Prepared in cooperation with the University of Washington and the Lower Columbia River Estuary Partnership

Columbia River Estuary Ecosystem Classification— 

Concept and Application

U.S. Department of the Interior

U.S. Geological Survey

Open-File Report 2011–1228
Cover: Photograph showing view of lower Columbia River estuary, approximately 55 km 

from the mouth, looking down-estuary with Welch Island in the foreground; the ocean 

entrance in the background. Photograph taken by Charles Simenstad, University of 

Washington, May 26, 2005.
Columbia River Estuary Ecosystem Classification—

Concept and Application

By Charles A. Simenstad and Jennifer L. Burke, University of Washington; Jim E. O’Connor and Charles Cannon,

U.S. Geological Survey; Danelle W. Heatwole and Mary F. Ramirez, University of Washington; Ian R. Waite and

Timothy D. Counihan, U.S. Geological Survey; and Krista L. Jones, Lower Columbia River Estuary Partnership

Prepared in cooperation with the University of Washington and the 

Lower Columbia River Estuary Partnership

Open-File Report 2011-1228

U.S. Department of the Interior

U.S. Geological Survey
U.S. Department of the Interior

KEN SALAZAR, Secretary

U.S. Geological Survey

Marcia K. McNutt, Director

U.S. Geological Survey, Reston, Virginia: 2011

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Suggested citation:

Simenstad, C.A., Burke, J.L., O’Connor, J.E., Cannon, C., Heatwole, D.W., Ramirez, M.F., Waite, I.R., Counihan, T.D.,

and Jones, K.L., 2011, Columbia River Estuary Ecosystem Classification—Concept and Application: U.S. Geological 

Survey Open-File Report 2011-1228, 54 p. 

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endorsement by the U.S. Government.

Although this report is in the public domain, permission must be secured from the individual 

copyright owners to reproduce any copyrighted material contained within this report.
iii

Contents

Executive Summary....................................................................................................................................................... 1

Introduction.................................................................................................................................................................... 2

Impetus for New Estuarine Ecosystem Classification ................................................................................................ 3

Objectives .................................................................................................................................................................. 6

Approach ....................................................................................................................................................................... 6

Columbia River Estuary, Processes and Ecosystems................................................................................................ 6

Setting of the Columbia River Basin and Estuary................................................................................................... 7

Contemporary Hydrologic and Geomorphic Processes and Landforms................................................................. 8

Floods and Tides ................................................................................................................................................ 8

Sediment Movement and Transfers.................................................................................................................... 9

Design of Columbia River Estuary Ecosystem Classification....................................................................................11

Methods........................................................................................................................................................................12

Data Criteria and Requirements................................................................................................................................12

Primary Criteria for Classification Design ..............................................................................................................12

Secondary .............................................................................................................................................................12

GIS Structure ............................................................................................................................................................13

Base Data and Analytical Steps................................................................................................................................13

Historical Flood Plain and Tidal Extent..................................................................................................................13

Level-Specific Data Sources .................................................................................................................................13

Levels 1 and 2— Ecosystem Province and Ecoregion ......................................................................................13

Level 3—Hydrogeomorphic Reach....................................................................................................................14

Level 4—Ecosystem Complex...........................................................................................................................15

Level 5—Geomorphic Catena............................................................................................................................16

Level 6—Primary Cover Class...........................................................................................................................17

Results..........................................................................................................................................................................18

Level 1—Ecosystem Province ..................................................................................................................................18

Level 2—Ecoregion...................................................................................................................................................18

Level 3—Hydrogeomorphic Reach ...........................................................................................................................18

Level 4—Ecosystem Complex ..................................................................................................................................22

Level 5—Geomorphic Catena...................................................................................................................................23

Level 6—Primary Cover Class ..................................................................................................................................23

Discussion ....................................................................................................................................................................24

General and Unique Applicability to Estuarine Classification Needs.........................................................................24

Utility and Application to Estuarine Science, Monitoring, Restoration and Management ..........................................24

Research...............................................................................................................................................................25

Change Analyses ..................................................................................................................................................25

Monitoring .............................................................................................................................................................26

Restoration and Preservation Planning .................................................................................................................27

Management .........................................................................................................................................................27

Constraints on Data Adequacy and Application of the Classification to the Entire Columbia River Estuary .............28

Validation Needs.......................................................................................................................................................29

Summary and Recommendations.................................................................................................................................29

Acknowledgments ........................................................................................................................................................30

References Cited..........................................................................................................................................................30
iv

Appendix A. Summary of location, geographic and geomorphic setting, major landforms, geologic content and history, 

characteristic geomorphic and hydrologic processes, and anthropogenic factors affecting key processes in eight 

Hydrogeomorphic Reach forming the Columbia River Estuary Ecosystem Classification. ...........................................39

Figures

Figure 1. Basic physiographic setting and geographic extent of the Columbia River estuary as applied to the 

Columbia River Estuary Ecosystem Classification....................................................................................................... 40

Figure 2. Classification Level 1-Ecoregion Provinces, adopting the EPA Ecoregion Level II classification................. 41

Figure 3. Classification Level 2-Ecoregions based on the EPA Ecoregion classifications .......................................... 42

Figure 4. Classification Level 3-Hydrogeomorphic Reaches indicating where the eight reaches are delineated by 

subdividing and adjusting the borders of EPA Ecoregion IV classes according to hydrological and physiographic 

discontinuities .............................................................................................................................................................. 43

Figure 5. Classification Level 4-Ecosystem Complexes illustrated for Hydrogeomorphic Reach F based on 

delineating mainstem and distributary channels using current bathymetry data and analyses of flood plain 

geology and geomorphology ....................................................................................................................................... 44

Figure 6. Classification Level 5-Geomorphic Catena illustrated for Hydrogeomorphic Reach F................................. 45

Figure 7. Classification Level 6-Primary Cover Class illustrated for Hydrogeomorphic Reach F based on 

2010 LCRE Land Cover Classification......................................................................................................................... 46

Figure 8. Comparison of Primary Cover Class in Hydrogeomorphic Reach F of Columbia River estuary 

between 1866 and 1901 and 2010 .............................................................................................................................. 47

Tables

Table 1. Sources and attributes of spatial data used to develop draft Columbia River Estuary Ecosystem 

Classification ............................................................................................................................................................... 48

Table 2. Preliminary list of ecosystem complexes mapped under Level 4 of the Columbia River Estuary 

Ecosystem Classification............................................................................................................................................. 50

Table 3. Preliminary list of geomorphic catenae mapped under Level 5 of the Columbia River Estuary 

Ecosystem Classification............................................................................................................................................. 51

Table 4. Classification hierarchy in relation to geology, time and human disturbances............................................... 53
v

Conversion Factors

SI to Inch/Pound

Multiply By To obtain

Length

centimeter (cm) 0.3937 inch (in.)

meter (m) 3.281 foot (ft) 

kilometer (km) 0.6214 mile (mi)

kilometer (km) 0.5400 mile, nautical (nmi) 

meter (m) 1.094 yard (yd) 

Area

square meter (m2) 10.76 square foot (ft2) 

square kilometer 0.3861 square mile

hectare (ha) 0.003861 square mile (mi2)

Volume

cubic meter (m3) 6.290 barrel (petroleum, 1 barrel = 42 gal)

cubic meter (m3) 264.2 gallon (gal) 

cubic meter (m3) 0.0002642 million gallons (Mgal) 

cubic centimeter (cm3) 0.06102 cubic inch (in3) 

Flow rate

cubic meter per second (m3/s) 70.07 acre-foot per day (acre-ft/d) 

cubic meter per year (m3/yr) 0.000811 acre-foot per year (acre-ft/yr) 

meter per second (m/s) 3.281 foot per second (ft/s) 

meter per year (m/yr) 3.281 foot per year ft/yr) 

cubic meter per second (m3/s) 35.31 cubic foot per second (ft3/s)

cubic meter per day (m3/d) 35.31 cubic foot per day (ft3/d) 

cubic meter per day (m3/d) 264.2 gallon per day (gal/d) 

cubic meter per second (m3/s) 22.83 million gallons per day (Mgal/d) 

cubic meter per hour (m3/h) 39.37 inch per hour (in/h)

millimeter per year (mm/yr) 0.03937 inch per year (in/yr) 

Specific conductance is given in microsiemens per centimeter at 25 degrees Celsius (μS/cm at 25°C).

Concentrations of chemical constituents in water are given either in milligrams per liter (mg/L) or micrograms per liter (μg/L).

Datums

Vertical coordinate information is referenced to the insert datum name (and abbreviation) here, for instance, “North American

Vertical Datum of 1988 (NAVD 88)”

Horizontal coordinate information is referenced to the insert datum name (and abbreviation) here, for instance, “North American 

Datum of 1983 (NAD 83)”

Altitude, as used in this report, refers to distance above the vertical datum.
vi

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1

Columbia River Estuary Ecosystem Classification: 

Concept and Application

By Charles A. Simenstad, Jennifer L. Burke, Jim E. O’Connor, Charles Cannon, Danelle W. Heatwole, Mary F. 

Ramirez, Ian R. Waite, Timothy D. Counihan, and Krista L. Jones

Executive Summary 

This document describes the concept, organization, and application of a hierarchical ecosystem 

classification that integrates saline and tidal freshwater reaches of estuaries in order to characterize the 

ecosystems of large flood plain rivers that are strongly influenced by riverine and estuarine hydrology. 

We illustrate the classification by applying it to the Columbia River estuary (Oregon-Washington, 

USA), a system that extends about 233 river kilometers (rkm) inland from the Pacific Ocean. More than 

three-quarters of this length is tidal freshwater. The Columbia River Estuary Ecosystem Classification

(“Classification”) is based on six hierarchical levels, progressing from the coarsest, regional scale to the 

finest, localized scale: (1) Ecosystem Province; (2) Ecoregion; (3) Hydrogeomorphic Reach; (4) 

Ecosystem Complex; (5) Geomorphic Catena; and (6) Primary Cover Class. We define and map Levels 

1-3 for the entire Columbia River estuary with existing geospatial datasets, and provide examples of 

Levels 4-6 for one hydrogeomorphic reach. In particular, three levels of the Classification capture the 

scales and categories of ecosystem structure and processes that are most tractable to estuarine research, 

monitoring, and management. These three levels are the (1) eight hydrogeomorphic reaches that 

embody the formative geologic and tectonic processes that created the existing estuarine landscape and 

encompass the influence of the resulting physiography on interactions between fluvial and tidal 

hydrology and geomorphology across 230 kilometers (km) of estuary, (2) more than 15 ecosystem 

complexes composed of broad landforms created predominantly by geologic processes during the 

Holocene, and (3) more than 25 geomorphic catenae embedded within ecosystem complexes that 

represent distinct geomorphic landforms, structures, ecosystems, and habitats, and components of the 

estuarine landscape most likely to change over short time periods.
2

Introduction

We describe the rationale, conceptual basis, and application of a hierarchical ecosystem 

classification for large-river, flood-plain estuaries, and provide examples from the application of this

controlling factor approach for the Columbia River estuary (Oregon-Washington, USA). A number of 

estuarine, delta and river-flood plain classifications based on geomorphology, hydrology, and salinity 

have been proposed as spatial frameworks for research and management (Hume and others, 2007). Few, 

however, completely integrate the estuarine to freshwater gradients or address the varying scales of 

geologic history and contemporary regional climate, watershed, ocean, riverine, and anthropogenic 

development factors that control estuarine ecosystem distributions and processes. 

The Columbia River Estuary Ecosystem Classification (hereafter “Classification”) described 

here addresses four prominent inconsistencies or gaps in existing estuarine ecosystem classifications and 

their application. These gaps are: (1) management applications (particularly in the USA) still tend to 

exclude significant tidal freshwater reaches of large-river estuaries, tidal flood (surge) plains, and deltas 

despite scientific recognition of the continuum of estuarine ecosystems from tidal saline to tidal fresh 

waters (see definition of ‘estuary’ below) and classifications that incorporate this breadth in estuary 

structure and processes; (2) focus by research and management efforts on the response attributes (for 

example, water quality, biota) rather than the ‘controlling factors’ and geological and hydrological 

processes that account for the occurrence, variation, and trends and patterns in change of ecosystem

types driven by estuary and watershed characteristics and processes (although, see Hume and others, 

2007); (3) little incorporation of large-scale and long-term “antecedent” processes, especially landscape 

modifying disturbance events, that over recent geologic time have shaped unique features of estuarine 

landscapes; and (4) no differentiation among features of estuarine landscapes and their component 

ecosystems that are formed by natural processes and those formed primarily by specific water and landuse management actions. Although we have attempted to address these needs specifically for the 

Columbia River estuary, we recognize that many of these inconsistencies continue to constrain the 

classification of large-river estuaries into ecosystem units that are useful for science and management 

decision-making in other systems around the world (McLusky and Elliott, 2007).

Our emphasis on the biophysical characteristics of ecosystems, factors that structure their 

occurrence and organization in estuaries, and consideration of regional to local scales of formative 

processes conforms with the more comprehensive definition of estuary from geological and 

geomorphological evidence that includes tidal freshwater reaches extending to the upper limit of tidal 

influence (Dionne, 1963; Dalrymple and others, 1992). Strong rationale for the initial geological and 

geomorphological perspective also has emerged from geochemical (Fairbridge, 1980) and biological 

disciplines (Schuchardt and Schirmer, 1991). Accordingly, we follow Perillo’s (1995, p. 26) inclusive 

definition of estuaries that embraces physical and biological attributes and includes complex, 

hierarchical forms of estuaries:

“An estuary is a semi-enclosed coastal body of water that extends to the effective limit of tidal 

influence, within which sea water entering from one or more free connections with the open sea, or 

any other saline coastal body of water, is significantly diluted with fresh water derived from land 

drainage, and can sustain euryhaline biological species from either part or the whole of their life 

cycle.” 
3

We adopt the definition of ‘head of tide’ that references water-level fluctuations affected by the 

tidal wave, which in turn influences shoreline and surgeplain vegetation and fauna assemblages because 

of their sensitivity to the regularity of water-level inundation and exposure. In adopting the head of tide 

as the ecotone between fluvial and estuarine ecosystems, we emphasize that more than just dilution of 

seawater by freshwater or current reversal structures the gradient from oceanic to fluvial ecosystems. 

