Prepared in cooperation with Green Point Consulting and the U.S. Environmental Protection 

Agency

Tidal Wetlands of the Yaquina and Alsea River Estuaries, 

Oregon: Geographic Information Systems Layer 

Development and Recommendations for National Wetlands 

Inventory Revisions

Open-File Report 2012–1038

U.S. Department of the Interior

U.S. Geological Survey
Cover. Photograph of Drift Creek and adjoining tidal marshes in the Alsea estuary, Oregon. Photograph by 

Christopher Janousek, U.S. Environmental Protection Agency, November 2010.
i

Tidal Wetlands of the Yaquina and Alsea River Estuaries,

Oregon: Geographic Information Systems Layer 

Development and Recommendations for National 

Wetlands Inventory Revisions

By Laura S. Brophy, Green Point Consulting; with contributions from: Deborah A. Reusser, U.S. Geological Survey;

and Christopher N. Janousek, U. S. Environmental Protection Agency

Prepared in cooperation with Green Point Consulting and the U.S. Environmental Protection 

Agency

Open-File Report 2012–1038

U.S. Department of the Interior

U.S. Geological Survey
ii

U.S. Department of the Interior

Sally Jewell, Secretary

U.S. Geological Survey

Suzette M. Kimball, Acting Director

U.S. Geological Survey, Reston, Virginia: 2013

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its natural and living resources, natural hazards, and the environment—visit 

http://www.usgs.gov or call 1–888–ASK–USGS

For an overview of USGS information products, including maps, imagery, and publications,

visit http://www.usgs.gov/pubprod

To order this and other USGS information products, visit http://store.usgs.gov

Suggested citation:

Brophy, LS., with contributions from: Reusser, D.A., and Janousek, C.N., 2013, Tidal wetlands of the Yaquina and 

Alsea River estuaries, Oregon: Geographic Information Systems layer development and recommendations for 

National Wetlands Inventory revisions: U.S. Geological Survey Open-File Report 2012–1038, 70 p.

Any use of trade, product, or firm names is for descriptive purposes only and does not imply 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

Contents ........................................................................................................................................................................iii

Figures...........................................................................................................................................................................iv

Tables............................................................................................................................................................................iv

Conversion Factors.........................................................................................................................................................v

Datums ...........................................................................................................................................................................v

Acronyms and Abbreviations .........................................................................................................................................vi

Definitions......................................................................................................................................................................vi

Abstract ......................................................................................................................................................................... 1

Introduction.................................................................................................................................................................... 1

Study Areas ............................................................................................................................................................... 2

Project Goals and Objectives..................................................................................................................................... 5

Methods......................................................................................................................................................................... 6

Plant Identification Workshop..................................................................................................................................... 6

Data Processing Steps............................................................................................................................................... 6

LiDAR Analysis .......................................................................................................................................................... 6

Wetland Classification................................................................................................................................................ 9

Estuarine versus Palustrine System (salinity regime)............................................................................................. 9

Cowardin et al. (1979) Modifiers........................................................................................................................... 10

Water Regime Modifiers ................................................................................................................................... 10

Special Modifiers .............................................................................................................................................. 11

Likely Former Tidal Wetlands Classified as Upland in the NWI................................................................................ 11

Creation of GIS Data for 1999 Tidal Wetland Prioritization Sites ............................................................................. 12

Results......................................................................................................................................................................... 15

Recommended Revisions to Cowardin et al. (1979) classifications ......................................................................... 15

Likely Former Tidal Wetlands Classified as Upland in the NWI................................................................................ 15

GIS Data for 1999 Prioritization Sites....................................................................................................................... 20

New Prioritization Sites......................................................................................................................................... 20

Revisions to Prioritization Site Attributes.............................................................................................................. 23

Recommendations....................................................................................................................................................... 23

Intended Uses and Limitations of Mapping .............................................................................................................. 23

Downloadable Wetland Shapefiles .............................................................................................................................. 24

Acknowledgments........................................................................................................................................................ 25

References Cited......................................................................................................................................................... 26

Appendix A: Landscapes and vegetation present across study areas in Yaquina and Alsea estuaries, Oregon......... 29
iv

Figures

Figure 1. Map of the Central Oregon Coast showing locations of the Yaquina and Alsea estuaries and associated 

drainage basins.. ........................................................................................................................................................... 3

Figure 2. Aerial image showing extensive intertidal area near the mouth of the estuary, Alsea Bay, Oregon. 

(Photograph by Laura Brophy, Green Point Consulting, September 2007). .................................................................. 4

Figure 3. Illustration of the relationship between prioritization site designation and National Wetland Inventory 

polygons.. .................................................................................................................................................................... 13

Figure 4. Map of recommended National Wetland Inventory Cowardin et al. (1979) classification revisions 

resulting from this project for the Yaquina estuary, Oregon, including areas identified as likely former tidal wetlands 

(“FTW”).. ...................................................................................................................................................................... 16

Figure 5. Map of recommended National Wetlands Inventory Cowardin et al. (1979) classification revisions 

resulting from this project for the Alsea estuary, Oregon, including areas identified as likely former tidal wetlands 

(“FTW”). ....................................................................................................................................................................... 17

Figure 6. Map of tidal wetlands and likely former tidal wetlands of the Yaquina River estuary, Oregon: prioritization 

sites from the 1999 tidal wetland prioritization (Brophy 1999), plus new sites identified in the current study (sites 

Y44 through Y49)......................................................................................................................................................... 21

Figure 7. Map of tidal wetlands and likely former tidal wetlands of the Alsea River estuary, Oregon: Prioritization 

sites from the 1999 tidal wetland prioritization (Brophy 1999), plus new sites identified in the current study (sites 

A38 through A41)......................................................................................................................................................... 22

Tables

Table 1. Common names for tidal wetland types frequently found in the Yaquina and Alsea estuaries, and their 

corresponding Cowardin et al. (1979) classifications..................................................................................................... 5

Table 2. Elevation zones used for LiDAR analysis (elevations in feet (ft) NAVD88), Yaquina and Alsea estuaries, 

Oregon........................................................................................................................................................................... 7

Table 3. Tidal datums for the Yaquina and Alsea estuaries, Oregon. ........................................................................... 7

Table 4. Table of attributes for GIS layer of prioritization sites to accompany 1999 tidal wetland prioritization........... 14

Table 5. Total area (acres) of recommended changes to NWI Cowardin et al. classification, by original NWI 

classification. Yaquina estuary, Oregon....................................................................................................................... 18

Table 6. Total area (acres) of recommended changes to NWI Cowardin et al. classification, by original NWI 

classification. Alsea estuary, Oregon........................................................................................................................... 19

Table 7. Downloadable Wetland Shapefiles................................................................................................................ 25
v

Conversion Factors

Inch/Pound to SI

Multiply By To obtain

Length

foot (ft) 0.3048 meter (m)

mile (mi) 1.609 kilometer (km)

Area

acre 4,047 square meter (m2)

acre 0.4047 hectare (ha)

acre 0.4047 square hectometer (hm2) 

acre 0.004047 square kilometer (km2)

Salinity is unitless.

Datums

UTM Zone 10N NAD83 HARN uses the NAD83(HARN) geographic 2D CRS as its base CRS and the 

UTM zone 10N (Transverse Mercator) as its projection.

Vertical coordinate information is referenced to the North American Vertical Datum of 1988 (NAVD 

88).

Horizontal coordinate information is referenced to the Oregon Lambert HARN (international feet).

