2007 The Dalles Lock and Dam – Tailrace – 

Main Unit 16 blade seals

Less than 1 gallon 

April 10, 2007 Bonneville Lock and Dam – Powerhouse 

2 head gate system reservoir 

314 gallons 

May 14, 2007 Lost Creek Reservoir - from privatelyowned submerged vehicle Up to 40 gallons 

May 18, 2007 Humboldt Bay, CA - from Corps’ dredge 

Essayons 

Approximately 7 gallons 

released 

May 27, 2007 Coos Bay Field Office - released from 

Corps’ dredge Yaquina 

Approximately 2 ounces 

June 13, 2007 Mouth of the Columbia River, South 

Jetty - released from contractor’s 

equipment 

Approximately 3 gallons 

hydraulic oil 

July 19, 2007 South Jetty construction at Mouth of the 

Columbia River - spilled from

contractor's equipment 

5 gallons of hydraulic oil 

August 6, 2007 South Coast Clamshell dredging project - 

from dredging contractor equipment 

during refueling operations 

Up to 15 gallons 

August 23, 2007 The Dalles Lock and Dam turbine oil 

spill 

1 gallon reported 

September 4, 2007 The Dalles Lock and Dam Less than 1 pint of oil 

discharged 

September 5, 2007 Willamette Falls Locks -upstream side of 

gate 1, lock chamber 

12 gallons of hydraulic oil 

September 20, 2007 Hills Creek Powerhouse Estimated leak of 1 gallon 

light turbine oil 

September 21, 2007 The Dalles Dam About .5 gallon of turbine oil 

In 1999, approximately 150 gallons of fuel were released near Fort Clatsop National Memorial 

by Willamette Industries. About 143 tons of potentially contaminated soil were tested for the 

presence of contaminants, but none were found (Spencer Environmental, Inc. 2000 in NPS 

2002). 

C.8. Land-based and Water-based Recreation 

The Fort Clatsop National Memorial Water Scoping Report (NPS WRD 1994) listed restricted 

access as a barrier to recreational activities, such as boating and fishing, along the Lewis and 

Clark River. Since 1980, however, Fort Clatsop National Memorial visitation has been steadily 

increasing. In preparation for the Lewis and Clark Bicentennial (2003-2006), the NPS estimated 

that approximately 400,000 to 500,000 visitors were expected (NPS 2002). 

50 
Fishing and boating are permitted on the Columbia River and Youngs Bay (NPS 2006c). 

According to some estimates, “more salmon are caught in the Columbia River and its tributaries 

than any other region in the state” (WDFW 2006). Regulations change annually (and sometimes 

weekly) to adjust to the status of the salmon runs (WDFW 2006). The mouth of the Columbia is 

popular for fall Chinook salmon and sturgeon fishing, while Youngs Bay is known for its spring 

Chinook fishery. The Youngs River is also a popular site for cutthroat trout (Trails.com 2006). In 

addition to fishing, non-motorized boating is available on the Lower Columbia River Water 

Trail, which runs from Bonneville Dam to the Pacific Ocean. 

C.9. Tsunami Hazards 

The potential threat of tsunami impacts on the Oregon-Washington coastal region has been 

summarized by WDOE (WDOE 2006j). The region is vulnerable to tsunamis generated by 

earthquakes on the Cascadia Subduction Zone, which is located about 70 miles off of the Pacific 

coast, as well as from distant sources (Walsh 2005). Recent studies suggest that tsunamis have 

struck the Oregon coast on a regular basis with wave heights between 20-45 feet at the shoreline 

(ODGMI 1995). According to some estimates, a tsunami would force the central portion of the 

Olympic Peninsula in Washington to rise, and coastal areas would be inundated with water, 

sinking below sea level. Maps developed by the Oregon Department of Geology and Mineral 

Industries (1995) show tsunami impacts from Clatsop Spit to Astoria as well as complete 

flooding of Cape Disappointment. 

C.10. Climate Change 

 

Climate projections suggest gradual regional warming and higher precipitation, especially in 

winter. This would likely lead to increased frequency of winter freshets and lower natural springfreshet flows (Bottom et al. 2005). Gradual regional warming makes the accumulation of 

snowpack less likely and smaller, decreasing spring freshet volume (LCREP Subbasin Summary 

2002). 