Interactions of tidal and river forcing modulates hydrological, geomorphological, geochemical, 

biological, and ecological processes across the tidally influenced freshwater (“tidal freshwater”) of 

lower watersheds in significantly different ways than in free-flowing fluvial ecosystems (for example, 

Schuchardt and others, 1993; Perillo, 1995; Elliott and McLusky, 2002; McLusky and Elliott, 2004; 

Wolanski, 2007). Whereas the European Communities Water Framework Directive’s definition of 

“transitional waters” includes “partially saline in character” (European Communities, 2000), the concept 

of transitional waters across the European Union has been applied more pragmatically as “aquatic areas 

which are neither fully open coastal nor enclosed or flowing freshwater areas” where boundaries may be 

defined by physiographic features and discontinuities, or by salinity or any other hydrogeographic 

feature” (McLusky and Elliott, 2007). Thus, the broad concept of transitional waters is attentive to 

distinctions and “discontinuities” among ecosystem transitions where tidal and fluvial processes interact 

and is similar to the more modern definition of estuaries.

In this analysis, we also adhere to the ecological literature’s distinction between “ecosystem” 

and “habitat” where an ecosystem is viewed as a community of plants, animals and micro-organisms 

and their abiotic environment interacting as an ecological unit whereas a habitat is a type of biotic and 

abiotic environment in which an organism (possibly specific to life history stage) lives. Because these 

terms are applied quite interchangeably in the conservation resource management literature, many 

‘habitat classifications’ would likely fall into the category of ecosystem classification.

This initial summary provides the rationale and utility for the Classification and our approach to 

its design concepts and methods. We define the six hierarchical levels of ecosystem function and 

structure underlying the Classification. With this structure, we delineate the three broadest levels for the 

entire Columbia River estuary with existing geospatial datasets. For finer levels of the Classification, we 

provide examples of application for a single hydrogeomorphic reach. We also suggest potential science 

and management applications for the Columbia River estuary.

Impetus for New Estuarine Ecosystem Classification

The need to recognize how controlling factors influence the organization of estuarine ecosystems 

may be most effectively addressed by understanding the hierarchy of spatial and temporal scales over 

which the formative processes operate (O’Neill and others, 1986; Klijn and Udo de Haes, 1994; Hume 

and others, 2007). The complex and dynamic nature of ecosystems presents challenges when attempting 

to characterize their structure and function at one, manageable scale; even more so when the features 

and processes of interest span multiple temporal and spatial scales. Increasing the challenge of 

characterization is that ecosystems tend to be self-organizing. However, the concept of a hierarchy in 

ecosystems suggests that it may be tractable to delineate boundaries and that the transition in ecosystem 

processes across these boundaries may be meaningful to science and management (Gonzalez, 1996).

In conceptualizing the Columbia River Estuary Ecosystem Classification, we surveyed the 

published literature, unpublished and other “gray” reports and the World Wide Web (WWW) for 

existing classification schemes possibly appropriate for application to the Columbia River estuary. 

Examination of commonly utilized riverine and wetland classifications, and especially those including 

hydrological and geomorphological descriptors (for example, Leopold and Wolman, 1957; Bovee, 1982; 

Rosgen, 1994; Sear and others, 2003) indicated that they seldom approached tidal freshwater regions of 
4

watersheds. Some classifications explicitly consider tidal freshwater and tidal flood-plain ecosystems, 

although these tend to originate from Europe, Australia, New Zealand, and Asia and most have not yet 

reached peer review publication. For instance, the Water Ecotope Classification (WEC) originated in 

The Netherlands (Van der Molen and others, 2003) and adopts a classification that comprehensively 

bridges watersheds and coastal waters with “transitional waters” and is based on morphodynamics, 

hydrodynamics, and land use. In WEC, flood-plain ecotypes are defined, however, the resolution of 

these ecotopes is not detailed enough for delineation of biotic habitats. In fact, application of the 

European Union’s (EU) Water Directive definition of “transitional waters” remains muddied around the 

differentiation between brackish and estuarine among broad seas, closed lagoons, or tidal estuaries 

(McKlusky and Elliott, 2007). Other estuary classifications (for example, Hume and Herdendorf, 1988; 

Simons and others, 2001) also include tidal freshwater and tidal flood plain ecosystems but do not 

classify estuarine features at the resolution of ecosystems. Although many recent approaches (for 

example, National Coastal/Marine Classification Standard for North America; Madden and Grossman,

2004) were developed to resolve deficiencies and inconsistencies in earlier classifications of habitat 

units and local structures for the estuarine and nearshore marine systems (Cowardin, 1979; Dethier,

1990; Brown, 1993; Wieland, 1993; Connor, 1997; Allee and others, 2000; Madley, 2002), none of 

these extended into tidal fluvial ecosystems and few provided much insight into tidal flood-plain 

ecosystems. However, Madden and Grossman (2004) make strong arguments for the need and 

mechanisms to link the National Coastal/Marine Classification Standard for North America to 

compatible freshwater classifications.

The large areas, high water velocities, and complex ecological interactions in large flood-plain 

rivers present substantial challenges to data gathering for comprehensive estuary classification. 

Hydraulic models are the basic tool for quantifying the interplay between hydrology and 

geomorphology and describing the physical aquatic habitat template. Hydraulic models have been used 

in the analysis and modeling of large rivers (Tiffan and others, 2002; Garland, 2004), but substantive 

differences in area, data requirements, and types of analyses dictate different approaches for using this 

tool on large rivers. For example, large rivers may stress computational resources for digital hydraulic 

models, and complex flow hydraulics around engineered structures and at the confluence of tributaries 

will require investigation of fine-scale enhancements and the utility of 2- and 3-dimensional models. At 

the same time, large rivers also offer opportunities to use high-resolution hydro-acoustic depth, velocity, 

and substrate-sensing instrumentation, new topographic data techniques such as Light Detection And 

Ranging (LiDAR), and extensive telemetry efforts that can provide datasets with high density and 

precision. 

Many of these methods and data sources have been applied to estuarine classification at varying 

spatial and temporal scales. Although typical land-cover classifications based on remote sensing 

imagery (for example, Coastal Change Analysis Program [C-CAP] using LANDSAT imagery) are 

excellent tools for capturing ecosystem status and change at a particular spatial scale, they do not 

necessarily capture larger landscape-scale features that account for some of the inherent diversity of 

estuarine ecosystems. Furthermore, it would be desirable to capture indicators of the more dynamic 

features of estuaries (such as bars and tidal channels), where strong fluvial and tidal forces interact and 

structure complex landscapes and frequent natural and anthropogenic disturbances continuously modify 

and re-arrange landscape structure. Efforts to characterize dynamic, large-scale estuaries may benefit 

from a comprehensive classification that is based primarily on ecosystem-forming processes. Capturing 

the status and trends of landscape-scale features can be particularly important when it is desirable for 

research and management to examine and manage transitions and connectivity among habitats of 

organisms with migratory life histories such as anadromous fishes.
5

Large rivers typically are affected by alterations to hydrologic and geomorphic processes. Flow 

regimes of large rivers frequently are altered by reservoir regulation or water diversions. As such,

restoration of the historical hydrograph often has been suggested as a primary action to restore 

ecosystem functions (National Academy of Sciences, 1992; Poff and others, 1997). This view assumes 

that the natural flow regime will return most, if not all, of the river’s physical habitat template. 

However, large rivers also are characterized by extensive physical alterations of channel morphology 

due to navigation, flood protection, flood-plain drainage, and bank stabilization structures. These 

features control the distribution of water and sediment and strongly influence physical features, thereby 

altering geomorphic adjustments of the river system (Gore and Shields, 1995; Jacobson and Galat, 

2006). Additionally, the development of dams on large-rivers systems alters the sediment transport 

regime, further influencing the river’s ability for geomorphic adjustments (Bayley, 1995; Syvitski and 

others, 2005a; Jacobson and others, 2009). Hence, the restoration of a natural hydrograph alone is 

unlikely to restore all physical features of large rivers unless other factors affecting hydrologic and 

geomorphic processes such as dikes and levees also are addressed. Much of the practical management of 

large rivers involves informed tradeoffs between hydrology and geomorphology, a decision-making 

process that can be guided by the relative ecological benefits and societal costs of altering these 

characteristics.

The Columbia River estuary exemplifies both the need and the challenges in classifying complex 

ecosystem structure along steep environmental gradients controlled by broad-scale regional tectonic and 

geologic processes, contemporary seasonally and annually variable hydrology and sedimentology, and 

even more rapid ecological responses. Flow regulation by the hydropower system and major alterations 

in channel configuration (for example, construction of dikes and levees and dredging to maintain the 

mainstem navigation channel) characterize present constraints on ecosystem-sustaining processes in the 

Columbia River estuary. For instance, loss of access to the natural flood plain and connectivity between 

habitats by the construction of levees has been implicated in habitat loss for juvenile salmon 

(Oncorhynchus spp., 13 populations of which are listed under the Endangered Species Act), both within 

the lower estuary (Thomas, 1983) and in tidal freshwater regions (Kukulka and Jay, 2003b).

In developing a strategy for a comprehensive ecosystem classification scheme appropriate to the 

entire tidally influenced region of the Columbia River estuary (fig. 1), we drew on the limited existing 

approaches to classifying and assessing functionality of large rivers, coastal flood plains, and estuaries. 

More than three-quarters of the length of the Columbia River estuary is tidal freshwater. Potentially at 

least 155 km of the 230 km estuary was historically exposed to effective tidal action (Syvitski and 

others, 2005b). Regulated flows have augmented dry-season discharges resulting considerably more 

persistent tidal freshwater under current conditions (Sherwood and others, 1990; Simenstad and others, 

1992). This is particularly relevant to the existing need for an ecosystem classification scheme because 

tidal freshwater regions, particularly of large tidal flood plain rivers such as the Columbia River, are 

seldom included in the currently accepted classifications for either estuaries or rivers. Although landcover classifications routinely include tidal freshwater vegetation and other unique surface features, 

hydrological, geomorphological, or landscape features are seldom included.

In presenting this classification, we recognize that it is an a priori approach at the levels 

(resolutions in hierarchy) which we found unresolved in most estuarine classifications. At this interim 

stage of the Classification, we have had no opportunity or mechanism to validate the more unique 

classes. By putting this forward, however, we invite rigorous, scientific testing of the Classification as a 

valid framework for the characterization and organization of estuarine ecosystems and as a management 

tool. In the Discussion, we present some examples of how the Classification could be, and is actually 

being tested and applied.
6

Objectives

Given the general lack of a documented estuarine ecosystem classification that met the setting 

and research and management needs of large-river and flood-plain estuaries such as the Columbia River 

estuary, we drew upon estuary classification literature (see prior discussion, particularly Perillo’s 1995 

comprehensive synopsis) and designed a hierarchical framework that would delineate useful classes 

across different scales of the diverse ecosystems and component fish and wildlife habitats. The primary 

purpose of the classification is to promote and facilitate systematic research, monitoring, and 

management of diverse ecosystems. We place particular emphasis on ecosystems that encompass the 

important fish and wildlife habitats that are much of the management focus in the Columbia River 

estuary. The Classification is, however, designed to provide a more utilitarian framework for 

understanding the underlying ecosystem processes that create the dynamic structure of the Columbia 

River and other, comparable large-river and coastal flood plain estuaries that possess extensive 

transitions and ecotones from tidal freshwater to euhaline ecosystems. As such, it is intended to assist 

scientists and managers who seek a broader scale of understanding required to study, manage, and 

restore these transitional ecosystems.

Approach

Columbia River Estuary, Processes and Ecosystems

Commensurate with the spatial extent of the Columbia River estuary, the geographic scope of 

the Classification (fig. 1) extends from the outer mouth (the oceanic end of the jetties) to the upstream 

extent of tidal variability in water level, which for the contemporary system is the downstream base of 

Bonneville Dam (about rkm 233); although the tidal wave is a minor component of the water-level 

fluctuation at this point, it is still distinguishable, particularly at low flow. This location also is close to 

the historical extent of tidal influence at the lower end of now-inundated Cascade Rapids. The lateral 

extent is defined as encompassing all elevations from deepest channel depths to the upper elevations of 

the historical flood plain, as well as flood plains of the tidally affected extent of tributary rivers. At 

present, we tentatively delineate the current flood plain as encompassing surfaces as high as 18 mm 

above North American Vertical Datum of 1988. The mapped floodplain extent will change during the 

process of mapping for the Classification as we refine our understanding of Holocene geology, floodplain morphology, and early pre-settlement flood elevations (based on U.S. Army Corps of Engineers, 

1968; Kukulka and Jay, 2003a, 2003b). The rationale for encompassing the entire area of the historical 

flood plain is that we intend the Classification to enable (a) comparison with historical ecosystem 

structure and (b) evaluation of restoration scenarios that may involve re-inundation of mainstem and 

tributary flood plains.