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

Acronyms and Abbreviations 

BLM U.S. Bureau of Land Management

DLCD Department of Land Conservation and Development

EPA U.S. Environmental Protection Agency

FTW Former Tidal Wetland

GIS Geographic Information Systems

HARN High Accuracy Reference Network

LiDAR Light Detection and Ranging

NAIP National Agricultural Imagery Program

NOAA National Oceanic and Atmospheric Administration

NWI National Wetlands Inventory

USFS U.S. Forest Service

MLLW Mean Lower Low Water

MHHW Mean Higher High Water

HMT Highest Measured Tide

Definitions

National Wetlands Inventory Wetland

Wetlands are lands transitional between terrestrial and aquatic systems where the water table is usually 

at or near the surface or the land is covered by shallow water. For purposes of this classification 

wetlands must have one or more of the following three attributes: (1) at least periodically, the land 

supports predominantly hydrophytes, (2) the substrate is predominantly undrained hydric soil, and (3) 

the substrate is nonsoil and is saturated with water or covered by shallow water at some time during the 

growing season of each year.

US Army Corps of Engineers and Oregon Department of State Lands Wetland

“Wetlands” means those areas that are inundated or saturated by surface or ground water at a frequency 

and duration sufficient to support, and that under normal circumstances do support, a prevalence of 

vegetation typically adapted for life in saturated soil conditions.
1

Tidal Wetlands of the Yaquina and Alsea River Estuaries,

Oregon: Geographic Information Systems Layer 

Development and Recommendations for National 

Wetlands Inventory Revisions

By Laura S. Brophy, Green Point Consulting; with contributions from: Deborah A. Reusser, U.S. Geological Survey; 

and Christopher N. Janousek, U.S. Environmental Protection Agency

Abstract

Geographic Information Systems (GIS) layers of current, and likely former, tidal wetlands in 

two Oregon estuaries were generated by enhancing the 2010 National Wetlands Inventory (NWI) data 

with expert local field knowledge, Light Detection and Ranging-derived elevations, and 2009 aerial 

orthophotographs. Data were generated for two purposes: First, to enhance the NWI by recommending

revised Cowardin et al. (1979) classifications for certain NWI wetlands within the study area; and 

second, to generate GIS data for the 1999 Yaquina and Alsea River Basins Estuarine Wetland Site 

Prioritization study. Two sets of GIS products were generated: (1) enhanced NWI shapefiles; 

and (2) shapefiles of prioritization sites. The enhanced NWI shapefiles contain recommended changes to 

the Cowardin et al. classification (system, subsystem, class, and/or modifiers) for 286 NWI polygons in 

the Yaquina estuary (1,133 acres) and 83 NWI polygons in the Alsea estuary (322 acres). These

enhanced NWI shapefiles also identify likely former tidal wetlands that are classified as upland in the 

current NWI (64 NWI polygons totaling 441 acres in the Yaquina estuary; 16 NWI polygons totaling 51 

acres in the Alsea estuary). The former tidal wetlands were identified to assist strategic planning for 

tidal wetland restoration. Cowardin et al. classifications for the former tidal wetlands were not provided, 

because their current hydrology is complex owing to dikes, tide gates, and drainage ditches. The scope 

of this project did not include the field evaluation that would be needed to determine whether the former 

tidal wetlands are currently wetlands, and if so, determine their correct Cowardin et al. classification.

The prioritization site shapefiles contain 49 prioritization sites totaling 2,177 acres in the Yaquina 

estuary, and 39 prioritization sites totaling 1,045 acres in the Alsea estuary. The prioritization sites 

include current and former (for example, diked) tidal wetlands, and provide landscape units appropriate 

for basin-scale wetland restoration and conservation action planning. Several new prioritization sites

(not included in the 1999 prioritization) were identified in each estuary, consisting of NWI polygons 

formerly classified as nontidal wetland or upland. The GIS products of this project improve the accuracy 

and utility of the NWI data, and provide useful tools for estuarine resource management.

Introduction

Wetlands in Oregon estuaries have been altered by past human land uses and will continue to

undergo changes owing to future human land use decisions and climate change effects, such as sea-level
2

rise, increased storm frequency and intensity, and changing temperature and precipitation patterns. 

Human alterations to tidal wetlands in several Oregon estuaries have been well documented through 

field surveys, aerial photograph interpretation of high resolution imagery, and Light Detection and 

Ranging (LiDAR) analyses (Brophy, 1999, 2005, 2012). However, some of these data were published as 

reports (for example, Brophy, 1999) and were not available in a format that could be used for modeling 

future changes in coastal habitats because of sea-level rise (SLR). In addition, although the National 

Wetlands Inventory (NWI) data layers had been updated by the U.S. Fish and Wildlife Service in 2010,

for the Yaquina and Alsea estuaries, preliminary SLR model runs for the Yaquina estuary by U.S. 

Geological Survey (USGS) indicated that some important wetlands were possibly miscoded. To 

improve SLR modeling results and enhance the accuracy and utility of the NWI for resource managers, 

the USGS provided funding to Green Point Consulting in 2010 to develop enhanced Geographic 

Information Systems (GIS) products for the Yaquina and Alsea drainage basins with recommended

NWI (Cowardin et al. 1979) classification revisions using information from previous studies and expert 

field knowledge. This report describes the methods used to enhance the NWI data layers and to develop 

the other GIS products, and summarizes the results of these changes. This report also includes 

photographs of wetland types and plant species that are common in these estuaries. Links to download 

the data are located in the data section of this document.

Study Areas

The Yaquina estuary is on the central Oregon coast adjacent to the town of Newport at latitude

44.62°N, longitude 124.02°W. The Alsea estuary is approximately 16 mi south of the Yaquina estuary

adjacent to the town of Waldport, Oregon (fig. 1). The project study areas include the entire Yaquina 

River estuary and the entire Alsea River estuary, from the Pacific Ocean to the upstream limit of tidal 

influence. Instead of the mapped head of tide, as published by the Oregon Department of State Lands 

(OR DSL) (2007), the study area included all land surfaces within tidal range (based on LiDAR-derived 

elevations), as described in section, “LiDAR Analysis”, even if those land surfaces were upstream of 

mapped head of tide. This was necessary because field experience has shown that the DSL head of tide 

mapping is sometimes inaccurate (for example, Brophy, 2012), and because this study included former 

tidal wetlands behind the tide gates and barriers that constitute the current head of tide in some water

bodies.

The Yaquina and Alsea estuaries are drowned river mouths with expansive intertidal mud flats 

near their mouths (fig. 2). Upslope and upstream of the mud flats are the three types of tidal wetlands 

addressed in this study: emergent tidal wetlands (tidal marsh), scrub-shrub tidal wetlands, and forested 

tidal wetlands. All three types can occur as either saline or freshwater wetlands. Their corresponding 

Cowardin et al. classes are shown in table 1. Woody-dominated (scrub-shrub and forested) tidal 

wetlands are collectively referred to as “tidal swamp”. The estuarine and tidally influenced palustrine 

wetland vegetation in both of these estuaries is species-rich and includes grasses such as Deschampsia 

cespitosa (fig. A1), Agrostis stolonifera (fig. A2), Hordeum jubatum (fig. A3), and Distichlis spicata; 

rushes (Juncus spp., figs. A4–A5); sedges such as Carex lyngbyei (fig. A6) and Carex obnupta (fig. 