The Climate Impacts Group (CIG) (2004) identified several impacts of warmer temperatures and 

increased winter precipitation on the Pacific Northwest (PNW) including: 

• Increased rain rather than snow during winter months; 

• Increased winter streamflow; 

• Increased winter flooding in transient basins; 

• Reduced amount of water stored as snow; 

• Earlier snow melt; and 

• Decreased late spring and summer streamflows 

Observed and predicted impacts of climate change in the Pacific Northwest (PNW) are 

summarized in Table 10. 

51 
Table 10. Observed and projected impacts of climate change in major climate and hydrologic 

indicators (CIG 2004) 

Indicator Observed 20th century changes Projected mid-century changes

Temperature Region-wide warming of about 1.5°F (1920-2000)

Warming has been fairly uniform and widespread,

with little difference between warming rates at 

urban and rural weather monitoring stations. 

1990s the warmest decade on record (warmer than 

any other decade by 0.9oF)

Most warming occurring during winter 

2020s: average increase of 2.7°F

2040s: average increase of 4.1°F

Temperature changes benchmarked to 

the decade of the 1990s. 

Precipitation Region-wide increase in precipitation since 1920

Median value: +22%

Changes upwards of 60% in northeast Washington

and British Columbia) 

Uncertain, although most models 

project wetter winters and drier 

summers 

April 1 

snowpack

Substantial declines (>30%) at most monitoring

stations below 6,000 feet

Continued decrease in April 1 

snowpack in mid- and low-elevation 

basins. 

Projected decrease in April 1 

snowpack for the Cascades Mountains

in Washington and Oregon relative to

20th century climate: 

 0 - 44% by the decade of the 

2020s (based on +3°F average temp

change) 

 0 - 58% by the decade of the 

2040s (based on +4.5°F average temp

change) 

Timing of peak

spring runoff 

Advanced 10-30 days earlier into the spring season 

during the last 50 years 

Greatest trends occurred in the PNW 

Earlier peak spring runoff expected 

on the order of 4-6 weeks 

Summer 

streamflow 

Declining in sensitive PNW basins

May-September inflows into Chester Morse Lake 

(WA) in the Cedar River watershed as a fraction of

annual flows 

have decreased 34% since 1946 

Losses in June-Sept flows at Dworshak Dam (ID) 

on the order of 10% in 82 years 

Continued and more wide-spread 

declines 

April-September natural streamflow 

in the Cedar River (WA) projected to 

decrease 35% by the 2040s (based on

a 2.5°F increase in average temp) 

July-October streamflows in the 

Tualatin Basin (OR) projected to 

decrease 10-20% by the 2040s; total 

average annual runoff projected to be

less than the historic average 

52 
Increased winter flooding, decreased summer streamflows, and elevated estuary temperatures 

will degrade estuarine salmon habitat. These changes will likely exacerbate stresses on salmon 

stocks from presently degraded freshwater and estuarine habitat (CIG 2004). 

Global climate change is projected to intensify many hazards and stresses currently present in the 

coastal zone including erosion, shoreline retreat, bluff landsliding, and flooding (CIG 2004). 

Coastal erosion, shoreline retreat and landslides are predicted to increase as a result of sea level 

rise and increased precipitation in winter. Some coastal areas may experience accretion, others, 

erosion. 

Sea level rise will depend on circulation changes in the Northeast Pacific and on local vertical 

land movements. Land subsidence along the northern Oregon coast is predicted to exacerbate sea 

level rise (CIG 2004). 

The potential impacts of climate change on the PNW are predicted to have adverse effects on 

both hydrologic and biological components. The potential management implications for 

mitigating these changes are discussed in Table 11. 

53 
Table 11. Potential management implications associated with projected climate change impacts 

on water resources in the Pacific Northwest (CIG 2004). 