The geologic history provides insight into the events that created the physiographic template for 

the estuary. Our interpretations of contemporary ecosystem structure originate from understanding of 

Quaternary geologic processes and events as well as of currently active processes. As should be evident 

in the descriptions of the features that define at least five of the six levels in the Classification, largescale, geologic and tectonic processes are responsible for much of the template for ecosystem structure 

in the estuary. 
7

Setting of the Columbia River Basin and Estuary

The Columbia River drains 660,480 km2 of western North America, flowing 2,000 km from its 

headwaters at Columbia Lake in southeastern British Columbia, Canada, to its confluence with the 

northeast Pacific Ocean near Astoria, Oregon. In terms of drainage area, the Columbia River is the 39th

largest river basin in the world (Vorosmarty and others, 2000), but it ranks higher with respect to mean 

discharge (23rd of primary rivers entering seas or oceans), mean elevation (7th of largest 50 rivers 

entering seas or oceans; Vorosmarty and others, 2000), and slope (5th of largest 50 rivers entering seas 

or oceans; Vorosmarty and others, 2000). By discharge volume, the Columbia River is the largest river 

to enter the northeast Pacific Ocean and conveys 77 percent of the total runoff from western North 

America (Hickey, 1998). The basin drains several physiographic regions, including the middle and 

northern Rocky Mountains, Columbia Plateau, Cascade Range, and Pacific border (Fenneman and 

Johnson, 1946). The basin includes parts of British Columbia, Canada, most of Idaho, large parts of 

Oregon and Washington, and small areas of Montana, Wyoming, Utah, and Nevada. The estuary forms 

the border between Washington and Oregon and traverses the Portland-Vancouver metropolitan area. 

Within the Columbia River estuary, the river crosses the Cascade Mountains and Pacific border 

provinces.

The Columbia River drainage basin is unique among the world’s largest rivers in that it drains 

toward the leading edge of a convergent tectonic margin. This setting is responsible for the relatively 

high basin elevation and mean channel slope. More specifically, this unique environment has a great 

effect on the lower river and estuary, where processes such as volcanism, seismicity, and mass 

movements significantly influence fluvial processes and the geomorphology of the river corridor. As 

discussed in more detail when we describe the Classification, the spatial and temporal scales of 

formative geologic processes and events correlate strongly with the proposed Classification, with 

broader subdivisions chiefly owing to tectonism and volcanism over the last 50 million years (Ma), and 

finer subdivisions primarily affected by processes and landscape history of the last 20,000 years. At the 

finest scales, modern and historical geologic, hydrologic, and ecologic processes exert primary 

influence.

Columbia River Basin hydrology reflects the interaction of topography resulting from the 

regional geologic environment and history, and the regional moist, maritime climate. Most Columbia 

River discharge is the product of Pacific frontal systems moving east with the mid-latitude westerlies, 

with most precipitation falling as winter snowfall in the Rocky Mountains and in the Cascade Range. 

Mean annual river discharge at the mouth is about 6,970 m3

/s) (Naik and Jay, 2005). Approximately 24

percent of this volume originates from west of the Cascade Range crest, despite a contributing area 

totaling only 8 percent of the river basin (Sherwood and others, 1990). Most of this discharge enters by 

the principal tributaries, the Willamette and Cowlitz Rivers, which drain large parts of the PugetWillamette forearc trough. The hydrologic imbalance between east and west of the Cascade Range owes 

to the rainy Maritime climate of the western Cascade Range and Pacific border provinces, where 

average annual runoff is 2.39 m; by contrast, the interior subbasin with its Middle Latitude Steppe 

climate yields only about 0.71 m/yr (U.S. Army Corps of Engineers, North Pacific Division, 1984).
8

Historically, mean monthly discharges at the mouth varied between late fall lows of about 3,500 

m3/s and May–June highs averaging about 15,000 m3/s. Annual peak discharges almost always resulted 

from snowmelt in the interior subbasin and peaked at 35,100 m3

/s (estimated at The Dalles, Oregon;

June 7, 1894). The lower basin typically does not add substantially to historical spring freshets, but has 

been a major contributor to large winter discharges on the Columbia River (Sherwood and others, 1990) 

and occasionally produced large (but typically short-duration) winter peaks on the lower estuary 

associated with regional rain-on-snow floods, such as those in December 1861 and December 1964. 

Both eastern and western subbasins of the Columbia River basin are subject to climate variation 

driven by two cycles originating from the Pacific Ocean: (1) the El Niño-Southern Oscillation (ENSO) 

conditions in the equatorial Pacific that is associated with warm, wet climate in the Pacific Northwest 

every 3–8 years and cold, dryer climate (”La Niña”) in the off-cycle (Ropelewski and Halpert, 1986); 

and (2) Pacific Decadal Oscillation (PDO), which is driven more by climate dynamics in the North 

Pacific Ocean and involves oscillating warm and dry climate eras every 20–30 years that is particularly 

manifest in cycling coastal ocean temperatures and biological productivity (Mantua and others, 1997). 

Both of these climate cycles are associated with hydrological and other climate disturbances that 

contribute to the dynamics of the Columbia River estuary’s landscape.

Contemporary Hydrologic and Geomorphic Processes and Landforms

The geologic history of the Columbia River has produced the background of physical conditions 

and landforms with which historical and modern processes interact to continue to shape the channel and 

flood plain. Inputs, outputs, and transfers of water, sediment, and organic debris are the key attributes of 

the geomorphic system constituting the estuarine corridor of the Columbia River. By understanding how 

these exchanges work in the context of the geologic history, one can better understand how changes to 

geomorphic processes and conditions, either by natural or anthropogenic means, might affect the 

physical character of the lower river. 

Floods and Tides

Flowing water exerts the fundamental force forming and altering most landforms of the estuary. 

As for most estuaries in this region, tidal forcing and basin runoff affect discharge direction, stage, and 

energy (Jay and others, 1990). River conditions, including stage and discharge energy, for the 

lowermost 21–56 km (depending on ambient discharge) are dominated by tidal forcing. In this reach, 

channel and flood-plain characteristics chiefly owe to tidal action. From rkm 21 to rkm 56, the estuary

undergoes a transition characterized by a minimum in “energy flux divergence” associated with salinity 

intrusion (Jay and others, 1990). Up-estuary of the transition, fluvial forcing becomes more influential, 

and the landforms in the uppermost reaches primarily result from flood processes. 

The tidal pattern affecting the estuary is mixed diurnal and semidiurnal, meaning two low and 

two high tides of unequal heights each lunar day (24.8 hours). Tidal amplitude ranges from 1.7 to 3.6 m 

at the ocean entrance, increasing to a maximum of 2.0 to 4.0 m near Astoria at rkm 29 before decreasing 

eastward to less than 0.2 m at Vancouver (rkm 171), but still affecting discharge stage at low river 

discharges as far upstream as Bonneville Dam at rkm 233 (Kukulka and Jay, 2003a). Tidal forcing has 

less effect when river discharge is extremely high; common historical flood discharges (for example, the 

June 1, 1946 discharge of 16,500 m3

/s) are tidally affected as far upstream as rkm 138, whereas the 

largest discharges are not measurably affected by tidal forcing upstream of Longview at rkm 106 (U.S. 

Corps of Engineers, 1968). Tidally forced current reversal penetrates to the Cowlitz River confluence at 

rkm 109 during periods of very low river discharge (Clark and Snyder, 1969), and saltwater intrusion as 

far upstream as rkm 37 (Fox and others, 1984). Tidal currents are strongest at the river entrance to the 
9

Pacific Ocean, where discharge is constricted by jetties and between Clatsop Spit and Cape 

Disappointment, and decrease inland. Within the estuary, Neal (1972) reported surface currents greater 

than 3.3 m/s during ebb tides, and 2.0 m/s during flood tides.

Floods probably bring more kinetic energy to the estuary than any other source, and for most of 

the lower estuary, floods are the primary agent of geomorphic change. For the 1858–1941 period predating significant discharge regulation in the basin, the mean peak Columbia River flood was 17,400

m3/s. Judging from a profile of stages measured during the 1946 flood of 16,500 m3/s (U.S. Army Corps 

of Engineers, 1968), floods of this magnitude have stages ranging from 8.8 to 3.0 m above the low 

water plane, with the greatest values being in the western Columbia River Gorge. The highest 

discharges of June 1894 and June 1948, both resulting from coincident snowmelt peaks from the upper 

Columbia and Snake River basins, had maximum stages as great as 13.4 m above low water (U.S. Army 

Corps of Engineers, 1968). The gradients of the flood profiles relate directly to discharge energy and 

dissipation. For all spring freshet flood profiles for the Columbia River estuary depicted on “U.S. Army 

Engineer District Portland Flood Profiles,” encompassing discharges ranging from 16,500 to 35,100 

m3/s, the steepest water-surface slopes (except for the short reach just down estuary of Bonneville Dam) 

are between Kalama (rkm 120) and Westport (rkm 80) (Hydrogeomorphic Reaches C and D, see 

section, “Results”). Consequently, these reaches have the greatest fluvial energy of the lower estuary. 

Distinctly lower gradients encompass the reaches from Kalama to the western end of the Columbia 

River Gorge, reflecting hydraulic ponding up estuary from the narrowed valley at Kalama. Gradients 

also flatten down estuary of rkm 65, due to the expansion of the estuary.

Discharge conditions lead to three basic geomorphic environments as outlined by Jay and others

(1990): (1) a zone between the river mouth and about rkm 8 (see Hydrogeomorphic Reach A, in section, 

“Results”) in which hydraulic energy is dominated by dissipation of tidal currents; (2) the reaches 

upstream of rkm 56 (see Hydrogeomorphic Reaches C-G, in section, “Results”) where fluvial energy 

dominates and little tidal energy persists; and (3) the intervening “energy flux divergence minimum” 

reach (the upstream part of Hydrogeomorphic Reach A and all of Reach B, in section, “Results”) 

between the fluvial and tidal reaches where fluvial energy and tidal energy dissipation are both small

(fig. 1). This categorization neatly organizes many of the geomorphic properties, discharge, and 

sediment movement in the lower estuary.

Sediment Movement and Transfers

Nearly all natural landforms within the flood-plain boundaries of the estuary are formed of 

clastic materials transported and deposited by the river. Most of this sediment is sand, silt, and clay. 

Most of the sediment along the lower river corridor comes from upstream or from tributaries entering 

the lower river; very little sediment enters the lower river from the ocean or by eolian transport from 

coastal beaches (Sherwood and Creager, 1990). From consideration of deposit volumes along the lower 

river, Gelfenbaum and others (1999) estimated that the long-term (about 10,000 years) sediment supply 

to the estuary has been about 20×106 m3

/yr), with about 75 percent of this sediment load exiting river 

for the Pacific Ocean. The balance of about 5×106 m3/yr has filled the estuary valley as it has aggraded 

in conjunction with Holocene sea-level rise. From measurements and hindcasting, Gelfenbaum and 

others (1999) estimated that the historical (1879–1934) rate of sediment inflow was much lower, with 

only about 8.7×106 m3

/yr entering the estuary. Compared to other large U.S. rivers, the modern sediment 

load of the Columbia River is low—about one-tenth that of the Colorado River, and about 40 percent of 

the Mississippi River on a load per unit drainage area basis (Ritter, 1967). Similarly, very few world 

rivers have sediment loads as low as the Columbia River (Sundborg, 1983, as cited in Cooke and 

Doornkamp, 1990). Annual fluxes probably vary tremendously in conjunction with discharge. Hindcast 
10

estimates of annual transport rates range from more than 35×106 m3/yr for the 1894 big-discharge year 

to less than 2×106 m3/yr for some of the low-discharge years of the last 3 decades, when discharge peaks 

have been significantly regulated and sediments have accumulated behind dams (Gelfenbaum and 

others, 1999).

The sources of sediment to the estuary are distinctly segregated by area and size (Whetten and 

others, 1969). Areas upstream of the Cascade Range chiefly provide fine-grained (fine sand and finer) 

non-volcanic sediment whereas tributaries from the Cascade Range provide coarser sediment (chiefly 

sand) of andesitic volcanic origin (Whetten and others, 1969). Measurements by Hauschild and others

(1966) indicate that the Snake River supplies substantially more sediment than the Columbia River at 

their confluence. The lower tributaries, in addition to providing most of the coarse component of the 

sediment load are also likely to provide a significant fraction of the total sediment load. Calculations 

summarized by Sherwood and others (1990) suggest that the Willamette River may contribute 

approximately 10 percent of the annual sediment load to the lower river.

Fluvial sediment transport is by two primary mechanisms—suspended and bedload. In the 

Columbia River and estuary, the suspended load consists primarily of the fine sand and finer materials 

supplied by the upper river basin (Whetten and others, 1969), but also at times including fine-grained 

material generated by Cascade Range volcanic eruptions (Hubbell and others, 1983). The coarser 

sediment—chiefly sand—moving on the bed is primarily volcanic rock fragments, presumably derived 

from the Cascade Range (Hauschild and others, 1966; Whetten and others, 1969). Suspended-load 

transport rates depend primarily on the volume of fine sediment introduced to the river system, which is 

primarily a function of watershed sediment supply processes. Bedload transport in the estuary is judged 

to be capacity-limited and is primarily a function of discharge strength, because much of the lower river 

channel is sand covered (Sherwood and others, 1990). Whetten and others (1969) estimated that bedload 

transport constitutes about 10 percent of the total sediment load, although few measurements support

this conclusion. During high discharges, bed material can be entrained into suspension, leading to 

substantial sand transport in suspension (Hauschild and others, 1966). Suspended load constitutes the 

bulk of the sediment load of the estuary. Although about 75 percent of the suspended load is transported 

to the ocean (Gelfenbaum and others, 1999), the balance is deposited in aqueous and tidal environments 

such as peripheral bays and side channels (Sherwood and others, 1990), as well as on terrestrial surfaces 

such as flood plains and mid-channel islands subject to overbank flooding and deposition. 

A large proportion of the bedload movement along the lower estuary is likely by migrating 

bedforms. Large sand waves and other channel bedforms along the estuary have been described by 

Hickson and Rodolf (1951), Jordan (1962), Hauschild and others (1966), Whetten and others (1969) and 

Sherwood and Creager (1990). Whetten and others (1969) mapped the lower river, noting that 45

percent of the channel between Bonneville Dam and the Willamette River confluence was covered in 

sand waves, with abundance increasing to 80 percent for the segment between the Willamette and 

Cowlitz River confluences, and 86 percent for the segment between the Cowlitz River and the ocean. 

Hauschild and others (1966) reported dunes in the Columbia River channel averaging 1.5 m high, and 

30–90 m in length; dimensions slightly smaller than those described by Jordan (1962) near Longview, 

which had amplitudes averaging about 2 m, lengths of about 500 m, and average spacing of about 100 

m. Smaller bedforms, primarily current ripples, are commonly superimposed on these large sand waves. 