A7); and succulent halophytes (Triglochin maritimum, fig. A8). Trees and shrubs found in Yaquina and 

Alsea tidal wetlands include Sitka spruce (Picea sitchensis) (fig. A9) and black twinberry (Lonicera 

involucrata) (figs. A10–A11). Additional representative landscapes and vegetation present across the 

study areas can be seen in figures A12–A32. Further information on Oregon tidal wetland habitats and 

vegetation can be found in Akins and Jefferson (1973), Jefferson (1975), Eilers (1975), Adamus and 

others (2005), and Brophy (2007a).
3

Figure 1. Map of the Central Oregon Coast showing locations of the Yaquina and Alsea estuaries and associated 

drainage basins. Oregon boundaries from the Nationalatlas.gov in geographic projection. Watershed boundaries 

and water polygons from U.S. Environmental Protection Agency classification project (Lee and Brown, unpublished 

data, 2009).
4

Figure 2. Aerial image showing extensive intertidal area near the mouth of the estuary, Alsea Bay, Oregon. 

(Photograph by Laura Brophy, Green Point Consulting, September 2007).
5

Table 1. Common names for tidal wetland types frequently found in the Yaquina and Alsea estuaries, and their 

corresponding Cowardin et al. (1979) classifications. 

[Table does not include all possible wetland types]

Common names – coarse scale Common names – fine scale Cowardin et al. classification

Tidal marsh, salt marsh

Low marsh, low salt marsh E2EMN

High marsh, high salt marsh, high 

brackish marsh E2EMP

Tidal swamp

Brackish scrub-shrub tidal wetland E2SSP

Brackish forested tidal wetland E2FOP

Freshwater scrub-shrub tidal wetland PSSR

Freshwater forested tidal wetland PFOR

Freshwater tidal marsh Freshwater tidal marsh PEMR

Like other Oregon estuaries, the Yaquina and Alsea estuaries are subjected to dry summers, 

during which river influence is low and ocean influence is high; and wet winters, where river influence

increases (Brown and Ozretich, 2009). During the summer months, strong upwelling events provide 

nutrient rich waters to Pacific coast estuaries. Estuaries contribute to coastal ecosystem services by 

cycling nutrients and providing critical habitat for native plants and animals including marine, 

anadromous, and resident fish, birds, and invertebrates (Adamus, 2006). 

Project Goals and Objectives

The goals of this project were to enhance the NWI data with expert local and regional 

knowledge for the Alsea and Yaquina estuaries, to improve the accuracy and utility of these GIS layers 

for resource management and to improve model results, for potential future wetland habitat distributions 

due to sea-level rise. To accomplish these goals, the following specific objectives were established: 

1. Educate USGS and Environmental Protection Agency (EPA) personnel on field identification of 

Oregon tidal wetland plants in the emergent, scrub-shrub and forested classes.

2. Generate enhanced NWI shapefiles containing recommended revisions to the Cowardin et al.

classification for tidal wetlands within the study area (emergent, scrub-shrub, and forested 

classes). 

3. Generate GIS datasets (shapefiles) for the tidal wetland prioritization sites identified in the 1999 

tidal wetland prioritization for the Yaquina and Alsea estuaries (Brophy, 1999), and characterize 

major changes at these prioritization sites since 1999.
6

Methods

Plant Identification Workshop

To improve and standardize knowledge of the local tidal wetland flora for USGS and EPA 

personnel, a 1-day workshop taught by Laura Brophy was held in May 2010. USGS and EPA staff

visited three tidal wetlands in the Yaquina estuary, representing a range of salinity regimes. Workshop 

training provided the foundation for subsequent large-scale estuarine vegetation surveys conducted by 

the USGS and EPA during 2010 in four coastal estuaries in Oregon.

Data Processing Steps

In February 2010, NWI shapefiles for the Yaquina drainage basin were downloaded from the 

NWI website (U.S. Fish and Wildlife Service, 2010) and merged into one data layer by EPA. In April 

2010, NWI shapefiles for the Alsea Bay drainage basin were downloaded from the NWI website and 

merged into one data layer by Green Point Consulting. Metadata for these NWI data list the date of the 

source imagery as “1977 to present”. The NWI data layers were then processed in the following ways:

1. LiDAR Analysis: LiDAR-derived elevation data (Watershed Sciences, Inc., 2009) were used to 

select NWI polygons within tidal range. Details on this process are provided in section, “LiDAR 

Analysis”.

2. NWI Wetland Classification: The Cowardin et al. classification for each NWI polygon within 

tidal range was reviewed and revised where necessary, based on the LiDAR-derived elevation, 

2009 aerial photography, salinity data provided by EPA, and field knowledge of the Yaquina and 

Alsea estuaries. Recommended revisions cover the Cowardin et al. system, subsystem, and class 

levels, hydrologic modifiers, and special modifiers. Details on this process are provided in

section, “NWI Wetland Classification”.

3. Creation of GIS data for 1999 tidal wetland prioritization: NWI polygons were merged to form a 

GIS layer of the prioritization sites defined in Brophy (1999). The wetland characteristics 

determined in 1999 were attributed to these prioritization sites. The LiDAR Digital Elevation 

Model (DEM), 2005 aerial photography, and field knowledge were used to identify any major 

changes that had occurred since 1999; these changes were attributed to the prioritization sites in 

the GIS data. Through the use of the new LiDAR data and 2009 aerial photography, several new 

prioritization sites were identified and attributed. Details on this process are provided in section,

“Creation of GIS Data for 1999 Tidal Wetland Prioritization”.

LiDAR Analysis

LiDAR-derived elevations were obtained from the “bare earth” digital elevation model 

developed for the Oregon LiDAR Consortium by Watershed Sciences, Inc. (Watershed Sciences, Inc., 

2009; Oregon Department of Geology and Mineral Industries, 2012). Standard (not water-penetrating) 

airborne LiDAR equipment was used. Data acquisition was not timed for low tide, but for this study 

area, all ground surfaces critical to the analysis (that is, surfaces above Mean Higher High Water) were 

above water in the LiDAR data. The vertical accuracy of the LiDAR data was 0.11 ft, determined 

through Real Time Kinematic ground survey on road surfaces, compared to the closest laser point 

(Watershed Sciences, Inc., 2009). Average laser pulse density was 0.80 per ft2 (Watershed Sciences, 

Inc., 2009). 
7

The LiDAR analysis focused on the upper limit of tidal influence, since NWI mapping of habitat 

classes lower in the tidal range (that is, low marsh, mud flat, aquatic bed) appeared to be accurate. To 

determine the upper limit of tidal influence, LiDAR derived elevations were analyzed to determine the 

percentage of each NWI polygon that occurred within three elevation zones (table 2). 

Table 2. Elevation zones used for LiDAR analysis (elevations in feet (ft) NAVD88), Yaquina and Alsea estuaries, 

Oregon.

Elevation zone Yaquina estuary Alsea estuary

1. Tidally inundated year-round <9 ft <8 ft

2. Seasonally inundated by combined tidal 

and fluvial flows 9–11 ft 8–11 ft

3. Potential tidal wetland 11–13 ft 11–13 ft

These elevation ranges were developed by reviewing tidal datums for the two estuaries (table 3) 

and comparing those datums to field knowledge of the Yaquina and Alsea estuaries gained during 

multiple projects (Brophy, 1999, 2003, 2004, 2006, 2009; Brophy and Christy, 2008, 2009, 2010; 

Brophy and others, 2011).

Table 3. Tidal datums for the Yaquina and Alsea estuaries, Oregon.

[MLLW= Mean Lower Low Water; MHHW= Mean Higher High Water; HMT=Highest Measured Tide.]

Yaquina estuary Alsea estuary

Source MLLW MHHW HMT MLLW MHHW HMT

National Oceanographic 

Atmospheric Administration

(2012)

-0.7 7.6 11.5 n/a n/a n/a

Brew and others (2007) -0.7 7.6 n/a -0.22 7.5 n/a

Buckley (2006) -0.8 8.2–8.81 12.3 n/a 6.5 10.7

Hamilton (1984) 2 -0.6 7.7 11.7 0.0 7.7 12.0

1 Where a range of values is provided, the range includes all locations within the specified estuary, as provided by the source

at left. The entry “n/a” indicates the value was not provided relative to the NAVD88 geodetic datum.