Projected Hydrologic Impact Potential Management Implications

Increased winter streamflow - Increases the risk for more winter flooding in

low (rain dominant) and midelevation 

(rain/snow mix) basins, possibly requiring

more active management of floods and 

floodplains 

- Increases the potential for more streambed 

scouring events (affecting salmon redds), 

possibly impacting salmon recovery and

management activities 

- Increases the potential for more winter

hydropower production, possibly

increasing revenues

Reduced snowpack - Reduces the amount of water available for 

spring reservoir refill and summer 

streamflows, potentially requiring operations 

adjustments to meet summer water demands 

(with implications for summer hydropower 

production and salmon) 

- Reduces the risk for spring flooding in large 

snowmelt dominant basins 

- Likely to increase competition for summer 

water uses

Earlier snowmelt and earlier peak runoff - Increases length of the summer low flow 

season, potentially increasing competition for 

summer water 

- May have implications for salmon 

management and recovery where there is a 

mismatch between salmon migration patterns 

and peak flows

Reduced summer streamflow - Increases frequency of significant low flow 

events and potential for drought, potentially 

increasing competition for water and stressing 

abilities to meet water quality parameters and 

instream flow requirements (re: warmer water 

temperatures)

54 
D. Recommendations 

D.1. Condition Overview 

We summarize the condition of water resources in LEWI in Tables 12-16 based on our review of 

available data and our best professional judgment. Our recommendations draw upon those 

previously offered by others. We incorporate uncertainty associated with the limited data 

available for assessing water resources in LEWI, especially with regard to the newly acquired 

park sites, for which water resource data are severely limited. 

We find that the greatest threats and stressors to water resources within LEWI emanate from

outside sources, for example, hydropower, land use (agriculture, forestry, development), and 

habitat modification (diking, dredging, and biological invasion). Furthermore, the potential for 

unpredictable catastrophic events such as a major oil spill, tsunami, or contamination from

nuclear wastes stored upstream must be recognized. 

The combination of anthropogenic changes, successional processes, and climate change requires 

that park managers determine ecosystem goals for LEWI that are both desirable and feasible, and 

nest these goals within the broader regional management goals. Assessment of potential changes 

associated with the cumulative effects of growth, development, and change impacts, and 

evaluation of management strategies will require a more comprehensive, quantitative basis from

which to determine change. 

55 
Table 12. Condition of water resources in and around LEWI. 

Legend: 

EP= 

existing 

problem

PP= 

potential 

problem 

IP= 

intermittent 

problem

OK= 

no 

detectable 

problem

ID= 

insufficient 

data to 

evaluate 

Stressor/ 

Environmental 

Indicator 

Lower 

Columbia 

River 

Estuary 

Youngs 

Bay 

Watershed

Wetlands, 

Lakes, 

Streams 

Outer Coastal 

Waters 

WATER QUALITY 

INDICATOR 

 Nutrients ID EP ID OK

 Dissolved Oxygen EP EP ID ID

 Fecal Bacteria EP EP ID OK

Toxic Compounds EP EP ID OK

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

IP IP EP OK

 Stormwater 

Runoff 

IP IP EP OK

 Agricultural 

Runoff 

IP IP EP OK

HABITAT

MODIFICATION 

Upland Habitat 

Modification 

EP EP EP OK

 Shoreline/Aquatic 

Habitat 

Modification 

EP EP EP EP

 Erosion EP EP EP EP 

RECREATIONAL 

USAGE 

Harvest/Collection 

of Organisms 

OK OK OK OK

OTHER 

STRESSORS/ 

INDICATORS 

Non-Native 

Invasive Species 

EP EP EP OK

Harmful Algal 

Blooms

ID ID ID ID

Fuel / Oil Spills PP PP OK PP 

56 
Table 13. Condition of water resources in the Lower Columbia River Estuary. 

Legend: 

EP= 

existing 

problem

PP= 

potential 

problem 

IP= 

intermittent 

problem

OK= 

no 

detectable 

problem

ID= 

insufficient 

data to 

evaluate 

Stressor/ 

Environmental 

Indicator 

Lower 

Columbia 

River 

Estuary 

Explanation 

WATER QUALITY 

INDICATOR 

 Nutrients ID Insufficient data to determine. No specific 

information on nutrients in the estuary or 

LEWI region (pg. 31) 

 Dissolved Oxygen EP Exceedances reported, although 

interpretation of data is difficult as many 

standards have not been established for 

measured parameters (Morace 2006) (pg. 23) 

 Fecal Bacteria EP Exceedances reported as Category 5 303(d) 

listings in WRIA 24 in Southwest 

Washington and in the Lower Columbia 

watershed in Oregon (Klaskanine and Lewis 

and Clark Rivers) (pg. 26). No reported 

exceedances for Cape Disappointment. 