Hauschild and others (1966) reported that the dunes in deeper parts of the channel evolved from long 

and low to short and high as discharge increased. Dune migration rate near Vancouver ranged from less 

than 1 m/d during low discharge periods, to as great as 60 m/d during high discharges (Hauschild and 

others, 1966). Bedform morphology in most of the lower Columbia River estuary indicates downstream 
11

transport, but reversing currents result in bidirectional bedform movement as far upstream as about rkm

25 (Sherwood and Creager, 1990). 

Summarizing sediment and sediment transport conditions from several lines of reasoning and 

observation, Sherwood and Creager (1990) conclude:

1. “Virtually all of the sediment in the estuary is derived from the Columbia River.”

2. “The lower estuary (see Hydrogeomorphic Reaches A and B, in Results) displays the most 

sediment-size variation because of the wide gradient of transport processes [fluvial to tidal] and 

depositional environments in the region.”

3. “The absence of coarse sand in the entrance and lower estuary, and the general fining-seaward 

trend exhibited in sediment size, suggest that the coarsest fraction of the fluvial sediment is not being 

transported through the estuary.” This observation, coupled with the Jay and others (1990) description 

of system energetics, leads to the strong probability that the region of the energy flux divergence 

minimum between rkm 21 and 56 is where most of medium and coarse sands is retained. Peterson and 

others (2003) refer to this region of active deposition in the Cathlamet Bay area as a “bay-head delta.”

In addition, Whetten and others (1969) came to the conclusion, also supported by the analyses of 

Hauschild and others (1966), that the majority of suspended load to the Columbia River basin is derived 

from the upper basin, and most bedload to the Columbia River is derived from the Cascade Range, and 

that these two sediment populations remain distinct as they move through the lower river. 

Design of Columbia River Estuary Ecosystem Classification

To develop a classification that captures the multiple and hierarchical scales of processes that 

influence estuarine ecosystems, we integrated information on riverine, oceanic, climatic and watershed 

factors that influence estuarine processes with information on geomorphic and biological features that 

vary across the estuarine gradient into a hierarchical framework classification. Similar to the 

“controlling factor” approach used in the Estuary Environment Classification (EEC) by Hume and 

others (2007), the Columbia River Estuarine Ecosystem Classification is based on systems hierarchy 

concepts (for example, O’Neill and others, 1986) and uses comparable proxies for regional, watershed, 

and estuarine ecosystem processes. This Classification extends into the tidal freshwater reaches of 

estuaries, thus addressing the EEC’s limited applicability to large rivers and flood plain estuaries and 

classification of individual estuarine components (Hume and others, 2007).

Based on the structure of other classification schemes developed for estuarine ecosystems 

described earlier, and common concepts of ecosystem geography (for example, Bailey, 1996), we 

developed an ecosystem classification for the Columbia River estuary that is organized in six 

hierarchical levels:

Ecosystem Province

Ecoregion

Hydrogeomorphic Reach

Ecosystem Complex

Geomorphic Catena

Primary Cover Class
12

The Classification is designed to aggregate land and aquatic cover classes (including culturally

modified land cover/land use classes and modifiers) according to the conceptualized ecosystem 

processes that structure landscape attributes, including biotic habitats at multiple spatial scales. The 

Classification methodology is based on digital geographic information systems (GIS), whenever 

possible using automated processes with minimal manual classification that facilitates an objective, 

repeatable, hydrogeomorphic class system. We use either scientifically based classification schemes that 

already exist for the area or develop rational rules adaptable to GIS-based analyses. Many data sources 

are readily available as GIS map layers. As these layers are updated and improved, they can be 

incorporated into revisions of the Classification methodology. In initially developing the Ecosystem 

Complex and Geomorphic Catena levels of the Classification, we have interpreted both digital and nondigital data (for example, cartographic geology) in order to delineate complexes and catenae.

Methods

Data Criteria and Requirements

We adopted the following primary and secondary selection criteria for the design of the 

classification and for selection of the data upon which it would be based.

Primary Criteria for Classification Design

Datasets used to develop the Classification primarily will be contemporary, 

comprehensive, complete, and widely available.

Landscape features must be mappable at appropriate scale to delineate important 

ecosystem components (cover types and shapes).

Because the influence of geology, physiography, and climate on hydrogeomorphic 

process regimes accounts for much of the variation in ecological attributes we 

observe through the estuary (particularly the tidal freshwater regions), we use 

indicators of hydrogeomorphic processes to delineate the classification level (Level 

3, Hydrogeomorphic Reaches) above those incorporating ecological features.

The Classification will capture scale of ecosystem dynamics (for example, development 

stage of ecosystems) that are anticipated to indicate ecological change over likely 

monitoring scales.

Finer scale levels of the Classification should capture ecosystem features that are 

indicative of habitat required by biota of concern (for example, species at risk, 

species listed as threatened or endangered).

The Classification should incorporate features of relevance to landscape and disturbance 

ecology of large tidal flood plain estuaries.

Secondary

Design should be enable delineation of some Classification levels using both historic 

spatial datasets and future spatial datasets.

Application of the Classification to historic and future spatial datasets will facilitate 

ecosystem change analyses for multiple points in time.
13

GIS Structure

All GIS data in the Classification methodology are readily available from State and Federal 

government agencies (table 1). Although the classification relies primarily on contemporary data 

sources, we utilize historical data to support ecosystem change analyses for areas where both historical 

and contemporary datasets are available.

For the preliminary mapping at the finer levels of the Classification, GIS processing utilized 

ESRI ArcGIS 9.3 ArcInfo with the Spatial Analyst extension. All data layers were imported to a 

geodatabase and projected to the State of Oregon standard (Lambert Conformal Conic, NAD 1983 

datum, meter map units) for processing consistency. Full implementation and reporting of the 

classification system and mapping will follow USGS standards for GIS products and associated 

metadata. 

Base Data and Analytical Steps

Historical Flood Plain and Tidal Extent

The spatial extent of the Classification is defined by our interpretation of the boundaries of the 

Holocene flood plains and extent of tidal influence (“head of tide”) in the estuary and tributaries. The 

limits of tidal influence up the Columbia River and for tributaries were determined using regional tidal 

elevation data (U.S. Army Corps of Engineers, 1968; Kukulka and Jay, 2003a) in combination with 10-

m digital elevation models (DEMs). The limits of the flood plain were derived from our interpretation of 

the extent of Holocene flood plain deposits (based on high-resolution LiDAR topography existing 

geologic maps) in conjunction with documented historical flood elevations (U.S. Army Corps of 

Engineers, 1968). 

Level-Specific Data Sources

The Classification has six levels; at the broadest scale, Levels 1 and 2 are derived from existing 

national scale ecologic classification systems and datasets and require only brief descriptions. The finer 

levels of Levels 3 through Level 6 are the aspects new to the proposed Classification and their source 

data and development are more fully described.

Levels 1 and 2— Ecosystem Province and Ecoregion 

We selected the EPA-adopted Ecoregion Levels II and III to provide regional context at the 

highest levels of the hierarchy (Classification Levels 1, 2, and partially 3). These ecoregion delineations 

reflect the regional variability of watersheds, which plays a strong peripheral (if not cumulative) effect 

on the structure of estuarine ecosystems such as the Columbia. For example, vegetation compositions 

differ dramatically in the different physiographic provinces defined by Ecoregion Levels II and III 

(Sowa and others, 2007). 

As initially developed by Bailey (1983, 1987, 1995), Bailey and others (1994), Omernik (1987, 

1995), and Omernik and Bailey (1997), the ecoregion concept provides a broad-scale framework in 

which ecological regions are distinguished by patterns and the composition of abiotic and biotic 

phenomena, such as climate, geology, physiography, hydrology, vegetation, soils, land use, and wildlife. 

Although there may be similarities among some of these characteristics, the relative importance of each, 

and the interrelationship among them, varies across regions. To encompass the coarsest scales of 

influence on the estuary, we adopted without modification the EPA Ecoregion Level II (Ecosystem 

Province) as Classification Level 1, and EPA Ecoregion Level III (Ecoregion) as Classification Level 2. 
14

The EPA Ecoregion II maps were derived through analysis of satellite imagery and appropriate 

natural resource source maps at small scales (approximately 1:40 million – 1:50 million) while 

Ecoregion III maps used similar resources to nest large ecological areas within Ecoregion Level II areas 

at a finer scale (approximately 1:20 million – 1:30 million) (Omernik, 1987, 1995; Omernik and Bailey, 

1997).

The biophysical framework of the Columbia River basin and the estuary in particular 

represented by these two levels of the Classification has been established by tectonic, volcanic, 

climatologic, and biologic processes operating over the last 50 Ma. Key elements include formation and 

uplift of the Coast and Cascade Ranges, uplift of the Rocky Mountains, and development and growth of 

the Columbia River basin. This broad context is helpful for understanding the overall physiography of 

the lower Columbia River (including hydrological, geological, and ecological factors associated with 

tributaries), but it encompasses temporal and spatial scales typically too coarse to provide a meaningful 

framework for management, restoration, and monitoring. 

Level 3—Hydrogeomorphic Reach

This level in the hierarchy diverges from the EPA ecoregion scheme, as well as other estuarine 

classifications, in order to incorporate indicators of ecosystem structure and process that encompass and 

assimilate tidal and freshwater controlling factors. To integrate watershed and tributary contributions 

and other influences with flood-plain processes and tidal-fluvial interactions along the estuarine 

gradient, and to recognize the importance of river network structure in classification hierarchy (Frissell 

and others, 1986; Rice and others, 2008), we adjusted the boundaries of EPA Level IV Ecoregions by 

incorporating tributary confluences, flood plain and other physiographic features and fluvial-tidal 

hydrologic and other discontinuities to delineate “hydrogeomorphic reaches” or Classification Level 3. 

Five primary factors were used to determine locations of hydrogeomorphic reach boundaries 

progressively (up-estuary) along the estuarine gradient:

1. Maximum (historic) salinity intrusion: Oligohaline and brackish salinities drive distributions of 

aquatic biota, and are regions of important geochemical transitions through processes such as 

flocculation; we positioned the up-estuary extent of historical salinity (0–0.5 practical salinity 

units [psu]) based on Sherwood and others (1990);

2. Up-estuary excursion of estuarine turbidity maximum (ETM): Although associated with the 

incursion of salinity, the ETM is a lower estuary feature where dynamic sedimentation, 

geochemical and biological processes (particularly food web interactions between bacteria and 

zooplankton) are primarily concentrated in the mainstem channel but may interact with 

peripheral bay environments (Jay and others 1990; Baross and others, 1994; Jay and Musiak, 

1994; Prahl and Coble, 1994; Reed and Donovan, 1994; Simenstad and others, 1994a, b; Small 

and Morgan, 1994; Crump and Baross, 1996; Morgan and others, 1997; Prahl and others, 1997; 

Crump and others, 1999; Fain and others, 2001). We used information from Simenstad and 

others (1994a&b; and unpublished data) to approximate the mean position of the ETM;

3. Up-estuary extent of current reversal: Much of the initial deposition of sediment, detritus and 

associated constituents that occurs in the mainstem estuary is associated with slack tide periods 

when particles have time to settle. Because this feature shifts daily and seasonally with discharge 

and tide levels, we adopted the mean position of the up-estuary extent of tidal reversal from 

predicted currents along the estuary using Tides & Currents Ver. 2.5, Nautical Software, Inc.; 
15

4. Convergences with major tributaries and slough systems. These features are important sources of 

dissolved and suspended materials (for example, suspended sediment, large wood, and detrital 

matter from upstream watersheds); anecdotal evidence suggest that tributaries and sloughs 

support high densities of fish and wildlife and are important staging areas for anadromous 

juvenile and adult salmon and smelt. However, potentially toxic water-soluble contaminants may 

be found in higher concentrations around confluences, for example, Columbia River confluences

with the Willamette River and Multnomah Channel (Fuhrer and others, 1996); and,

5. Transitions in maximum flood (pre-regulation) tide level: Maximum water elevation and the 

frequency and duration of flood events are major factors determining wetland community 

structure, particularly in the flooding disturbance regime in a tidal flood (surge) plain; we used 

flood profiles available for the length of the estuary to interpret major inflections in flood 

elevations due in part to marked changes in the elevation of the river bed and other channel 

morphology changes that affect conveyance (U.S. Army Corps of Engineers, 1968; Kukulka and 

Jay, 2003a, 2003b).

The level of the Hydrogeomorphic Reach in the Classification represents the intersection of 

broad-scale geologic processes and events over the last 50 Ma with more modern or recent geologic and

hydrologic processes of the Holocene. The overall physiography of the reaches relates primarily to the 

broad-scale geologic environment, including the Cascade and Coast Ranges, and the Portland Basin, 

whereas many of the defining criteria such as current and tide conditions reflect modern and recent 

geological conditions and processes. 

The Hydrogeomorphic Reach level is the coarsest level of the Classification that encompasses 

the entire flood plain, albeit for lengths of Columbia River (and major tributaries) of similar overall 

character as defined by the above criteria. Within the Columbia River estuary, overall flood-plain 

morphology is dominated by Holocene aggradation since the sea-level low about 15,000 years ago. This 

aggradation typically has resulted in the flood plain abutting older bedrock units, but in places the flood 

plain is flanked by Quaternary alluvium deposited by the ancestral Columbia River, deposits of large 

ice-age floods, and volcanogenic deposits from eruptions of nearby Mount Hood and Mount St. Helens 

(Evarts and others, 2009).

Level 4—Ecosystem Complex

Unlike the higher levels in the Classification, ecosystem complexes are biophysical patches 

formed by long-standing geologic and hydrologic processes that establish long-term geomorphic 

templates in the estuary and its flood plain in addition to continuous and more recent hydrologic and 

geomorphic processes that result in changing landscape mosaics of landform and vegetation patches. 