2 Hamilton (1984) provides elevations relative to the NGVD29 or NGVD29(47) datum. Elevations relative to the NAVD88 

datum were determined by applying the elevation adjustments at http://www.ngs.noaa.gov/cgi-bin/VERTCON/vert_con.prl. 

The elevation zones defined in table 2 were deliberately broad to reflect the range of published 

values in table 3 and the limited number of field studies of inundation regimes in the Yaquina and Alsea 

estuaries. Because this analysis focused on the upper limits of tidal influence, the elevation zones in 

table 2 did not subdivide elevations below Mean Higher High Water (MHHW). 

The elevation zones in table 2 extended well above MHHW for several reasons: First, studies 

have documented that brackish high marsh and brackish to freshwater tidal swamps (scrub-shrub and 

forested tidal wetlands) in Oregon generally are found at elevations well above MHHW. For example, at 

the Bandon Marsh National Wildlife Refuge in the Coquille River estuary, the elevation of a forested 

tidal wetland in the lower estuary (bay fringe) was 8.2 ft NAVD88, which is 1.2 ft above MHHW 
8

(Brophy and van de Wetering, 2012). At a strongly fluvial site in the Siuslaw River estuary, the 

elevation of a freshwater tidal wetland was 8.6 ft NAVD88 (1.5 ft above MHHW); model simulations

showed that this site is tidally inundated about 2 percent of the time during typical months of December 

and January (Brophy, 2009). Second, inundation at these high tidal wetlands is the product of both tidal 

forces and river flows (fluvial forces). As indicated in table 2, inundation in elevation zone 2 is 

primarily seasonal. Combined tidal and fluvial inundation occurs more often in winter when river flows 

are high (Brophy, 2009; Brophy and others, 2011). The contribution of river flow to tidal amplitude is 

particularly strong in the middle and upper estuary where river valleys are more confined (Brophy, 

2009; Brophy and others, 2011; Huang and others, 2011). Model simulations have not yet fully explored 

the highest potential elevations of this combined fluvial-tidal inundation. 

Finally, dense vegetation may interfere with the LiDAR signal, resulting in “bare earth” 

elevations that are higher than the actual ground surface elevation (Gopfert and Heipke, 2006). This 

effect is particularly pronounced in the freshwater tidal zone (upper estuary) in dense monotypic stands 

of slough sedge (Carex obnupta) and reed canarygrass (Phalaris arundinacea) (Brophy and van de 

Wetering, 2012). 

Land surfaces within the lowest elevation zone (<8 ft for the Alsea estuary, <9 ft for the 

Yaquina) are clearly tidal wetlands, based on information from previous studies (Brophy, 2009; Brophy 

and others, 2011), tidal datums (table 3), and data provided by EPA. For example, EPA analysis of 

National Oceanic and Atmospheric Administration (NOAA) tidal height records from 2004 to 2008 

show that in the lower Yaquina estuary, wetlands at 9.0 ft NAVD88 (1.4 ft above MHHW) are 

submerged by tidal waters at least once per month year-round (J. Stecher and C. Janousek, unpub, data, 

2011). The next elevation range (8–11 ft for the Alsea, 9–11 ft for the Yaquina) includes land surfaces 

likely to experience tidal inundation during winter, or in spring and fall during spring tide cycles or high 

river flows. The top elevation range (11–13 ft) covers the range of NOAA values for HMT (Highest 

Measured Tide) recorded at NOAA’s local tidal stations and therefore includes potential waters of the 

State, as either Tidal Waters (OAR 141–085–0515(2)) or wetlands (OAR 141–085–0510(97)), as 

described in Oregon administrative rules. However, this higher range was not used in our final analysis, 

as tidal wetlands in the Yaquina and Alsea estuaries generally occurred below this elevation range. 

To determine the percentage of each NWI polygon that occurred within the elevation zones in 

table 2, the NWI data were first reprojected to Oregon Statewide Lambert NAD83 HARN to match the 

projection of the LiDAR-derived elevation datasets. The LiDAR raster dataset (DEM) for each estuary 

was then reclassified using Environmental Systems Research Institute (ESRI) Spatial Analyst to create 

two new discrete raster datasets: Dataset 1: Value of 1 = <9 ft (Yaquina) or <8 ft (Alsea), value of 0 =

other elevation; Dataset 2: Value of 1 = 9–11 ft NAVD88 (Yaquina) or 8–11 ft (Alsea), value of 0 =

other elevation. The NWI polygons were then intersected with these two discrete raster datasets using 

the “Isectpolyrst” command with proportion = TRUE in the ArcMap Geospatial Modeling Environment. 

This created a new attribute in the NWI layer showing the percent of each NWI polygon with a value of 

1 or 0 for each of the two elevation classes (<8 ft versus 8-11ft for the Alsea; <9 ft versus 9–11 ft for the 

Yaquina). 

NWI polygons with more than 25 percent of their area in these two elevation zones were 

compared to aerial photographs, field knowledge of the estuaries, and data from other studies (Brophy, 

2003, 2004, 2007b, 2007c, 2009; Brophy and Christy, 2008, 2009; Brophy and others, 2011). The 25

percent threshold was based on these studies and data from other Oregon estuaries (Brophy and van de 

Wetering, 2012), and allowed for potential vegetation interference with the LiDAR signal as well as the 

fluvial contribution to water levels previously described. NWI polygons, which were considered very 

likely to be current or former tidal wetlands (based on aerial photograph interpretation, field knowledge, 
9

and other data), were selected and the appropriate Cowardin et al. classification was assigned (see 

section, “Wetland Classification”). The selected NWI polygons were then merged (Editor/Merge tool in 

ESRI ArcMap) to form the Prioritization Sites identified in the 1999 Yaquina and Alsea River Basins 

Estuarine Wetland Site Prioritization (Brophy, 2009) (see section, “Creation of GIS Data for 1999 Tidal 

Wetland Prioritization”).

For extensive tide gated lands like Boone Slough, Nute Slough, Depot Slough, and Olalla 

Slough in the Yaquina estuary, few visual indicators remain of former tidal status. Substantial portions 

of these tide gated lands are within the <9 ft and 9–11 ft elevation zones, but are classified in the NWI 

as upland; however, these were very likely tidal wetlands prior to construction of the tidal flow barriers. 

A separate procedure to map these likely former tidal wetlands was developed to assist planning for 

future restoration projects (see section, “Likely Former Tidal Wetlands Classified as Upland in the 

NWI”).

As in the 1999 prioritization (Brophy, 1999), lands that have been filled and converted to 

developed uses were excluded from this study, even if they were within tidal range. Examples include 

the former log storage yard at the Siletz Tribes mill just downstream of Mill Creek, on the northern bank 

of the Yaquina River, and industrial lands on the banks of the Yaquina in the city of Toledo. 

Wetland Classification

Expert knowledge of the Yaquina and Alsea estuaries, LiDAR-derived elevations, salinity data 

provided by EPA, and recent aerial photographs were used to determine the correct Cowardin et al.

system, subsystem, class, hydrologic modifiers, and special modifiers for each NWI polygon identified 

as a tidal wetland using the methods described in the “LiDAR Analysis” Section. For consistency, these 

revisions followed the same definitions of wetland systems, subsystems, and classes used in the NWI 

(Cowardin et al. 1979). The elevation zones in table 1 were not used to classify the wetlands; they were 

used only for the previously described LiDAR analysis. 