Toxic Compounds EP PCBs, dioxins, other compounds detected as 

Category 5 and 4A 303(d) listings in WRIAs 

24 and 25 in Southwest Washington (pg. 26). 

Sources of contaminants believed to include 

sources upstream of Bonneville Dam, 

surface water runoff, and erosion, and have 

been found in salmon tissue and sediments 

(Feist et al. 2005; CRK 2006b; Morace 

2006; Johnson et al. 2007)

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

IP Intermittent releases reported. Discharges 

from mills, dams, and industrial and 

municipal facilities blamed as sources (CRK 

2006b) (pg. 34, 39). 

 Stormwater 

Runoff 

IP Seasonal runoff causes intermittent problems

 Agricultural 

Runoff 

IP Intermittent releases reported

57 
HABITAT

MODIFICATION 

Upland Habitat 

Modification 

EP Agriculture, forestry, and urban/suburban 

development have modified habitat. 

Irrigation practices and dam projects have 

reduced flow (pg. 43-44)

 Shoreline/Aquatic 

Habitat 

Modification 

EP Diking and dredging have substantially 

modified habitat. Alterations can reduce 

availability of estuarine habitat for salmonids 

(pg. 45, 47). Dikes have caused a 10-12% 

reduction in the estuary’s tidal prism

(NOAA Fisheries 2006) (pg. 45).

 Erosion EP Natural processes disturbed by dredging and 

diking, which have reduced sediment load in 

the river by about 24-50% since the 1800s 

(WDOE 2001).

RECREATIONAL 

USAGE 

Harvest/Collection 

of Organisms 

OK No indication that decline of salmon runs is 

related to direct removal (pg. 42). 

OTHER 

STRESSORS/ 

INDICATORS 

Non-Native 

Invasive Species 

EP Invasive species present; some problematic. 

At least 81 new organisms have been 

introduced since the mid-1800s (Systma et 

al. 2004).

Harmful Algal 

Blooms

ID No data available on HABs specific to 

estuary. 

Fuel / Oil Spills PP Small but chronic spills could have 

cumulative impacts (see Table 9). Shipping 

traffic on the river makes the region 

susceptible to future problems, especially 

navigation around the river mouth (pg. 48).

58 
Table 14. Condition of water resources in the Youngs Bay Watershed. 

Legend: 

EP= 

existing 

problem

PP= 

potential 

problem 

IP= 

intermittent 

problem

OK= 

no 

detectable 

problem

ID= 

insufficient 

data to 

evaluate 

Stressor/ 

Environmental 

Indicator 

Youngs 

Bay 

Watershed

Explanation 

WATER QUALITY 

INDICATOR 

 Nutrients EP Exceedances reported near Fort Clatsop 

(NPS WRD 2000), low levels near Lewis 

and Clark River in 1996 (NPS 2002), and 

throughout watershed (Table 1, pg. 25).

 Dissolved Oxygen EP Exceedances reported near Fort Clatsop 

(NPS WRD 2000).

 Fecal Bacteria EP Exceedances reported throughout 

watershed except for Lower Lewis and 

Clark River (Table 1, pg. 25).

Toxic Compounds EP PCBs, dioxins, other compounds detected 

in Lewis and Clark River near Fort Clatsop 

(NPS 2002) in soils believed to be caused 

by sources upstream (pg. 23).

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

IP Intermittent releases reported from Fort 

Clatsop in the 1990s from three septic 

tank/leachfield systems (NPS WRD 1994) 

(pg. 33) and other discharges (NPS WRD 

2000) (pg. 36) and (Bischoff et al. 2000) 

(pg. 37).

 Stormwater 

Runoff 

IP Seasonal runoff causes intermittent 

problems. National Park Service operations 

at Fort Clatsop found to be a source (NPS 

WRD 1994) (pg. 33).

 Agricultural 

Runoff 

IP Intermittent releases reported near Fort 

Clatsop (NPS WRD 1994) (pg. 33, 37).

HABITAT

MODIFICATION 

Upland Habitat 

Modification 

EP Agriculture, forestry, and urban/suburban 

development have modified habitat (pg. 32, 

pg. 35, 37).