For the most part, the Ecosystem Complex category reflects geomorphic process regimes and episodic 

geologic events of the Holocene (last 10,000 years), resulting in landforms such as terraces, dune fields, 

flood plains, volcanogenic deltas, and channels. Thus, Ecosystem Complexes are influenced by the 

overlapping effects of massive Holocene disturbances (such as landslide and volcanic sediment pulses, 

large floods, storm surges, or tectonic movements), shorter-term biophysical processes (such as erosion 

and sedimentation associated with localized flooding, vegetation succession, local extinction and 

recruitment events), and anthropogenic modifications of the landscape (such as diking and filling, 

channel hardening, and urban and suburban development on the flood plain).
16

Numerous data sources (table 1) and GIS processes are used to derive Classification Level 4—

Ecosystem Complex level of the Classification. Each hydrogeomorphic reach is evaluated and 

processed individually for complexes, building on basic GIS rules but with modifications commensurate 

with changes in geomorphic and ecosystem structure by hydrogeomorphic reach. The foundation of the 

Ecosystem Complex level was the delineation of major aquatic features of the estuary based on

bathymetry, while the flood plain and other episodically and partly inundated features were based on 

interpretation of topographic, geologic and geomorphic features.

Complete mapping the Ecosystem Complexes across all reaches awaits full implementation of 

the Classification1

, but for purposes of describing the Classification, we show proposed ecosystem 

complexes for Hydrogeomorphic Reach F. This reach extends along the Columbia River’s flood plain 

from (and including) the confluence of the Willamette River to the confluence of the Lewis River (fig.

1). 

Ecosystem Complexes (table 2) within the aquatic domain (areas continuously submerged or 

typically submerged during the tidal cycle) were mapped by rule sets applied to bathymetric data: (1) 

Deep water channels were delineated where depths were greater than the fourth quartile of the entire 

bathymetry dataset (>8 m relative to North American Vertical Datum of 1988); and (2) Distributary 

channels were delineated where depths were greater than 1 m and less than 8 m.

Flood-plain Ecosystem Complexes required more interpretative mapping to distinguish 

landforms coinciding with various hydrologic and geomorphic process regimes (table 2). This mapping 

primarily was accomplished on the basis of topographic characteristics supported by existing geologic 

and soils mapping.

The Ecosystem Complexes (as well as features mapped at finer levels of the Classification) 

mapped for Hydrogeomorphic Reach F will not encompass all types of Ecosystem Complexes for the 

Columbia River estuary. We anticipate that most Hydrogeomorphic Reaches will have Ecosystem 

Complexes (as well as features at finer Classification levels) unique to that reach and that the total 

number of types of Ecosystem Complexes will be much larger for the Columbia River estuary. 

Similarly, application of the Classification for different fluvial estuary systems will certainly produce a 

different set of Ecosystem Complexes. 

Level 5—Geomorphic Catena

Geomorphic catenae form the mosaic of physical and biological features nested within 

ecosystem complexes. Because both natural ecosystem processes and the intrinsic characteristics of 

catena vary and change over space and time, catenae occur in a 3-dimensional shifting mosaic of 

ecosystems along the river-ocean continuum (Stanford and others, 2005). In the Stanford and others 

(2005) typology, the Classification’s ecosystem complexes tend to persist but can be constrained or 

eliminated by human alteration while the geomorphic catenae form the shifting mosaic that, “...changes 

spatially over time due to primary drivers, particularly flooding, channel avulsion, cut and fill 

alluviation (erosion and deposition of fine and coarse sediments), deposition of wood [, and] recruitment 

and regeneration of riparian vegetation.” For the Columbia River estuary, Geomorphic Catenae consist 

chiefly of individual landforms created during the last 2,000 years since rate of sea-level rise diminished 

markedly (table 3). Examples of such landforms include individual bars, levees, islands and ponds. The 

 1 Collection of high-resolution bathymetry data was completed in 2010, and classified land-cover data will be available in mid2011, under the auspices of the Lower Columbia River Estuary Partnership (LCREP) and is being incorporated into 

delineation of the Ecosystem Complexes for all estuary reaches.
17

dynamics of these processes result in more temporal variation of landscape patches categorized at this 

level of the classification. At the Geomorphic Catena level, the Classification provides potential coastal 

flood plain and estuary classes that would extend the typologies proposed by Stanford (1998), Ward and 

others (2002), and Stanford and others (2005) to the sea.

Geomorphic catenae are classified and delineated in two steps: (1) within ecosystem complexes, 

multiple mapping criteria and sources are used to distinguish water body and flood-plain features 

occurring within each complex; and (2) Level 6—Primary Cover Class data are applied in conjunction 

with other geospatial data (for example, LiDAR) to delineate discrete biological communities associated 

with the geologic/geomorphic units delineated in step (1). In addition to bathymetry, the primary data 

sources for the first step included: (1) aerial photography; (2) topographic maps; (3) soils maps; and (4) 

geology maps; the primary sources for the second step included the LiDAR, bathymetry and LANDSAT 

land-cover data (table 1).

Level 6—Primary Cover Class

The Primary Cover Class Structure is the finest level of the hierarchical scheme. It includes the 

elements that compose spatial coverage of classes in the Classification Level 5—Geomorphic Catena. 

Although land cover is the highest resolution level of the Classification, we do not use it as the ultimate 

dependent variable in the hierarchy. Although land cover of natural ecosystems implies some level of 

equilibrium adjustment of vegetation communities to abiotic variables at a landscape scale, land cover 

of highly altered ecosystems is more static and provides less insight into the relationship between 

abiotic variables and vegetation (or absence thereof). For this reason, we used land cover selectively for 

two purposes: (1) to modify the least altered (“reference”) conditions of abiotic catenae (table 3) to 

relate ecosystem responses and states to geologic and other physicochemical processes; and (2) identify 

cultural modifications that can inform restoration and management decisions for ecosystem 

rehabilitation and recovery. We are utilizing the most recently completed 2010 Lower Columbia River 

Estuary (LCRE) Land Cover Classification that was derived using a high resolution image segmentation 

and object based classification process that integrated data from: (1) 2009 4 band, 1 m resolution 

airborne imagery acquired by the USDA National Agriculture Inventory Program (NAIP); (2) archived 

30 m LANDSAT TM5 imagery from various dates ranging from 2007 to 2009; and (3) 2009–10 LiDAR 

elevation data acquired by the U.S. Army Corps of Engineers (table 1). This classification was

supported by extensive training data in some regions of the system. However, work is underway in the 

study area to provide an updated (for example, 2009–10) land-cover dataset to facilitate finer resolution 

catenae delineation for the completion of the Classification. In addition to cultural features (such as

dikes, roads, fill, and other infrastructure) identified in the delineation of the geomorphic catenae, any 

artificial or otherwise modified Primary Cover Class (such as agricultural fields, park and other lawns) 

is additionally distinguished by a modifier. In the pilot example, 24 Primary Cover Classes are 

represented for Reach F.
18

Results

Each level of the Classification encompasses different scales of influence on ecosystem 

structure, where the highest levels in the scheme describe regional-scale structure and the lowest levels 

compose the finer scale components of the strata in the hierarchy levels. For example, each of the 

Geomorphic Catena in Level 5 is composed of sets of the Primary Cover Classes in Level 6. These sets 

or aggregations of cover classes are not necessarily unique other than their association with larger scale 

features (described below under Level 6—Primary Cover Class). Similarly, each Hydrogeomorphic 

Reach in Level 3 is composed of various compositions and arrangements of Ecosystem Complexes, 

which are expected to vary among the different reaches. Table 4 provides a framework for the 

classification hierarchy in relation to geology, time, and human disturbance.

We describe Levels 1 through 3 of the Classification for the entire estuary. Levels 4-5 are not 

complete because of incomplete bathymetry and land-cover data (Level 6) over the entire study area. As 

a demonstration, we present one hydrogeomorphic reach (Reach F) as an example of the potential 

delineations of features at the ecosystem complex and geomorphic catena scales. 

Level 1—Ecosystem Province

As described in section, “Setting of the Columbia River Basin and Estuary,” the Basin is 

distinctly divided by the Cascade Mountain Range into the warmer and wetter Marine West Coast 

Forest Province to the west and the drier Western Cordillera and Cold Deserts provinces to the east—

east of the Range (fig. 2). Although the Marine West Coast Forest Province makes up only 8 percent of 

the Basin area, this Province contributes 24 percent of the fluvial forcing that differs in timing, 

magnitude, and constituents (for example, sediment, organic matter) relative to freshwater discharge 

from the large eastern region of the Basin [see Whetten and others (1969); Sherwood and others (1990); 

and Prahl and others (1998) for more detail about the various contributions from these different 

provinces to the estuary.]

Level 2—Ecoregion

Moving from the Columbia River estuary’s mouth upstream to Bonneville Dam, the Coast 

Range Ecoregion extends more than100 km from the Pacific Ocean to Willamette River (fig. 3A). On 

the Washington side of the Columbia River, the Puget Lowland Ecoregion includes the Cowlitz River 

valley and influences about a 10 km length of the estuary at that river’s confluence with the Columbia 

River near Longview, Washington. Along both the Oregon and Washington sides of the Columbia

River, the Willamette Valley Ecoregion surrounds the broad flood-plain region of the lower Willamette 

River and its confluence with the Columbia River. Lastly, the Cascades Ecoregion extends from the 

beginning of the estuarine flood plain to the Columbia River Gorge and Bonneville Dam. 

Level 3—Hydrogeomorphic Reach

The EPA’s eight Level IV Ecoregions (fig. 3B) are the foundation of the Classification’s Level 

3-Hydrogeomorphic Reaches and relate to estuarine ecosystems primarily by the character and 

magnitude of fluxes of water, sediment, nutrient, contaminant, and other constituents delivered by 

tributaries draining different ecoregions. The EPA’s Coast Range Ecoregion includes four more detailed 

ecoregions (the Coastal Lowlands, Coastal Uplands, Willapa Hills, and Volcanics). The larger Puget 

Lowland Ecoregion is distinct and does not include more detailed Ecoregions at the EPA’s Level IV. 

Level III Willamette Valley Ecoregion is divided into two smaller Ecoregions, the Portland/Vancouver 
19

Basin and Valley Foothills. At the western end of the Gorge, the Level III, Cascades Ecoregion includes 

the West Cascades Lowlands and Valleys Ecoregion and a tongue of the Valley Foothills Ecoregion.

Revising the EPA Level IV ecoregions based on additional hydrological and physiographic 

criteria (see Level 3—Hydrogeomorphic Reach in section, “Methods”), we delineated the following 

eight reaches (fig. 4; appendix A). For each of these Hydrogeomorphic Reaches, tentative flood-plain 

boundaries (as shown in figs. 1 and 4) were determined by a simple elevation criterion of 18 m above 

North American Vertical Datum of 1988. These floodplain boundaries will be refined, as they have been 

for Reach F (fig. 5), on the basis of mapping at Levels 4 (Ecosystem Complex) and 5 (Geomorphic 

Catana). For each reach, we summarize the dominant channel features, major geologic events, sediment 

inputs, and tidal influence.

1. Coastal Lowlands Entrance-Mixing (rkm 0–23 )—Level IV Coastal Lowlands, encompassing 

euhaline salinities and the region of most extensive mixing of estuarine and ocean waters around the 

estuary’s entrance and surrounding bays and tributary entrances. Broad mud and sand flats are 

particularly prominent features in the peripheral bays. This reach may have some of the most 

dynamic environmental conditions in terms of timing, frequency, and duration of disturbances. On 

regular and predictable tidal scales, factors like water salinity, velocity, and turbidity are affected by 

turbulent mixing of fluvial and oceanic waters across the estuary’s entrance. More stochastic 

disturbance events also are accentuated at the fluvial-tidal interface, where high perigean tides, 

storm surges and fluvial flooding can produce extreme coastal flooding events that occur 

approximately once per decade (Pacific County Historical Society and Museum , 2000) despite the 

extensive flood control capacity of the Columbia River Basin hydrosystem. This region also 

experiences extreme coastal disturbances associated with periodic subduction zone earthquakes 

including tsunami and episodes of coseismic subsidence (2–3 m) following by tectonic uplift

(Atwater and Hemphill-Haley, 1997). In addition to the massive subduction zone earthquake last 

experienced on January 26, 1700, more than 20 significant earthquakes and 12 tsunami have been 

reported in the vicinity of Astoria and Willapa Bay since 1840 (Pacific County Historical Society 

and Museum , 2000). As a result of coastal tectonics, this hydrogeomorphic reach continues to 

experience coastal uplift, resulting in an average sea level fall of 0.7 to 1.7 mm/yr (Burgette and 

others, 2009), partly offset by episodic subsidence during subduction zone earthquakes. 

2. Coastal Uplands Salinity Gradient (rkm 23–61)—Level IV Coastal Uplands and Willapa Hills 

ecoregions combined, including the strongest salinity gradient from mesohaline to oligohaline at the 

up-estuary extent of salinity intrusion (about rkm 45). Through this reach, the estuary converges 

from open and peripheral bays and bay head delta into a confined fluvial valley. Perhaps the most 

unique feature of this reach is the broad, complex mosaic of mid-channel islands, shoals and 

distributary and tidal channels. Sea level fall continues in this reach, producing emergence of up to 

1.2 mm/yr east of rkm 52 (Burgette and others, 2009). The combination of sea level fall and 

sediment accretion had produced 1–6 mm/yr of shoaling that is particularly evident in the “bay-head 

delta” of this reach (Sherwood and others, 1990; Peterson and others, 1999). As a result, 

successional development of sand and mud flats to emergent marshes, and emergent marshes to 

woody scrub-shrub and forested tidal wetlands appears to have occurred on islands in the reach (for 

example, Russian Island; Elliot 2004); conversely, very little erosion and disturbance is evident over 

the same period.
20

3. Volcanics Current Reversal (rkm 61–103)—although dominantly a fluvial environment, Level IV 

Volcanics Ecoregion encompasses most of the up-estuary extent of current reversal (to rkm 85 

during low discharge): Reach C extends through a confined valley that bisects the eastern Coast 

Range but still contains large, swampy mid-channel islands, distributary channels and sloughs, and 

flood plains. Tidal influence diminishes extensively throughout the reach, such that the seasonal 

river discharge range at the eastern end of the reach is about 4.4 m but the maximum tidal influence 

is only 0.34 m. The primary natural disturbance regimes include energetic floods, downstream 

sediment deposition from episodic inputs from Mount St. Helens, and coastal subsidence from the 

massive subduction zone earthquakes up to about 80 rkm.