The highest-resolution aerial photographs available at the time of this study were color infrared 

photographs acquired jointly by Department of Land Conservation and Development (DLCD) and EPA

during 2004–06 (Oregon Department of Land Conservation and Development and others, 2007a,

2007b). These images had 0.25 m ground pixel resolution. The DLCD-EPA imagery was supplemented 

by 2005 true color NAIP imagery (digital ortho quarter-quads, 0.5 m ground pixel resolution). 

Photograph interpretation was used to identify tidal channels, brackish versus freshwater vegetation, 

topographic transitions, developed lands, dikes, restrictive culverts, and tide gates, and other features 

that helped distinguish between tidal wetlands and nontidal wetlands or uplands, and to provide other 

information needed for wetland classification. Recommended classifications also drew on other field 

studies of tidal wetlands in the Yaquina, Alsea, and other Oregon estuaries (Brophy, 2003, 2004, 2007b, 

2007c, 2009, 2012; Brophy and Christy, 2008, 2009, 2010; Brophy and others, 2011), and salinity data 

provided by EPA (C. Brown and C. Janousek, written commun, 2011).

Estuarine versus Palustrine System (salinity regime) 

Wetlands with salinity equal to or greater than 0.5 (originating from marine salts) during low 

flow (summer and early fall) are classified in the Cowardin et al. system as estuarine wetlands 

(Cowardin et al. 1979). Tidal wetlands with salinities less than 0.5 (freshwater tidal wetlands) are 

classified as palustrine wetlands, and are assigned a “water regime modifier” to indicate tidal influence. 

Cheryl Brown of EPA provided a shapefile containing salinity data for the Yaquina estuary 

originating from many sources (more than 8,000 data points originating from EPA and the Oregon 

Department of Environmental Quality). Almost all measurements were on the main stem river, but
10

sampling depth was variable (Cheryl Brown, written commun., 2011). Despite the NWI’s classification 

of tidal wetlands as palustrine upstream of river mile 14, these data showed late summer and early fall 

salinities in the range of 5–10 as far upstream as river mile 19.5, near the upstream limit of tidal 

wetlands in the estuary. Therefore, only very limited areas were classified as palustrine, tidally

influenced wetlands. Additional data from upper Poole Slough on the Yaquina likewise revealed that 

other wetlands designated as palustrine tidal in the NWI are actually brackish habitats (C. Janousek and 

C. Folger, unpub. data, 2011).

For the Alsea estuary, data from previous field studies (Brophy, 2003, 2006; Brophy and 

Christy, 2008, 2009, 2010) were used to determine which wetlands should be classified in the estuarine 

system versus the palustrine system. Field observations of vegetation were the primary means for this 

classification; dominance by brackish-tolerant species (based on field knowledge and Adamus, 2005) 

indicated wetlands that should be placed in the estuarine system.

Salinity in a tidal wetland may differ from salinity in the adjacent tidal water body. For example, 

a forested tidal wetland near the hillslope base may have much lower salinity than the nearby tidal river 

because of freshwater drainage from the nearby uplands (Brophy, 2009; Brophy and van de Wetering, 

2012). Where specific field data were not available, the aerial photographs (previously described) were 

used to help determine estuarine versus palustrine classification. Reed canarygrass (Phalaris 

arundinacea) (fig. A14) and red alder (Alnus rubra) (figs. A15–A16) are two species that are 

identifiable in aerial photographs and do not tolerate much salinity, based on our field experience and

Adamus (2005). Aerial photographs were used to identify tidal wetlands that were dominated by these 

species, and these areas were classified as tidally influenced palustrine wetlands. 

Cowardin et al. (1979) Classification Modifiers

Water regime (hydrologic) modifiers and special modifiers were included in our recommended 

Cowardin et al. classifications. Although the mapping standard used by the NWI does not require 

special modifiers for estuarine habitats (Federal Geographic Data Committee, 2009), the special 

modifiers we have provided in our mapping contain crucial information and should therefore be 

retained. Modifiers were used according to the definitions provided in Cowardin et al. (1979).

Water Regime Modifiers

When the Cowardin et al. classification is applied to Oregon estuaries, low salt marsh generally

is assigned the “N” modifier, which is defined as “regularly flooded” (“tidal water alternately floods and 

exposes the land surface at least once daily”) (Cowardin et al. 1979, p. 21), and high estuarine marsh is

generally assigned the “P” modifier, which is defined as “irregularly flooded” (“tidal water floods the 

land surface less often than daily”) (Cowardin et al. 1979, p. 21). In general, the water regime modifiers 

for wetlands already classified as estuarine in the NWI were not revised, because they were fairly 

accurate. However, “irregularly flooded” is not an accurate description of the high marsh inundation 

regime. Field measurements and model simulations indicate that high marsh is in fact regularly flooded, 

although much less often than low marsh. The typical pattern is inundation during higher high tides on 

spring tide cycles, once or twice a month (Brophy, 2009; Brophy and others, 2011). For NWI polygons 

that were classified as palustrine but the correct classification was estuarine (based on salinity data, as 

previously described), the “N” and “P” modifiers were applied as appropriate, based on elevation and 

our knowledge of the specific location. Estuarine scrub-shrub and estuarine forested wetlands (E2SS 

and E2FO) were assigned the “P” modifier, because in our study area these wetland types generally do 

not flood daily. 
11

For tidally influenced palustrine wetlands, the Cowardin et al. classification offers the same 

hydrologic regime modifiers used in nontidal systems, but with the word “tidal” added: R = seasonally 

flooded (tidal), S = temporarily flooded (tidal), T = semipermanently flooded (tidal), and V =

permanently flooded (tidal). These modifiers are not well-suited to the observed flooding regimes in 

freshwater tidal wetlands of Oregon. Regular flooding of tidally influenced palustrine wetlands has been 

documented during spring tide cycles throughout the year, with more frequent flooding during high 

winter flow periods (Brophy, 2007b, 2009; Brophy and others, 2011). Given limited classification 

options, the best-suited hydrologic modifier from the Cowardin et al. system (seasonally flooded (tidal)) 

was used for all tidally influenced palustrine wetlands in our study areas.

Special Modifiers

Special modifiers generally describe wetland alterations. These modifiers were applied based on 

local knowledge and aerial photograph interpretation. As previously described, these modifiers contain 

crucial information and should not be viewed as optional in the revised NWI classification, although the 

NWI mapping standard does not require their use (Federal Geographic Data Committee, 2009). 

Former tidal wetlands behind dikes, tide gates, and restrictive culverts should be classified in the 

NWI as diked wetlands (modifier “h”). However, many of these areas lack the “h” modifier in existing 

NWI mapping. In some cases, this may be because of the NWI’s reliance on remote data. Field work is 

often needed to identify hydrologic alterations, especially restrictive culverts and tide gates. 

Identifying lands protected by dikes was of critical importance for the USGS climate change 

project modeling efforts targeted at identifying potential estuarine habitats at risk to sea-level rise. In an 

analysis of elevation ranges for NWI classes, lands behind dikes without the “diked” modifier created an 

artificially low elevation range for some wetland classes (D. Reusser and R. Loiselle, unpub. data,

2012).

The diked modifier was added to all NWI polygons which were considered likely to be former 

tidal wetlands with hydrology affected by dikes, tide gates, or restrictive culverts (identified using 

LiDAR-derived elevations, aerial photographs, and expert local knowledge of the estuaries). The 

polygons to which the diked modifier was applied were at low elevations (usually below 8 or 9 ft

relative to MLLW), and were located behind (landward of) the dikes, tide gates, and restrictive culverts. 