59 
 Shoreline/Aquatic 

Habitat 

Modification 

EP Diking and dredging have substantially 

modified habitat. Dikes along the Lewis 

and Clark River has destroyed or altered 

almost 70% of the wetlands, and dredging 

of the Lewis and Clark River to facilitate 

navigation and timber transport has 

influenced the habitat (NPS WRD 1994; 

Bischoff et al. 2000) (pg. 33). 

 Erosion EP Natural processes disturbed by dredging 

and diking

RECREATIONAL 

USAGE

Harvest/Collection 

of Organisms 

OK No indication that decline of salmon runs is 

related to direct removal (pg. 42). 

OTHER 

STRESSORS/ 

INDICATORS

Non-Native 

Invasive Species 

EP Invasive species present; some problematic. 

At least 81 new organisms have been 

introduced since the mid-1800s (Systma et 

al. 2004). 

Harmful Algal 

Blooms

ID No data available on HABs specific to the 

Youngs Bay watershed. 

Fuel / Oil Spills PP Small but chronic spills could have 

cumulative impacts. Most in the Columbia 

River itself (ACOE 2006b), but potential 

exists in the Youngs Bay watershed. In 

1999, about 150 gallons of fuel was 

released near Fort Clatsop although no 

contaminants were found in the soil (NPS 

2002) (pg. 50). 

60 
Table 15. Condition of water resources in freshwater wetlands, lakes, and streams. 

Stressor/ 

Environmental 

Indicator 

Wetlands, 

Lakes, 

Streams 

Explanation 

WATER QUALITY 

INDICATOR 

 Nutrients ID No data available specific to freshwater 

bodies. 

 Dissolved Oxygen ID No data available specific to freshwater 

bodies.

 Fecal Bacteria ID No data available specific to freshwater 

bodies.

Toxic Compounds ID No data available specific to freshwater 

bodies.

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

EP Intermittent releases reported

 Stormwater 

Runoff 

EP Seasonal runoff causes intermittent 

problems; National Park Service operations 

at Fort Clatsop found to be a source (NPS 

WRD 1994) (pg. 33).

 Agricultural 

Runoff 

EP Intermittent releases reported near Fort 

Clatsop (NPS WRD 1994) (pg. 33, 37).

HABITAT

MODIFICATION 

Upland Habitat 

Modification 

EP Agriculture, forestry, and urban/suburban 

development have modified habitat (pg. 32, 

pg. 35, 37). Irrigation practices and water 

withdrawals (pg. 43).

 Shoreline/Aquatic 

Habitat 

Modification 

EP Diking and channel modification have 

substantially altered habitat. See Figure 18 

for locations of dikes along wetlands, lakes, 

and streams.

 Erosion EP Natural processes modified by diking and 

channel modification. 

Legend: 

EP= 

existing 

problem

PP= 

potential 

problem 

IP= 

intermittent 

problem

OK= 

no 

detectable 

problem

ID= 

insufficient 

data to 

evaluate 

61 
RECREATIONAL 

USAGE 

Harvest/Collection 

of Organisms 

OK No indication that decline of salmon runs is 

related to direct removal (pg. 42).

OTHER 

STRESSORS/ 

INDICATORS 

Non-Native 

Invasive Species 

EP Invasive species present; some problematic. 

At least 81 new organisms have been 

introduced since the mid-1800s (Systma et 

al. 2004), which could spread through 

freshwater system.

Harmful Algal 

Blooms

ID No data available specific to freshwater 

bodies. 

Fuel / Oil Spills OK No indication of problems in freshwater 

system. 

62 
Table 16. Condition of water resources in outer coastal areas. 

Stressor/ 

Environmental 

Indicator 

Outer 

Coastal 

Waters 

Explanation 

WATER QUALITY 

INDICATOR 

 Nutrients OK No indication of problems specific to outer 

coastal areas. 

 Dissolved Oxygen ID No data available specific to outer coastal 

areas. 

 Fecal Bacteria OK Only low levels of bacteria found at Fort 

Stevens and Seaside, Oregon outside of the 

estuary in 2004. 

Toxic Compounds OK No indication of problems specific to outer 

coastal areas. 

LAND-USE 

RELATED 

STRESSORS

 Septic / 

Wastewater 

OK No indication of problems specific to outer 

coastal areas.

 Stormwater 

Runoff 

OK No indication of problems specific to outer 

coastal areas.

 Agricultural 

Runoff 

OK No indication of problems specific to outer 

coastal areas. 