4. Western Cascades Tributary Confluences (rkm 103–119)—most of the Level IV Puget Lowland 

Ecoregion, including the confined valley along the mainstem river and the broad bottomlands at the 

confluences of the Cowlitz and Kalama Rivers. Back channels and tidal channels dissect the flood 

plains. The river current seldom reverses within this reach although there is still about 0.2 m range 

of tidal influence. This reach receives episodic sediment inputs from the watershed and tributaries 

up-estuary as well as volumetrically prominent pulses of volcanogenic sediments from Mount St. 

Helens eruptions that enter the estuary as sediment or lahars through the Cowlitz River and Kalama 

River valleys. In the last several centuries, Mount St. Helens has erupted multiple times producing 

large amounts of sediment from 1480 to 1482 and in 1980 when it released about 100×106 m3 of 

sediment that entered the estuary by 1987 (Gates, 1994). Additionally, in this reach, un-diked 

islands and flood plains have actively accreting and eroding margins (Atwater, 1994), resulting in 

local bar-and-swale morphology on islands and flood plains (for example, Cottonwood Island; 

Carrolls Channel).

5. Tidal Flood Plain Basin Constriction (rkm 119–137)—up-estuary segment of Level IV Puget 

Lowland Ecoregion and lower segment of the Level IV Portland/Vancouver Basin, divided at the 

major constriction in the estuary’s flood plain near the community of St. Helens and including the 

confluence of the estuary with the Lewis River: Other than the bottomlands formed at the 

confluences of the Lewis and Kalama Rivers, Reach E is narrowly confined by Tertiary bedrock 

valley sides and Pleistocene terrace and volcanic deposits. Both the Kalama and Lewis Rivers have 

conveyed volcaniclastic debris to the Columbia River from eruptions of Mount St. Helens, including 

large volume inputs about 2500 and 500 BP (Vogel, 2005). Tidal fluctuation has small influence

(about 0.8 m range at Kalama), especially during peak flood stages of 7–9 m. Most of the flood plain 

islands, Columbia River flood plains and Lewis and Kalama Rivers deltas are thinly capped by fine 

sediments deposited from overbank flooding. Flood discharges have produced prominent channel 

migration bar-and-swale morphology on the islands and flood plains. The results of these processes 

are evident at Deer Island, where lateral bars and natural levees have formed from river migration

during the late Holocene, leaving lower, swampy areas in the flood plain formed to the west.
21

6. Middle Tidal Flood Plain Basin (rkm 137–165)—portion of the Columbia and Willamette Rivers 

(including Multnomah Channel) flood plains in the Level IV Portland/Vancouver Basin downestuary of the major confluence of the estuary with the Willamette River: This is the widest flood 

plain reach of the upper estuary where the wide alluvial valley (including Sauvie Island) is bounded 

by the Portland Hills uplift to the west and the Cascade volcanic arc to the east. The flood plain is 

composed of wetlands and many seasonal ponds within bar-and-swale deposits and scoured bedrock 

areas, as well as terraces and rocky outcroppings. Many of the wetland complexes are separated 

from the mainstem Columbia River channel by the slightly higher flood plain bar-and-swale 

deposits generated by lateral channel migration. The flood plain is circumscribed by distributary 

channels, most notably Multnomah Channel; many circuitous sloughs and tidal channels connect 

swale wetlands embedded in the bar-and-swale topography. Dikes, levees, road grades and drainage 

ditches have locally altered the hydrology and inundation characteristics of this reach. Tributary 

sediment delivery has not kept pace with the high rates of the Columbia River aggradation from 

downstream sedimentation, resulting in drowned tributary valleys, such as Scappoose Bay, that are 

integrated into the flood plain mosaic. Positioned downstream of the confluence of the Willamette 

and Columbia Rivers, this reach has been particularly vulnerable to flooding from combined 

Columbia River Basin freshets and coastal storms prior to completion of the substantial flood 

control capacity in the Willamette River basin during the mid- to late-20th century. Flooding from 

the “pineapple express” coastal storms (Colle and Mass, 2000) can influence this reach, including 

five floods of 3 m above Willamette River flood stage since 1876, with the most recent in 1996. 

This reach has little tidal influence, particularly during high river discharge.

7. Upper Tidal Flood Plain Basin (rkm 165–204)—portion of the Level IV Portland/Vancouver Basin 

from just upstream of the Willamette-Columbia Rivers confluence up-estuary to the western 

entrance to the Columbia River Gorge. Reach G is the up-estuary continuation of the wide alluvial 

valley centered around Holocene flood plain bounded by Pleistocene fluvial deposits and isolated 

Quaternary volcanic centers on the north and south. The Sandy and Washougal Rivers confluences 

in the eastern end of the reach are associated with narrow deltas and flood-plain wetlands. Sediment 

inputs from Mount St. Helens are primarily multiple limited-depth episodes of air-fall tephra 

deposition. Mount Hood, however, has been a large source of volcanogenic sediment, mainly by 

way of the Sandy River which joins the Columbia River at the upstream end of this reach. Mount 

Hood has erupted during two major periods since the 16th century, most recently from 1879 to about 

1900, producing at least three lahars that entered the Columbia River about 1,500 years ago and 

depositing 340–640×106 m3 within 15 km downstream of confluence (Rapp, 2005). Mid-channel 

islands (for example, Government, Reed Islands) appear to have been formed only in the last 500 

years (Evarts and O’Connor, 2008), likely growing in a down-estuary direction from sediment 

deposition initiated by accumulations of large woody debris. Major portions of the flood plain have 

been modified by levees and fill, particular in North Portland. Tidal variability in water level 

generally is obscured by river freshets and daily power peaking cycles of Bonneville Dam.
22

8. Western Gorge (rkm 204–233)—Level IV West Cascades Lowlands and Valleys to Bonneville 

Dam: The terminal reach of the estuary is confined to the western end of the Columbia River Gorge, 

which was cut through the uplifted Cascade Range during the last 3–3.5 Ma (Evarts and others, 

2009). The Holocene valley fill is locally flanked by Missoula Flood deposits and Pleistocene 

terraces, but much of the river is bordered by bedrock, coarse-grained alluvial fans, colluvium, and 

large landslide complexes, especially on the northern slopes (O’Connor and Burns, 2009). The few 

peripheral flood plains (for example, Franz Lake) and wetlands occur mostly in the downstream lee 

of rocky valley projections but not at the outlets of major tributaries as in other reaches (for 

example, Sandy River in Reach G). Many of the prominent mainstem features like the large islands 

(for example, Bradford, Hamilton, Pierce Islands) were formed by the breaching of the A.D. 1415–

1445 Bonneville Landslide sometime before A.D. 1479, producing a peak discharge as great as 

110,000 m3/s and diverting the river channel south (abandoning the river course that is now 

Greenleaf Slough). This flood left distinctive overbank deposits down-estuary as far as Wallace 

Island in Hydrogeomorphic Reach C (Atwater, 1994; O’Connor, 2004; O’Connor and Burns, 2009). 

Evidence of late Holocene sand dune formation and growth over the last 2,500 years are still evident 

on Sandy Island and east of Rooster Rock. Steep valley walls provide episodic inputs of coarsegrained debris-discharge sediment, especially around the Warrendale area where large active fan 

complexes convey sediment from the steep walls of the Columbia River Gorge into the Columbia 

River. The influence of the tides (range less than 0.3 m) is much less than that of the power peaking 

cycle created by discharges from Bonneville Dam.

Level 4—Ecosystem Complex

At this time, complete mapping of ecosystem complexes throughout the entire Columbia River 

estuary has been limited by gaps in recent bathymetry datasets, which are a critical component for 

mapping aquatic ecosystem complexes. However, we here provide an example of ecosystem complexes 

for Hydrogeomorphic Reach F (fig. 5) where bathymetric and terrestrial data are mostly complete. The 

first step was refinement of the flood-plain boundary on the basis topographic, pedologic, and 

geomorphic criteria, resulting in a more accurate boundary encompassing the areas flanking the lower 

Willamette River and Columbia River subject to fluvial inundation, erosion, and deposition. Within this 

refined flood-plain in this reach, 16 classes of complexes were delineated. Primary complex classes are 

associated with flood-plain features, primary and tributary channels, and regularly flooded features. We 

delineate some natural features within the reach, such as rocky outcrops in the Holocene flood plain, 

which are never inundated (or essentially “terrestrial”). With the exception of landforms completely 

obscured by extensive modifications (the “Developed” class), we do not distinguish anthropogenic 

modifications of the system because they are assumed to be nested at finer scale within a complex; 

however, we recognize that in some cases, human modification may encompass an entire complex such 

as construction of dikes or levees around the perimeter of flood plain islands.
23

Ecosystem complexes in Reach F include six types of channels that are permanently flooded and 

three channel margins that are intermittently exposed (wetlands). The dominant features are flood plain 

and channel islands (four). As indicated in table 2, not all ecosystem complexes are represented in 

Hydrogeomorphic Reach F. 

Level 5—Geomorphic Catena

Geomorphic catenae are individual landforms nested within Ecosystem complexes and 

consisting of distinctive Primary Cover Class types. Development of geomorphic catenae for the entire 

Columbia River estuary also is impeded at this time by missing datasets, such as bathymetry data for 

Level 4 and recent, complete land-cover data for Level 6 (see below, Level 6—Primary Cover Class). 

Here, we combined the Level 4–Ecosystem Complexes developed for Hydrogeomorphic Reach F and 

2010 land-cover data to generate an initial delineation of geomorphic catenae for Reach F (fig. 6). We 

have identified 27 classes of geomorphic catenae in Reach F, including 4 aquatic classes (including the 

Unknown Depth class), 3 tributary or other channel classes (including Tributary Valley), 13 tidal flood 

plain classes, 5 artificial or developed (including Unknown) classes, and 2 relict classes (bedrock, 

terrace) that occur throughout the reach; 5 modifiers that distinguish extensive anthropogenic 

alterations.

Although many of the geomorphic catenae are discrete or slightly clustered (for example, 

terraces) other catenae are extensively interconnected. For instance, flood plain channels typically 

connect to lakes, marshes, and forests on flood plains. Similarly, as indicated in the hydrogeomorphic 

reach descriptions, flood plain bar, and scroll features are often associated with flood plain lake/ponds 

and herbaceous low marshes within the scroll features.

Unlike the ecosystem complexes, the classification and delineation of geomorphic catenae are 

more variable (and even ephemeral) because complexes are partially dependent on short-term, 

instantaneous “snap-shot” datasets such as aerial photography, LiDAR, and satellite remote sensing 

imagery. Catena classes that expand and contract with variable hydrologic conditions are the most 

vulnerable to this source of variation and mapping uncertainty.

Level 6—Primary Cover Class

The Level 6–Primary Cover Class data that we are using to integrate biological and other 

attributes with the geological and geomorphic features for Level 5–Geomorphic Catena in Reach F is 

based on integrated high resolution image segmentation and object based classification of NAIP and 

LANDSAT TM5 imagery and LiDAR elevation data (table 1). Using these preliminary 2010 LCRE

data, we have preliminarily identified 26 classes in Reach F (fig. 7). Among the vegetated classes, in 

addition to agriculture, aquatic beds and tree farms, 4 are upland and 12 are wetland classes. Water, 

rock, mud, sand, urban, and “other” classes (for example, bare ground and developed open space) 

constitute the un-vegetated classes. Among the vegetation classes are: (1) five tidal wetland classes

(coniferous, deciduous, mixed forest, scrub-shrub, and herbaceous); and (2) the equivalent classes for 

both non-tidal and upland areas of the Reach F. 
24

Discussion

General and Unique Applicability to Estuarine Classification Needs

We have developed the Columbia River Estuary Ecosystem Classification to address the same 

need for estuaries as described by Poole (2002) for dynamic, patchy, and strongly hierarchical river and 

stream networks: “...a hierarchical patch dynamics perspective [that] can be used as a framework for 

visualizing interactions between structure and function...” While the landscape-scale relationships 

between structure and function in fluvial ecosystems is increasingly understood (Mertes, 2002; Poole, 

2002; Poole and others, 2002; Wiens, 2002; Stanford and others, 2005; Strayer and others, 2006), 

similar research is lacking in large, freshwater dominated estuaries and deltas. The Classification offers 

a template for more detailed, process-based tests of those structure-function relationships. Moreover, the 

Classification is based primarily on spatially explicit datasets, which are key resources for interpreting 

estuarine hydrology, geomorphology, and ecosystem structure (Gilvear and others, 2004; Hume and 

others, 2007). Additionally, as spatial datasets are collected over time, the Classification provides a 

framework for assessments of ecosystem change and examinations of structure and function over 

multiple time scales and with respect to multiple stressors (for example, climate conditions, land use, 

and large-scale geologic events).

As tidal freshwater ecosystems cannot be disassociated from saline ecosystems in estuaries, we 

propose that pursuing fundamentally different approaches to ecosystem classification in fluvial and 

estuarine systems misses potentially strong controlling factors of rivers and their watersheds on 

estuarine structure and function (Hume and others, 2007). As illustrated by the challenges at developing 

a common definition and understanding of the term “transitional waters” (McLusky and Elliott, 2007) in

the European Communities’ Water Framework Directive (European Communities, 2000), estuaries 

encompass a continuum near coastal ocean, estuarine, and fluvial environments. At a minimum, the 

Classification addresses the identified need for the “division of transitional water system into 

management units that can usefully inform the decision-making process” (Ferreira and others, 2006) as 

well as effective management and rehabilitation. 