In major tributary and slough systems like Boone Slough, Nute Slough, Depot Slough, and Olalla 

Slough, some of these polygons were located at a considerable distance from the dike or tidal restriction. 

Nevertheless, use of the diked modifier seemed appropriate because elevations generally were low, and 

these large slough systems were likely to have had strong tidal forcing prior to alteration.

Likely Former Tidal Wetlands Classified as Upland in the NWI 

In the major diked tributaries of the Yaquina estuary—Boone Slough, Nute Slough, Depot 

Slough, and Olalla Slough—low-elevation land surfaces were extensive and were classified as upland in 

the NWI. These lands generally were less than 9 ft NAVD88. Similar low-elevation lands classified as 

upland in the NWI were identified in the middle and upper Alsea estuary. It seems likely that these were 

once tidal wetlands. However, the hydrology is currently altered by tide gates and extensive ditching 

and diking, so field investigation would be needed to determine whether these low-elevations lands are 

currently wetlands, and if so, their correct Cowardin et al. classification. We added these low-lying 

former tidal wetlands to the Enhanced NWI maps by cutting the upland polygon at an elevation of 11 ft

NAVD88 based on the LiDAR data, using Editor/Split in ArcMap. An 11 ft elevation cutoff was used 

for consistency with the previously described LiDAR analysis (table 2). In lieu of a Cowardin et al.

classification, the code FTW (Former tidal wetland) was assigned to these polygons, with the note
12

“likely former tidal wetland/tidal waters of the State.” The former tidal wetland polygons also were 

added to the Prioritization Sites by merging them with the adjacent NWI polygons, as described in 

section, “Creation of GIS Data for 1999 Tidal Wetland Prioritization Sites”.

Creation of GIS Data for 1999 Tidal Wetland Prioritization Sites

As described in section, “Project Goals and Objectives”, one goal of this study was to generate 

GIS data (shapefiles) for the prioritization sites defined in the 1999 tidal wetland prioritization for the 

Yaquina and Alsea estuaries (Brophy, 1999) and characterize any major changes at the prioritization 

sites since 1999. The 1999 study identified and characterized current and likely former tidal wetlands in 

the Yaquina and Alsea estuaries, and divided the wetlands into 78 sites suitable for action planning 

purposes (43 in Yaquina, 35 in Alsea). These sites are referred to as prioritization sites in this report. 

The 1999 study then used ecological criteria to prioritize these 78 sites for conservation and restoration 

activities. Paper maps of the approximate locations of the 78 prioritization sites were provided with the 

1999 report, but no GIS data were produced. The current project updated the 1999 study by providing

GIS layers of the prioritization sites. The 1999 project and the current study are intended for use in 

strategic planning of voluntary conservation and restoration efforts; note however, that these products 

are not intended for regulatory use (Brophy, 1999). Consistent with the Oregon Estuary Assessment 

method (Brophy, 2007a), the 1999 study and the current study included emergent, scrub-shrub, and 

forested wetlands, but algal beds, seagrass beds, and mudflats were not included.

GIS mapping and characterization of prioritization sites for the current study drew upon many 

data sources. Primary data sources were the LiDAR-derived elevations, NWI maps, and aerial 

photographs previously described. Other data included mapping of tidal wetlands and potential tidal 

wetlands provided by Scranton (2004), historical vegetation data, other GIS and tabular data sources, 

and expert local knowledge of the two estuaries derived from previous field studies ((Brophy, 2003, 

2004, 2007b, 2007c, 2009; Brophy and Christy 2008, 2009; Brophy and others, 2011).

The Oregon Watershed Assessment Manual, Estuary Assessment module (Brophy, 2007a)

describes in detail how prioritization sites are created. Because individual NWI polygons are too small 

and numerous, they were merged to form larger analysis units based on hydrology, alterations, and land 

use history (fig. 3). These units (prioritization sites) are suitable for planning wetland restoration and 

conservation actions at the basin scale. In some cases, a prioritization site consisted of a single NWI 

polygon. However, in a few cases NWI polygons were split because of differences in the level of habitat 

alteration within a single polygon. Details on methods for defining prioritization sites are described in 

Brophy (2007a). The availability of LiDAR-derived elevations and recent aerial photography enabled 

identification of several new prioritization sites that had not been identified in the 1999 study (see

section, “New Prioritization Sites Added to 1999 Study”). New prioritization sites were created only if 

the underlying NWI polygons totaled more than 1 acre.
13

Figure 3. Illustration of the relationship between prioritization site designation and National Wetland Inventory

polygons. In this example from the Alsea estuary, Oregon, the pink shaded area is a single prioritization site (Site 

A21 in fig.7) composed of 12 underlying NWI polygons (dark pink outlines). The NWI polygons were merged to 

form the prioritization site, based on their similar alteration level, land use history, and hydrologic connectivity. NWI 

polygons outside the pink prioritization site are non-tidal wetlands or wetlands in tidal wetland classes not included 

in this study (brown and green shaded areas plus the white river channel); or uplands (white areas at edges of 

figure).

Action planning for wetland restoration and conservation requires knowledge of conditions such 

as habitat alterations, dominant vegetation, land use, and potential restoration actions. The 1999

prioritization for the Yaquina and Alsea estuaries (Brophy, 1999) provided this information for each 

prioritization site in spreadsheet format. These prioritization site characteristics (table 2) were 

transferred as attributes to the GIS data generated in this project. In addition, major changes in 

prioritization site conditions since 1999 were identified through interpretation of the LiDAR data and 

aerial photographs, and by incorporating expert local knowledge, as previously described. These 

changes were listed as attributes in the prioritization site GIS shapefiles (attributes 8, 11, 13, 16, 18, 20,

and 22 in table 4).
14

Table 4. Table of attributes for GIS layer of prioritization sites to accompany 1999 tidal wetland prioritization.

[ Note: the value “n/a” for any attribute indicates that field was not used in the 1999 report.]

Attribute 

number Attribute name Description

1 FID Feature ID (generated by ArcMap)

2 Shape Feature type (generated by ArcMap)

3 GPC_site GPC site number

4 Area_acres Site size (acres)

5 Site_name Name of site (if any)

6 TRS TRS location (Township, Range, Section)

7 Descrip99 General description of wetland conditions and location (1999 data)

8 Descr2010 General description of wetland conditions and location in 2010 (if different from 

1999)

9 Own_num99 Approximate number of landowners (1999 data)

10 Veg_typ99

Vegetation description, using classification from Oregon Estuary Plan Book 

(Cortright and others 1987) (1999 data). Dominant species listed where possible, 

based on field observation.

11 Veg_2010

Vegetation description in 2010 (if different from 1999), using classification from 

Oregon Estuary Plan Book (Cortright and others 1987). Dominant species listed 

where possible, based on field observation.