HABITAT

MODIFICATION 

Upland Habitat 

Modification 

OK No indication of problems specific to outer 

coastal areas. 

 Shoreline/Aquatic 

Habitat 

Modification 

EP Mouth of Columbia River modified by jetties. 

Portions have been weakened by wave action, 

causing concern that jetties could breach as a 

result of a large storm event, which could 

transport sand directly into the navigation 

channel (ACOE 2006a). 

 Erosion EP Natural processes modified by jetties. Wave 

action and marine supply of sediment has been 

limited, sand and gravel has been exported out 

of the estuary at a rate three times higher than 

that at which they enter (NOAA Fisheries 

2006). Currents and wave action have also 

been altered in Baker Bay, causing migration 

of mid-channel islands and the creation of 

tidal marsh habitat in some areas (pg. 47). 

63 
RECREATIONAL 

USAGE 

Harvest/Collection 

of Organisms 

OK No indication that decline of salmon runs is 

related to direct removal (pg. 42). 

OTHER 

STRESSORS/ 

INDICATORS 

Non-Native 

Invasive Species 

OK No indication of problems specific to outer 

coastal areas. 

Harmful Algal 

Blooms

ID Limited data specific to outer coastal areas 

despite projects to monitor phytoplankton 

blooms (ODFW 2006). Elevated domoic acid 

levels in razor clams at Clatsop Spit found by 

Trainer (2002) and ODA (2006) (pg. 40). 

Fuel / Oil Spills PP Area vulnerable to oil spills because of 

location of shipping lanes along the coast (pg. 

48). 

64 
D.2 Recommendations 

D.2.a. Context and General Recommendations 

The water resource management environment within which LEWI exists is complex and 

dynamic at several scales. Multiple park sites are distributed around the Lower Columbia River 

Estuary and along outer coastal shores across two states. Human activities that influence the 

quality of water resources (e.g., shoreline and upland habitat modification, agriculture, forestry, 

urban and suburban development, hydropower operations, commercial shipping) occur across 

multiple spatial scales and vary in intensity through time. Consequently, we consider multiple 

scales and make recommendations for water resource management within LEWI at 1) the 

regional scale, in the context of the Lower Columbia River Estuary; 2) the watershed scale, in the 

context of the Youngs Bay Watershed; and 3) the scale of the park itself. Achieving integration 

across all three scales presents a substantial challenge that can be met only through partnering 

with other agencies and entities. 

Regional Scale: Lower Columbia River Estuary 

LCREP (2004) articulated five action-oriented strategies for the Lower Columbia subbasin: 

1) Reduce the effects of the Columbia River hydropower system

2) Protect and restore habitat 

3) Address toxic contaminants 

4) Slow introductions of non-native species 

5) Reduce predation on focal species 

Based on our review of water resources within LEWI, these five strategies address several of the 

most prominent threats to regional water resources. Consequently, we recommend that LEWI 

retain these as priority strategies, track their implementation by LCREP, and contribute expertise 

and support for such implementation where appropriate, recognizing that full implementation 

will require far more capacity than exists within LEWI alone. 

Within the LCREP framework, LEWI has the opportunity to participate in the design of the 

LCREP monitoring program to ensure that it meets NPS water resource needs. In addition, 

LEWI might reasonably expand its own water resource monitoring program to include newly 

acquired sites within the park in a design that simultaneously serves its own needs and is 

integrated with a larger LCREP monitoring program. Priority sites could include Fort Clatsop 

National Memorial, Station Camp, and estuarine habitat(s) within Cape Disappointment. 

USFWS and NOAA are engaged in recovery planning processes under the US ESA for the 

marbled murrelet and several species of salmon that utilize the Lower Columbia River Estuary 

during some portion of their life history. These recovery planning processes are consonant with 

LEWI’s interest in restoring the ecosystem to conditions encountered by Lewis and Clark in 

1805-1806. Currently, as many as 30 tribes, federal and state agencies, and NGOs are engaged in 

65 
salmonid recovery. LEWI can leverage these activities by actively participating in recovery 

planning processes, particularly those with relevance to habitats within or adjacent to park sites. 