Utility and Application to Estuarine Science, Monitoring, Restoration and Management

The Classification assesses biophysical datasets to develop a hierarchical representation of 

estuarine ecosystems where the ecosystem units at finer spatial scales (Level 3–Hydrogeomorphic 

Reach to Level 5–Geomorphic Catena) have particular geomorphic and hydrologic relevance to 

estuarine resource management issues. The Classification provides a visualization tool for examining 

the diversity and spatial distribution of ecosystem units across multiple spatial scales. Because the 

Classification also will be applicable to other estuarine systems where the necessary data (table 1) are 

available (Hume and others, 2007), it will help to promote and facilitate research, monitoring, 

restoration/preservation, and management efforts at regional and other spatial scales.
25

Research

The Classification provides a viable template that scientists can apply to stratify large, dynamic 

systems like the Columbia River estuary into manageable, discrete units for intensive and/or spatially 

extensive study and formulation of testable hypotheses. The structure of the Classification and the 

inherent integration of data necessary to formulate the hierarchical levels will allow scientists to assess 

landscape-level changes in the estuary (see section, “Change Analyses”). Using the Classification as a 

template and data resource, many possibilities exist to conduct research assessing the relationships 

between landscape-scale metrics and population dynamics and viability of important fish and wildlife 

species in estuarine ecosystems (Turner, 2005). Although the current lack of high-resolution data 

prevents us from final delineation of all hierarchical levels in the Classification, the rapid advancement 

of the technologies needed to efficiently collect the necessary data suggest that the data will become less 

expensive to collect and increase in widespread availability over time. 

Alternatively, research may focus on relating physical conditions and biota within specific 

ecosystem complexes and/or geomorphic catenae. This type of research may yield information on those 

ecosystems that support vegetation, fish, and wildlife assemblages of concern or contribute substantial 

fluxes of organic matter, nutrients, and other basal food web resources to estuarine ecosystems. In this 

respect, an important validation of the Classification will be to test whether Geomorphic Catena can 

serve as identifiable habitats of estuarine fish and wildlife species of concern in the Columbia River 

estuary, such as juvenile Pacific salmon as they migrate through the estuary. Because of the threatened 

and endangered status among many of the Columbia River’s salmon populations, understanding the 

association between prevalent controlling factors such as hydrology (including anthropogenic flow

regulation) and the structure and evolution of habitat features (primarily at the geomorphic catena level) 

required by juvenile salmon is a critical step to enhancing habitat diversity for salmon recovery (Bottom 

and others, 2005). 

Change Analyses

In addition to spatial analyses within and between systems, a standardized method for 

delineating ecosystems provides a framework for temporal analyses of ecosystem change. These 

analyses are particularly relevant for dynamic estuarine systems where the distribution, area, and 

maturity of different ecosystems vary in response to interacting controlling factors such river inflow, 

tidal variation, sediment inputs, and management actions such as regulation of river discharge and 

constructions of dikes and levees. Because the Classification’s method for ecosystem delineation is not

apt to change substantially over time, monitoring agencies could apply the Classification to datasets as 

they become available in order to identify and assess changes in ecosystem types. With this information, 

monitoring entities could examine effects of management actions (for example, discharge regulation, 

diking, dredging, and restoration actions) and climate change on estuarine ecosystems and communities 

over time.
26

As an example, we have applied the Classification’s geospatial processing procedures for Level 

6—Primary Cover Class to the 1866–1901 United States Coast and Geodetic Survey (USCGS) “t-sheet” 

topographic surveys for Reach F and compared the symbology for distinguishable land cover vegetation 

classes against our current draft of Level 6–Primary Cover Class (fig. 7) for a segment of the flood plain

(fig. 8). This comparison suggests that while the basic structure of ecosystem complexes within the 

original survey area has not changed significantly over the past about 100 years, landscape metrics 

derived for five comparable vegetation cover classes (embedded in geomorphic catenae) quantify 

changes in complex dimensions and shapes and may indicate changes in their function in the estuary. 

Overall, the total area of floodplain forest and wetland forest ecosystems decreased significantly 

between 1866–1901 and 2010, less prominent floodplain scrub-shrub and wetland herbaceous 

ecosystems increased somewhat, and wetland scrub-shrub was a minor component historically and 

currently. In contrast, several metrics of patch complexity (total edge, shape, and perimeter:area ratio) 

have uniformly increased from historical to current conditions, especially wetland herbaceous (total 

edge and shape) and wetland forest (perimeter:area ratio). From a landscape ecology perspective, these 

trends could be associated with patch fragmentation, which has complex implications for changes in 

ecosystem function. However, how these changes may relate to altered hydrogeomorphic processes and 

resulting shifts in geomorphic catenae requires considerably more analysis.

Monitoring

The Classification’s standardized delineation of ecosystem components is an effective

communication tool for entities collecting, analyzing and sharing monitoring datasets within and

between estuaries. The Classification also can be used to design robust status and trend monitoring 

efforts. Habitat and fish monitoring programs within the Columbia Basin inform various management 

needs; including the requirements of Biological Opinions on the operation of the Federal Columbia 

River Power System, tracking the recovery of species listed under the Endangered Species Act, and 

addressing the needs of the Northwest Power and Conservation Council’s Fish and Wildlife Program. 

Like the Columbia River estuary, the management of other estuarine systems typically is multijurisdictional in nature. As an example, the Columbia River estuary (1) is within the jurisdiction of two 

States (Oregon and Washington) and numerous Federal, Tribal, watershed council, county, and 

municipal entities; (2) is the focus of ongoing recovery efforts for four ESA listed anadromous salmonid 

species (coho, chum, Chinook, and steelhead) and bull trout, and (3) has diverse land use and increasing 

human population pressures. Although there is a growing need for an integrated approach to long-term 

status and trend monitoring programs (Pacific Northwest Aquatic Monitoring Partnership , 2009), the 

Classification can help facilitate the evaluation of the status and trends of ecosystem attributes at 

multiple scales that accommodate the multi-jurisdictional monitoring needs of estuarine systems. 

Furthermore, if the resources were available to support a comprehensive status and trend monitoring 

program of indicators that are ecologically significant to listed salmonids in the Columbia River estuary, 

the hierarchical levels of the Classification could be used as attribute data in status and trend monitoring 

designs, such as a rotational split-panel design (Johnson and others, 2008; see:

http://www.pnl.gov/main/publications/external/technical_reports/PNNL-17300.pdf; Appendix B) and/or 

to weight site selection using a Generalized Random-Tessellation Stratified (GRTS) framework (Larsen 

and others, 2008). Using the Classification to inform a master sample could enable management entities 

to stratify sampling locations by specific ecosystem complex or geomorphic catena classes relevant to

culturally and economically important fish and wildlife species.
27

The Classification is intended to support metadata analyses of abiotic and biotic conditions

among different estuary systems. Such analyses would provide a heuristic exercise for testing our 

scientific understanding of these systems and enable assessments of estuarine conditions at regional and 

international levels, such as among the large estuaries of western North America (including San

Francisco Bay and Delta, Columbia River, Puget Sound, and the Fraser River), which have (or did 

historically have) extensive tidal freshwater ecosystems. Hydrographic reaches based on seasonal water 

and sediment quality attributes have been developed for the San Francisco estuary (San Francisco 

Estuary Institute , 2005) in a similar manner to the Classification’s hydrogeomorphic reaches. Analyses 

among these systems could explore topics including the capacity of Pacific Rim estuaries to sustain wild 

salmonid populations and interactions among tidal vegetation assemblages and rising sea levels.

Restoration and Preservation Planning

We also consider the Classification useful for ecosystem restoration and preservation 

applications where the goal is to restore and protect functional ecosystems. With directed research, the 

Classification could be used as a tool in support of restoration planning efforts at different spatial scales. 

At the project level, Classification datasets provide the basis for assessments of the complexity and 

diversity of complexes and/or catenae using landscape ecology metrics. Initial actions could then focus 

on restoring and protecting sites with high ecosystem complexity and diversity. At larger scales, 

Classification datasets in conjunction with ecosystem stressor datasets (for example, road densities, 

urban and industrial locations, and sites with known toxic contamination, Evans and others, 2006) can 

be used to determine the proximity of candidate restoration sites to stressors of concern and account for 

potential confounding impacts at project sites. At the estuary-wide scale, restoration implementers could 

incorporate information on complexes and catenae that support fishes and wildlife of concern (as these 

data become available) in order to select projects that establish refuge habitats, or “stepping stones,” 

along estuarine and tidal-freshwater corridors. These habitats would facilitate the movement of 

organisms between less hospitable ecosystems and throughout estuarine systems.

Management

Relative to estuarine resource management, the Classification provides a system-wide context 

for linking ecosystem spatial and temporal dynamics and management actions. In particular, the 

Classification’s delineation methods reflect a process-based approach where geomorphic and hydrologic 

processes act at multiple time scales and vary longitudinally and laterally throughout the estuary of 

focus. These processes emphasize ecosystem formation and change over time instead of a static 

distribution of ecosystems. Furthermore, Classification datasets reflect a “snap shot” of conditions when 

ancillary datasets were collected (fig. 8). As research quantifies key geomorphic and hydrologic drivers 

of ecosystem condition in estuaries, agencies can use this information to implement management actions 

(such as releases of river discharges that form and maintain ecosystems; removal or setbacks of dikes to 

improve connections between mainstem and off-channel ecosystems) that support dynamic estuarine 

systems. These types of actions are apt to support recovery efforts for fish and wildlife populations of 

concern that are adapted to variable estuarine conditions (for example pertaining to salmonids, Bottom 

and others, 2005).
28

We acknowledge that the context of the Classification is extensively embedded in the 

management issues surrounding the Columbia River estuary. Since completion of the Estuary 

Partnership’s Comprehensive Conservation and Management Plan (LCR-CCMP) (Lower Columbia 

River Estuary Program, 1999), organization of monitoring, management and education has depended to 

a large degree on understanding the distribution and status of ecosystems and biota-specific habitats. 

Included among 43 discrete actions recommended in the LCR-CCMP plan are those that would: (a) 

“inventory and prioritize habitat types and attributes needing protection and conservation”; (b) “identify 

habitats and environmentally sensitive lands that should not be altered”; (c) “protect, conserve and 

enhance identified habitats, particularly wetlands, on the mainstem of the lower Columbia River”; and 

(d) “adopt and implement consistent wetland, riparian, and instream habitat protection standards to

increase the quality and quantity of habitat to protect aquatic species.” Although considerable 

information was available for the lower about 75 km of estuary (Thomas, 1983; see also dedicated issue 

of Progress in Oceanography, 1990, 24(1-4), L.F. Small, guest ed.), the lack of a clear accounting of the 

types and spatial organization of the diverse ecosystems that composed the about 230 km of the lower 

River and estuary was cited as a critical limitation in implementing the recommended actions. 

Commensurate with this information gap was the lack of an ecosystem classification that would allow 

scientifically-based delineation of habitats at a variety of scales required for different monitoring, 

planning and management needs.

Constraints on Data Adequacy and Application of the Classification to the Entire Columbia River 

Estuary

Current constraints on application and validation of all levels of the Classification to the entire 

Columbia River estuary include incomplete and outdated bathymetric datasets for the estuary, LiDAR 

gaps for low elevation tidally influenced features like mudflats, and low accuracy for wetland features in 

available land-cover datasets (for example, LANDSAT 7 from 2000). Of these datasets, the bathymetry

is the least consistent due to the dynamic nature of the Columbia River riverbed and differences in 

spatial resolution of the original surveys and propagation of errors associated with combining surveys 

from a 7-year period. 

The completion of the lower three levels of the Classification (Ecosystem Complex, Geomorphic 

Catena, and Primary Cover Class) is anticipated to be complete by late 2011 in cooperation with the 

Estuary Partnership. GIS data layers, metadata, and final report will be made available to regional 

partners by the Estuary Partnership. Combined, these surveys are anticipated to provide a consistent 

bathymetric dataset for the lower and middle estuary, enabling completion of Level 4–Ecosystem 

complexes. Training and field checking for a new classified land-cover dataset are scheduled for 2010–

11 and subsequent processing in winter 2011 under coordination by LCREP. This new land-cover 

dataset and the bathymetry data will support delineation of Level 5–Geomorphic Catena and Level 6–

Primary Cover Class for the entire estuary.
29

Validation Needs

At this time, the Classification has not been formally validated with field data. Upon completion 

of all Classification levels for the entire estuary, a statistically rigorous, field-based validation of the

Classification should be conducted to test for the appropriateness of the ecosystem complex and 

geomorphic catena levels and the classes and subdivisions within each level.

Summary and Recommendations

This description of the concept and framework for the Columbia River Estuarine Ecosystem 

Classification also explains the rationale for advancing an ecosystem process-based classification that 

captures the variation and mechanisms in formative processes that shape estuarine ecosystems along the 

continuum from the head of tide to the ocean entrance. This Classification was developed to reflect the 

complex physiographic setting and geologic history of the Columbia River estuary and dynamic 

processes reworking that landscape in a domain of significant tidal and riverine discharge modifications. 

As such, this Classification may be more complex than classifications developed for estuaries in less 

dynamic settings. However, we suggest that the scope and scale of this classification would serve as a 

robust starting framework for analysis of other estuarine systems.

Based on our experience developing the Classification template and recognition that the three 

most complex levels have yet to be fully delineated for the Columbia River estuary, we recognize these

persistent science and information gaps:

1. Considerably more scientific investigations are needed to understand the processes and 

associated rates of change that structure the estuarine ecosystem, especially in tidal 

freshwater reaches where tidal influence generally is mediated by freshwater discharge.

2. More effort should be expended to compare estuarine classification systems that are 

similarly based on hydrogeomorphic controlling factors, such that classifications for 

different regions and types of estuaries can at least be cross-walked and ecosystem 

composition and structure compared.