12 Alter99 Alteration type(s) (1999 data)

13 Alt2010 Alteration type(s) in 2010, if different from 1999

14 Altdate99 Date of alteration, determined from historic aerial photographs (1999 data)

15 Action99 Possible restoration actions (1999 data)

16 Actn2010 Possible restoration actions in 2010 (if different from 1999)

17 LandUse99 Current land use (1999 data)

18 LndUs2010 Current land use in 2010 (if different from 1999 data)

19 LandAdj99 Adjacent land use (1999 data)

20 LndAdj10 Adjacent land use in 2010 (if different from 1999)

21 Stream99 Connections to streams (1999 data)
15

Attribute 

number Attribute name Description

22 Strm2010 Connections to streams (2010, if different from 1999 data)

23 Expert991 Comments from experts, part 1 (1999 data)

24 Expert992 Comments from experts, part 2 (1999 data)

25 Nxtstp991 Recommended next steps for action planning for wetland restoration/conservation, 

part 1 (1999 data)

26 Nxtstp992 Recommended next steps for action planning for wetland restoration/conservation, 

part 2 (1999 data)

27 Reprts991 Other reports that mention the site, part 1 (1999 data) – see full report (Brophy, 1999) 

for key to abbreviations

28 Reprts992 Other reports that mention the site, part 2 (1999 data) – see full report (Brophy, 1999) 

for key to abbreviations

29 GIS_2010 Notes on creation of GIS layer in 2010

Results

Recommended Revisions to Cowardin et al. (1979) Classification

The enhanced NWI shapefiles contain recommended revisions to the Cowardin et al.

classification (system, subsystem, class, and/or modifiers) for 286 NWI polygons in the Yaquina estuary 

(1,133 acres) and 83 NWI polygons in the Alsea basin (322 acres) (figs. 4 and 5). Many of the changes 

consisted of adding the “diked” modifier to diked former tidal wetlands that are currently palustrine 

wetlands. For example, PEMC was changed to PEMCh for 514 acres in the Yaquina estuary, and 

PEMA was changed to PEMAh for 32 acres in the Alsea estuary (tables 5 and 6). Other common 

changes were the addition of a tidally influenced hydrologic modifier to palustrine wetlands, and a 

change from the palustrine to the estuarine class based on field measurements of salinity data. 

Substantial acreages of likely former tidal wetland were identified that are currently classified as upland 

in the NWI (tables 5 and 6; see section, “Likely Former Tidal Wetlands Classified as Upland in the 

NWI”)

Likely Former Tidal Wetlands Classified as Upland in the NWI 

Analysis of LiDAR data revealed many likely former tidal wetlands that were classified as 

upland in the National Wetlands Inventory (64 NWI polygons totaling 441 acres in the Yaquina estuary, 

and 16 NWI polygons totaling 51 acres in the Alsea estuary) (figs. 4 and 5; tables 5 and 6). Cowardin et 

al. classification of these former tidal wetlands was beyond the scope of this project because field 

evaluation would have been needed to determine the hydrologic status of these areas. 

.
16

Figure 4. Map of recommended National Wetland Inventory Cowardin et al. (1979) classification revisions resulting from this project for the Yaquina 

estuary, Oregon, including areas identified as likely former tidal wetlands (“FTW”). NWI polygons without recommended revisions are shown as 

outlines only (fill=background color). Source data: Table 7-Yaquina_tidal_NWI_2011. Projection: UTM Zone 10N NAD83.
17

Figure 5. Map of recommended National Wetlands Inventory Cowardin et al. (1979) classification revisions resulting from this project for the Alsea 

estuary, Oregon, including areas identified as likely former tidal wetlands (“FTW”). NWI polygons without recommended revisions are shown as 

outlines only (fill=background color). Source data: Table 7-Alsea_tidal_NWI_2011. Projection: UTM Zone 10N NAD83.
18

Table 5. Total area (acres) of recommended changes to NWI Cowardin et al. classification, by original NWI classification. Yaquina estuary, Oregon. 

[Table includes only those original and revised classifications that totaled more than 1 acre]

Recommended revised Cowardin et al. classification (or other designation*): area in acres

E2EM/SSP

E2EMP

E2FOP

E2SSP

FTW1

PABF

PEM/SSCh

PEM/SSR

PEMAdh

PEMAhPEMCh

PEMFhPFOAh

PFOR

PSS/EMAhPSS/EMCh

PSSAhPSSCh

PSSR

Total

Original NWI classification

PABF 5.8 5.8

PEM/SSA 15.9 15.9

PEM/SSC 18.1 14.3 32.4

PEMA 4.0 38.9 170.1 10.1 227.4

PEMAh 19.5 19.5

PEMC 3.3 514.3 518.0

PEMCd 46.3 46.3

PEMF 21.3 21.3

PEMR 49.3 1.1 51.2

PFOA 1.8 6.4 16.1 24.6

PFOC 2.4 0.4 5.7

PSS/EMA 8.8 8.8

PSS/EMC 36.6 36.6

PSSA 9.0 10.9 6.1 27.8

PSSC 60.3 60.3

PSSR 3.8 2.9 6.7

U 1.8 441.0 442.8

Total 18.1 128.2 5.5 13.5 441.0 5.8 14.3 15.9 38.9 170.1 525.5 21.3 6.4 16.8 8.8 36.6 10.9 63.2 6.1 1574.4

1

FTW is not a Cowardin et al. classification, but a designation indicating a likely Former Tidal Wetland, currently disconnected from tidal flow but with land 

surfaces at elevations within tidal range.
19

Table 6. Total area (acres) of recommended changes to NWI Cowardin et al. classification, by original NWI classification. Alsea estuary, Oregon. 

[Table includes only those original and revised classifications that totaled more than 1 acre]

Recommended revised Cowardin et al. classification (or other designation*): area in acres

E2EMN

E2EMP

E2FOP

E2SSP

E2USN

FTW1

PEMAdh

PEMAhPEMCh

PEMR

PFOAh

PFOR

FOAh

PSS/

FOCh

PSS/

PSSAh

PSSR

Total

Original NWI classification

PEMA 21.8 31.8 13.2 66.8

PEMAd 75.3 75.3

PEMC 2.7 9.9 4.5 17.1

PEMCh 7.3 7.3

PEMR 51.3 51.3

PEMS 8.3 8.3

PFOA 1.5 10.5 12.0

PFOB 1.7 1.7

PFOCh 2.4 2.4

PFOR 4.4 4.4

PSS/FOA 24.3 24.3

PSS/FOC 3.2 3.2

PSSA 1.5 1.8 1.9 5.2

PSSR 6.6 6.6

R1UBV 2.2 2.2

R1UBVh 5.9 5.9

U 12.5 4.5 0.6 51.0 6.3 74.9

Total 12.5 84.1 12.9 7.2 8.0 51.0 75.3 31.8 9.9 24.9 10.5 11.0 24.3 3.2 1.8 1.9 373.0

1

FTW is not a Cowardin et al. classification, but a designation indicating a likely Former Tidal Wetland, currently disconnected from tidal flow but with land 

surfaces at elevations within tidal range.
20

GIS Data for 1999 Prioritization Sites

GIS datasets were created for the 1999 prioritization sites as well as for several new 

prioritization sites in each estuary (figs. 6 and 7). The GIS datasets contain 49 prioritization sites 

totaling 2,177 acres in the Yaquina estuary, and 39 prioritization sites totaling 1,045 acres in the Alsea 

estuary. The prioritization sites consisted of 494 and 192 underlying NWI polygons in the Yaquina and 

Alsea estuaries, respectively. 

New Prioritization Sites

Previously described LiDAR-derived elevations and NWI classification analysis allowed us to 

identify tidal wetlands (or former tidal wetlands) that had not been described in the 1999 study. In most 

cases, these tidal wetlands were already classified as wetlands in the NWI, but they were not previously 

classified as tidal wetlands nor did they have special modifiers suggesting hydrologic alterations that 

would restrict tidal flows. In two cases, new sites were identified that were classified as upland in the 

NWI, but which were at elevations within tidal range. These two cases were prioritization sites A38 and 

A40, on land owned by U.S. Forest Service (USFS) and U.S. Bureau of Land Management (BLM), near 

the Drift Creek tidal wetland restoration project (prioritization site A26) (fig. 7). LiDAR data were used 

to digitize new prioritization site boundaries using the methods described in section, “Likely Former 

Tidal Wetlands Classified as Upland in the NWI”. 

The new prioritization sites in each estuary are listed, with approximate acreages. Field visits by 

a knowledgeable wetland scientist are recommended to determine the state and federal regulatory 

status of these areas.