Watershed Scale: Youngs Bay Watershed 

Bischoff et al. (2000) made the following recommendations with regard to managing coastal 

habitats in the Youngs Bay watershed: 

1) Prioritize areas that salmonids are known to use for spawning and rearing, especially 

those with sufficient water quality (low temperature, low turbidity) and “good stream

channel characteristics (responsive channel habitat type, good geomorphologic conditions, 

good riparian shade and recruitment potential).” 

2) Create a strategy to collect “continuous discharge data in the primary rivers that flow into 

Youngs Bay....Discharge data are essential to evaluate current low flow and peak flow 

conditions in the watershed.” 

3) “Develop or expand the continuous temperature monitoring network with monitors at 

strategically located points such as the mouths of tributary streams, locations of known 

spawning beds, at the interface between major land use types, or downstream of activities 

with the potential to influence water temperature.” 

4) “Locate and map potential sources of nitrogen, phosphorus, and bacteria in the 

watershed.” 

While these four recommendations focus primarily on salmon habitat, they are consistent with 

monitoring water quality parameters that are essential to maintaining healthy estuarine habitats. 

LEWI should encourage the development of a sustained monitoring program and participate in 

such monitoring activities where feasible. In particular, LEWI can contribute site-specific water 

quality data to regional databases in order to increase the power to detect regional trends. 

Watershed-level impacts to LEWI’s resources that originate outside the park must be identified 

and, where possible, minimized or mitigated. This requires that the park keep apprised of landuse activities within the watershed and engage in partnerships to address the impacts of such 

activities where feasible. Where outside funds are available for activities such as restoration, 

LEWI can partner with local entities and agencies to plan and implement projects that would 

benefit water resources within the park. 

Park-wide Scale 

The recent expansion of LEWI from the original Fort Clatsop National Memorial site to a larger 

park encompassing several disjunct sites requires that management of water resources be 

extended to the new park sites. Prior water resource data collection and management for these 

sites is largely lacking. Although a park-wide system of water resource management is desirable, 

differences in site history, use, location, and ecology will require the development of site-specific 

strategies that are compatible with park-wide goals and objectives. 

66 
LEWI has maintained a water resource monitoring program at the Fort Clatsop National 

Memorial site since 1998. Consistent with both a watershed and parkwide approach, this 

monitoring program could be expanded to include newly acquired park sites and to address new 

or emerging threats to water quality. Monitoring sediments for toxins and pollutants would add 

information that could be essential to restoration activities. Monitoring storm-water runoff from 

roads and parking lots within the park would add valuable information and could help guide 

remedial action. Rare freshwater resources should be included in any expansion of the 

monitoring program. Resources for monitoring could be leveraged by partnering with local 

entities, state agencies, and academic institutions.

LEWI has demonstrated a commitment to wetland restoration. Restoration is an important tool to 

address habitat loss and modification due to diking, shoreline hardening, forest practices, and 

biological invasion. In many park areas, restoration will be required to return wetlands to 

conditions approximating those encountered by Lewis and Clark. Consequently, wetland 

restoration will be important to meeting park management goals and should remain a priority 

activity within LEWI. Candidate restoration sites from across all park sites should be prioritized 

by level of threat, feasibility of restoration, and likelihood of restoring ecological function. As 

partnerships and funds allow, sites can be selected from such a list. 

Elsewhere in coastal Oregon, the US Forest Service has pioneered the ‘Suislaw Process’ as a 

means of catalyzing wetland restoration programs on lands under the agency’s ownership. The 

process is led by a multidisciplinary graduate student team working closely with an advisory 

board and project manager over a short period (weeks to months) to develop a detailed plan for a 

restoration site (Chase 2006). The benefits of the process as implemented by the USFS are 1) 

low cost; 2) stakeholder participation and support for the process; 3) leveraged resources and 

expertise. The process has been used successfully to design a restoration plan for the Lower Drift 

Creek Estuary in the Alsea watershed and has been extended to the Salmon River estuary. Given 

the importance of wetland restoration within and around LEWI and the current limitations on 

funding and personnel, the park could consider implementing a program similar to the Suislaw 

Process at priority restoration sites. 

High volumes of shipping traffic coupled with habitat modification and upland land use render 

the Lower Columbia River Estuary particularly vulnerable to invasion by non-native species. 