3. Considerable more attention needs to be given to the geologic and tectonic processes that 

shaped estuaries as we know them, and particularly those processes that are still active, 

even if on very low frequency (but potentially very high magnitude) time scales. The 

prospects of sea-level rise and other manifestations of climate change makes this processbased understanding of large, landscape-scale influences on estuarine structure even 

more important.

4. Management applications of ecosystem classifications need to be tested with regional 

experts. The practicality and feasibility of monitoring large, dynamic estuaries based on a 

classification (such as proposed here) may have to balance statistical rigor and ecological 

significance.
30

Acknowledgments

Under the coordination of the Lower Columbia River Estuary Partnership, and through the 

support of the Bonneville Power Administration (BPA) and the U.S. Geological Survey (USGS), we 

have since 2004 been formulating an estuarine ecosystem classification that addresses these needs for 

the Columbia River and other comparable, large-river flood-plain estuaries. The Estuary Partnership has 

provided substantial assistance in coordinating acquisition of new bathymetric, land-cover and other 

critical datasets, as well as facilitating review of and refinements to the Classification throughout its 

development; we are particularly indebted to Keith Marcoe, Estuary Partnership GIS and Data 

Management Specialist, for facilitating acquisition and classification of new land cover/land use data for 

the estuary and for reviewing the emerging Ecosystem Complex and Geomorphic Catena classes. 

Support for preparing this document was provided by the Estuary Partnership while support for 

publication of this document was provided by a USGS Assistance Award (#05HQAG0096). Valuable 

technical support was provided by James Hatten and Tom Batt (USGS) who compiled a single 

bathymetric dataset of points from numerous data sources. 

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39

Appendix A. Summary of location, geographic and geomorphic setting, major 

landforms, geologic content and history, characteristic geomorphic and 

hydrologic processes, and anthropogenic factors affecting key processes in 

eight Hydrogeomorphic Reach forming the Columbia River Estuary Ecosystem 

Classification.

Reach A

Reach B

Reach C

Reach D

Reach E

Reach F

Reach G

Reach H

Appendix A is a Microsoft© Excel file and can be downloaded at 

http://pubs.usgs.gov/of/2011/1228. 
40

Figure 1. Basic physiographic setting and geographic extent of the Columbia River

estuary as applied to the Columbia River Estuary Ecosystem Classification. Tentative 

flood-plain outline estimated by inclusion of all surfaces less than 18 m above the 

NAVD 1988.
41

Figure 2. Classification Level 1-Ecoregion Provinces, adopting the EPA Ecoregion Level II classification.
42

Figure 3. Classification Level 2-Ecoregions based on the EPA Ecoregion classifications. A. EPA Ecoregion Level 

III classification. B EPA Ecoregion Level IV classification, which is nested in the Level III classes. Both maps show 

outline of tentative Columbia River estuary flood plain. 
43

Figure 4. Classification Level 3-Hydrogeomorphic Reaches indicating where the eight reaches are delineated by 

subdividing and adjusting the borders of EPA Ecoregion IV classes (see Figure 3) according to hydrological and 

physiographic discontinuities (see Methods). 
44

Figure 5. Classification Level 4-Ecosystem Complexes illustrated for Hydrogeomorphic Reach F (see fig. 4) based 

on delineating mainstem and distributary channels using current bathymetry data and analyses of flood plain 

geology and geomorphology (see Methods, table 1). Classified area reflects flood-plain boundary revised from 

initial elevation-based criteria (shown in inset and by area “outside Holocene flood plain” to only include area of 

Holocene fluvial deposition and modification as inferred from topographic, geological and soils maps.
45

Figure 6. Classification Level 5-Geomorphic Catena illustrated for Hydrogeomorphic Reach F (see fig. 4). 

Classified area reflects flood-plain boundary revised from initial elevation-based criteria (shown in inset and by area 

“outside Holocene flood plain”) to only include area of Holocene fluvial deposition and modification as inferred from 

topographic, geological, and soils maps.
46

Figure 7. Classification Level 6-Primary Cover Class illustrated for Hydrogeomorphic Reach F (see fig. 4) based on 

2010 LCRE Land Cover Classification. The classification encompassed the slightly larger area of the earlier 

tentative Hydrogeomorphic Reach boundary as shown in figure 4. 
47

Figure 8. Comparison of Primary Cover Class in Hydrogeomorphic Reach F of Columbia River estuary between 

1866 and 1901 (top left; based on analysis of USCGS ‘t-sheet’ survey data; table 1) and 2010 (top right; see 

Ecosystem Complex under Results, above). FRAGSTATS (McGarigal and Marks, 1995) metrics are generated for 

land cover vegetation classes as landscape patches illustrate in the lower panels (a, middle left) total area, (b, 

middle right) total edge, (c, lower left) shape index, and (d, lower right) perimeter:area ratio.
48

Table 1. Sources and attributes of spatial data used to develop draft Columbia River Estuary Ecosystem Classification.

[rkm 75 = rm 46,rkKm 214 = rm 133, rkm 230 = rm 145]

Data type Year Spatial extent Resolution Data sources Online availability

Land cover

Land cover 2000 rkm 0– 230 30-m Landsat 7 Thematic Mapper 

imagery

http://edcsns17.cr.usgs.gov/NewEarthExplorer/

Wetlands 1974 rkm 0230 1:24,000 U.S. Fish and Wildlife Service 

National Wetland Inventory

http://www.fws.gov/wetlands/Data/

Aerial imagery 2009 rkm 0–230 1-m U.S. Department of Agriculture 

digital orthophotographs

http://datagateway.nrcs.usda.gov/

Ecoregions 1984–2007 RKm 0 to 230 varies U.S. Environmental Protection 

Agency ecoregion 

classification

http://www.epa.gov/wed/pages/ecoregions.htm

Bathymetry

Bathymetry varies RKm 0 to 230 varies Lower Columbia River Estuary 

Partnership bathymetry 

compilation

http://lcrep.org/

Historical 

Bathymetry 

1866 to 1901 RKm 0 to 214 1:10,000 to 

1:20,000

U.S. Coast and Geodetic Survey 

hydrographic maps, provided by 

National Oceanographic and 

Atmospheric Administration 

Coastal Services Center

https://catalyst.uw.edu/workspace/wet/14965/82924
49

Table 1. Sources and attributes of spatial data used to develop draft Columbia River Estuary Ecosystem Classification.—Continued

Topography

Topography and 

cultural features

varies RKm 0 to 230 1:24,000 U.S. Geological Survey 

topographic maps 

http://edcsns17.cr.usgs.gov/NewEarthExplorer/

Historical 

Topography and 

Land Cover 

1866 to 1901 RKm 0 to 214 1:10,000 U.S. Coast and Geodetic Survey 

topographic maps, provided by 

National Oceanographic and 

Atmospheric Administration 

Coastal Services Center

https://catalyst.uw.edu/workspace/wet/14965/82924

Elevation varies RKm 0 to 230 10-m U.S. Geological Survey 

National Elevation Dataset

http://ned.usgs.gov/

Elevation 2010 RKm 0 to 230 1-m U.S. Army Corps of Engineers 

LiDAR survey

https://www.nwp.usace.army.mil/services/home.asp

Hydrology varies RKm 0 to 230 30-m Earth Design Consultants, Inc. 

flood-plain extent

Geology and soils

Soils varies RKm 0 to 230 varies Natural Resources Conservation 

Service (NRCS)

http://datagateway.nrcs.usda.gov

Geology varies RKm 0 to 

230, Oregon 

only

varies Oregon Department of Geology 

and Mineral Industries 

statewide geologic map

http://spatialdata.oregonexplorer.info

Geology varies RKm 0 to 

230, 

Washington 

only

1:100,000 Washington State Department 

of Natural Resources Division 

of Geology and Earth Resources 

statewide geologic map

http://www.dnr.wa.gov/ResearchScience/Topics/GeosciencesData/Pages/gis_data.aspx

Geology varies RKm 122 to 

150, 185 to 

206

1:24,000 U.S. Geological Survey 

geologic maps

http://ngmdb.usgs.gov/
50

Table 2. Preliminary list of ecosystem complexes mapped under Level 4 of the 

Columbia River Estuary Ecosystem Classification.

Complex Brief description

Aquatic complexes

backwater embayment large indentations of the shoreline, connected by a smaller 

opening or slough

embayment large, open indentations of the shoreline

primary channel primary channel of river

tributary channel larger river tributaries 

tributary secondary channel channel beginning in a tributary and connected to a larger 

channel at both ends at least seasonally

Flood-plain complexes

bedrock bedrock above surface of flood plain

developed areas where flood plain is completely obscured by development

dune deposit accumulation of wind-blown sediment

flood plain undifferentiated Holocene flood plain 

flood plain backswamp low areas away from primary channel, generally with many 

wetlands and lakes

flood plain bar and scroll bar and swale topography

landslide deposits and associated topography resulting from mass 

movements

secondary channel channel that is connected to primary channel at both ends at least 

seasonally

terrace pre-Holocene alluvial deposit surrounded by Holocene flood 

plain or elevated Holocene flood plain surfaces above historically 

active flood plain

tributary fan alluvial fans at mouths of tributaries

tributary flood plain flood plains of tributaries
51

Table 3. Preliminary list of geomorphic catenae mapped under Level 5 of the Columbia River 

Estuary Ecosystem Classification.

Catena Brief description

Aquatic catenae

deep channel deepest part of channel

intermittently exposed sparsely vegetated beaches and shallow water areas within channels

permanently flooded permanently flooded part of channel, excluding the deepest part

side channel secondary or distributary channels on major tributaries, for which there is no 

bathymetric data

unknown depth channel areas lacking bathymetric data

Flood-plain catenae

artificial beach/bar beach resulting from anthropogenic activity

artificial water body undifferentiated artificial water body 

bedrock bedrock above surface of flood plain

crevasse splay lacustrine delta deposit that is not from a channel originating outside the flood 

plain

developed flood plain areas where flood plain is completely obscured by development

dune deposit accumulation of wind-blown sediment

filled areas filled in areas; generally are shallow water or islands on historic maps, includes 

dredge spoils.

flood plain undifferentiated flood plain

flood-plain channel island islands in flood-plain channels

flood-plain channel channels that do not originate outside the flood plain and are not connected to a 

primary channel at both ends

lake or wetland low areas that cannot be resolved as wetland or lake/pond, generally are drained 

lakes.

lake/pond bodies of water, generally not channelized, includes cut off channels and 

seasonally inundated areas. 

lake/pond island island in a non-channelized water body

landslide deposit mass-wasting deposit on flood plain

natural levee ridges from lateral migration of channels, may include shallow swales where 

ridges coalesce and ridge/swale distinction is ambiguous; often are sub-parallel 

to a present or former channel.
52

Table 3. Preliminary list of geomorphic catenae mapped under Level 5 of the Columbia River 

Estuary Ecosystem Classification.—Continued

Catena Brief description

Flood-plain catenae—Continued

terrace pre-Holocene alluvial deposit surrounded by Holocene flood plain or elevated 

Holocene flood plain surfaces above historically active flood plain

tributary (minor) tributary channels of smaller streams 

tributary fan alluvial fans at mouths of tributaries

tributary valley (outside flood plain) low parts of tributary valleys that extend outside the Holocene flood plain

unknown insufficient information to permit classification

wetland low relatively flat areas in flood plain that are or historically were seasonally 

inundated

Flood-plain modifier

Artificial completely artificial feature

Altered feature whose geometry has changed because of anthropogenic activity

Altered hydrology feature whose hydrology has changed because of anthropogenic activity

Diked area not hydrologically connected with primary channel because of dike

Partially diked area of limited hydrologic connection with primary channel because of dike
53

Table 4. Classification hierarchy in relation to geology, time and human disturbances.

Classification level Main geologic controls and major (including anthropogenic) 

events Temporal scales Potential application to management and restoration

Ecosystem Province Plate tectonics, global continental position, and 

topography

50-250 Ma Flow and sediment transport, alteration by basin-wide 

flow regulation, land-use practices, and sensitivity to 

global climate change vary by province.

Ecoregion Formation and uplift of Cascade and Coast Ranges, 

subsidence of Portland Basin

1-50 Ma Flow and sediment transport, alteration by basin-wide 

flow regulation, land-use practices, and sensitivity to 

global climate change vary by ecoregion.

Hydrogeomorphic Reach Establishment of Columbia River drainage, Columbia 

River Basalt flows, Columbia River aggradation since last 

glacial maximum

0.01-20 Ma Flow and sediment transport, alteration by basin-wide 

flow regulation, land-use practices, sensitivity to global 

climate change vary by hydrogeomorphic reach.

Ecosystem Complex Holocene aggradation and Columbia River sediment 

transport since last glacial maximum sea-level low, 

episodic volcanogenic sediment inputs, landslides, landuse changes, engineering effects including dam 

construction, bank stabilization, levee construction, 

channel dredging.

20-10,000 yrs Information to guide management and restoration actions 

including siting of conservation easements/purchases, 

levee setbacks, altered dredging strategies, and flowregime restoration.

Geomorphic Catena Columbia River floods, sediment transport processes, 

episodic subsidence and tectonic warping associated with 

Cascadia earthquake cycle since sea- level stabilization, 

land-use changes, engineering effects including dam 

construction, bank stabilization, levee construction, 

channel dredging.

1-2,000 yrs Information to guide management and restoration actions 

including siting of conservation easements/purchases, 

levee setbacks, altered dredging strategies, and flowregime restoration.

Primary Land Cover Columbia River flow, sediment transport and tidal 

processes, land-use changes, engineering effects including 

dam construction, bank stabilization, levee construction, 

channel dredging.

hours to 100 yrs Information to guide management and restoration actions 

including siting of conservation easements/purchases, 

levee setbacks, altered dredging strategies, restoration of 

native species, control of invasive species, and flowregime restoration.
54

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 Simenstad and others—Columbia River Estuary Ecosystem Classification— Concept and Application—Open-File Report 2011-1228