Control of invasive species is especially appropriate at small scales, for example, site-specific 

removals in sensitive areas with the park. The park can continue to remove invasive species on a 

case-by-case basis (as has been done in the past), and can become proactive by developing an 

invasive species management plan that includes aspects of prevention, detection, control, and 

eradication in a systematic framework that allows rapid response, sustained activity, and 

prioritization by species and anticipated threat to habitats. Invasive species management should 

be coupled with restoration activities to 1) prevent invasion of restored habitats and 2) to restore 

invaded habitats. 

67 
D.2.b. Specific Recommendations 

Based on recommendations reported in Section D.2.a. and on our review and assessment of 

water resource condition and stressors in and around LEWI, we offer the following specific 

recommendations (Table 17). The order in which the recommendations are presented does not 

reflect relative importance or urgency. In offering these recommendations, we acknowledge that 

moderate uncertainty exists in our evaluation of several aspects of water resource condition. 

This uncertainty reflects the limitations of the data. Consequently, our recommendations include 

suggestions for closing data gaps, especially those pertaining to water resources that could 

become degraded in the near-to-mid-term. 

Table 17. Specific Recommendations 

• Maintain and expand the current water quality monitoring program to include new park 

sites. 

• Integrate the water quality monitoring program with regional programs (e.g., LCREP 

monitoring program). 

• Determine feasibility of restoring aquatic habitats within LEWI to the approximate 

conditions encountered by Lewis and Clark; prioritize habitats by feasibility, and modify 

management goals for aquatic habitats deemed not feasible for restoration.

• Where feasible, partner with local groups and tribes to restore degraded freshwater and 

estuarine habitats, especially those that provide essential fish habitat. 

• Develop a plan for managing non-indigenous marine, estuarine, and freshwater species. 

• Work with other agencies and entities to reduce the impacts of hydropower and land use 

on water resources within LEWI. 

• Encourage NACP to update the Oil Spill Geographic Response Plans for the Lower 

Columbia River Estuary and outer coastal regions. Consider whether the definition of 

sensitive areas under existing Oil Spill Contingency Plan rules could be expanded to 

include sensitive areas within LEWI. 

• Measure stormwater runoff and manage to reduce impacts to estuarine environments. 

• Measure the amounts of toxins and contaminants introduced to coastal streams and rivers 

and to beach areas by surface water flow from primary and secondary roadways and 

parking areas. Determine whether toxins and contaminants from roadway sources impair 

water resources in LEWI.

• Plan for impacts due to climate change, including impacts to restoration sites. 

68 
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78 
Appendix A. Water Quality Standards 

Table A1. EPA Water Quality Standards for Marine Waters 

EPA Water Quality Standards for Marine waters Source 

Dissolved Oxygen (DO) Criteria evaluated for freshwater levels only. Coldwater values

were used because the EPA identifies the presence of salmonid 

species to be indicative of coldwater areas. The acute lethal limit 

for salmonids is at 3 mg/L, but the coldwater minimum has been

established at 4 mg/L due to more sensitive insect populations. 

Because the criteria are generalized, it is required that states

evaluate the species in their own waters to establish appropriate

minimum levels of dissolved oxygen. 

U.S. EPA. 1986. Ambient 

Water Quality Criteria for 

Dissolved Oxygen. EPA 

440/5-86-003; EPA Gold 

Book 

Temperature For marine aquatic life, the maximum increase in the weekly

average temperature due to artificial causes is 1°C (1.8°F) during all 

seasons of the year, and daily temperature cycles of a body of water 

are not to be altered, neither in amplitude nor frequency.

EPA Gold Book 

pH Shall fall between the range of 6.5-8.5 EPA Gold Book

Turbidity 

Toxic Substances 

Primary Contact Recreation Source 

Fecal Coliforms The median value for a fecal coliform standard is 15 per 100mL and 

the 90th percentile should not exceed 43 for a 5-tube, 3-dilution 

method. 

EPA Gold Book 

79 
The Department of the Interior protects and manages the nation’s natural resources and cultural heritage; provides scientific and 

other information about those resources; and honors its special responsibilities to American Indians, Alask Natives, and affiliated

Island Communities. 

NPS D-80, September 2007
National Park Service 

U.S. Department of the Interior 

Natural Resource Program Center

Natural Resources Program Center 

Water Resources Division 

1201 Oakridge Drive, Suite 250

Fort Collins, CO 80525 

www.nature.nps.gov/water 

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