• Yaquina estuary: New prioritization sites (fig. 6)

o Site Y44 (7 acres): Partially filled forested tidal wetland at the mouth of Olalla Slough.

o Site Y45 (13 acres): Diked pasture in the upper estuary, probably former tidal swamp. 

o Site Y46 (4 acres): Diked pasture in the upper estuary, probably former tidal swamp.

o Site Y47 (12 acres): Undiked tidal swamp (forested and scrub-shrub tidal wetland) in the upper 

estuary.

o Site Y48 (2 acres): Fringing marsh on south bank of the Yaquina River, just upstream of site Y3.

o Site Y49 (3 acres): Undiked tidal marsh just outside the tide gates on Depot Slough.

• Alsea estuary: New prioritization sites (fig. 7)

o Site A38 (8 acres): Tidal marsh and tidal swamp (forested tidal wetland) on the northern bank of 

Drift Creek at river mile 2. This is a USFS restoration site.

o Site A39 (6 acres): Freshwater tidal marsh (probably former tidal swamp) at river mile 3 on Drift 

Creek.

o Site A40 (9 acres): Forested tidal wetland or former tidal wetland, immediately east of the large 

USFS tidal marsh restoration area on Drift Creek. A site visit or information from USFS is 

needed to determine the current hydrologic status.

o Site A41 (2 acres): Small possible tidal swamp opposite mouth of Risley Creek and Bain 

Slough.
21

Figure 6. Map of tidal wetlands and likely former tidal wetlands of the Yaquina River estuary, Oregon: prioritization sites from the 1999 tidal wetland 

prioritization (Brophy 1999), plus new sites identified in the current study (sites Y44 through Y49). Prioritization sites, created by merging NWI 

polygons, provide analysis units suitable for action planning for tidal wetland restoration and conservation. Colored areas are prioritization sites; each 

site is colored separately, and labels indicate site numbers. Background is NWI mapping (gray lines). Projection: UTM Zone 10N NAD83.
22

Figure 7. Map of tidal wetlands and likely former tidal wetlands of the Alsea River estuary, Oregon: Prioritization sites from the 1999 tidal wetland 

prioritization (Brophy 1999), plus new sites identified in the current study (sites A38 through A41). Prioritization sites, created by merging NWI 

polygons, provide analysis units suitable for action planning for tidal wetland restoration and conservation. Colored areas are prioritization sites; each 

site is colored separately, and labels indicate site numbers. Background is NWI mapping (gray lines). Projection: UTM Zone 10N NAD83. 
23

Revisions to Prioritization Site Attributes

New information on prioritization site characteristics (changes since 1999, or information not 

provided in 1999) was generated for 15 of 49 prioritization sites in the Yaquina estuary and 8 of 39 

prioritization sites in the Alsea estuary. The new information can be found in the attribute tables of the 

prioritization site shapefiles (see section, “Downloadable Wetland Shapefiles”). Most of the new 

information relates to restoration activities or field observations since 1999.

Recommendations 

Time limitations prevented digitization of all likely former tidal wetlands. For example, many

narrow bands of floodplain were classified as upland in the NWI, but had elevations within our defined 

9–11 or 11–13 ft elevation zones. These floodplains also are likely tidal wetlands, former tidal wetlands, 

and/or tidal waters potentially subject to State and Federal regulations, but these areas were not added to 

the NWI shapefile. Despite their narrow width, tidal floodplains provide important ecosystem services 

for aquatic organisms using the main stem rivers. We recommend using LiDAR to map tidal floodplains 

so they can be included in planning for coastal resource conservation and restoration.

This analysis relied heavily on interpretation of high-resolution aerial photographs acquired in 

2005 by Oregon Department of Land Conservation and Development (DLCD) and EPA (Oregon 

Department of Land Conservation and Development and others, 2007a, 2007b). Field observations in 

2010 indicated that changes have occurred at some prioritization sites since production of these 2005 

photographs. NAIP (National Agricultural Imagery Program) orthophotographs were flown in 2009, but 

were not yet available as of the writing of this report. Regular review of field conditions is 

recommended to update the information provided in this report. Field visits by knowledgeable wetland

scientists (after obtaining landowner permission for access) would be particularly useful.

Since completion of the data layers in 2010, GIS inventories of dikes and tide gates in Oregon 

estuaries have become available (Mattison, 2011a, 2011b). The information in these GIS inventories 

generally is consistent with this project’s products; additional detail is provided for some dikes and tide 

gates. Review of the dike and tide gate inventories is recommended when updating this project’s 

shapefiles, and when planning site-specific actions. 

LiDAR data constitute a powerful new tool for studies like this one, with potential utility beyond 

the present report. For example, the LiDAR data could be used to digitize new boundaries for NWI 

polygons, provided on-site validation of wetland conditions is conducted. Additional effort is 

recommended to fully utilize the LiDAR data to assist strategic planning for tidal wetland conservation 

and restoration. 

In some parts of the estuary, particularly the freshwater tidal zone, it is likely that the LiDAR 

signal did not successfully penetrate dense herbaceous vegetation, resulting in “bare earth” elevations 

that are higher than the actual land surface. Vegetation interference with the LiDAR signal has been 

documented (Gopfert and Heipke, 2006). In Oregon, LiDAR-derived elevations are sometimes 1–2 ft 

higher than actual ground surfaces in areas of dense slough sedge and reed canary grass (Brophy, 2012;

Brophy and van de Wetering 2012). Because of this potential inaccuracy, ground-truthing of the 

LiDAR bare earth model is recommended, particularly for site-specific planning and restoration design.

Intended Uses and Limitations of Mapping

These data are intended to be used for planning purposes only and are non-regulatory in nature. 

The recommended revisions should be included in the NWI to improve its accuracy, but our methods 
24

and suggested wetland classification revisions should be reviewed by NWI staff to ensure they meet 

NWI standards. As is always the case with NWI mapping, users should be aware that there may be 

upland areas within mapped wetlands, and there may be unmapped wetlands and tidal waters that are 

subject to State and/or Federal regulation per State Removal-Fill Law, Federal Clean Water Act or 

Federal Rivers and Harbors Act. Furthermore, because the NWI uses the Cowardin et al. definition of a 

wetland, which differs from the definition of a regulatory wetland subject to State and Federal 

regulations, not all NWI wetlands are necessarily subject to regulation.

Downloadable Wetland Shapefiles

This report contains Geographic Information System (GIS) data in georeferenced vector 

(polygon) format. The vector (polygon) data are available as Environmental Systems Research Institute 

(ESRI) shapefile files. Shapefiles generally include *.shp, *.shx, *.xml, and *.dbf files at a minimum. 

All these data also include *.prj files which contain the dataset projection information. The GIS 

shapefiles have been bundled with their corresponding Federal Geographic Data Committee (FGDC)-

compliant metadata into compressed zip files.

To download the data, right-click on the appropriate filename hotlink below. Then select 'Save 

Target As...' to save the file to your local hard drive.

The following products were created in the course of this study:

1. GIS datasets (shapefile format) of NWI polygons in the Yaquina and Alsea estuaries, 

containing recommended revisions to the NWI classification 

(Yaquina_tidal_NWI_2011.shp and Alsea_tidal_NWI_2011.shp, respectively). Datasets 

include metadata, based on the metadata provided by EPA for the original Yaquina NWI 

layer.

2. GIS datasets (shapefile format) of the prioritization sites identified in the 1999 prioritization 

of tidal wetlands in the Yaquina and Alsea estuaries (Brophy, 1999): 

Yaquina_tidal_wetlands_2011.shp for the Yaquina estuary, and 

Alsea_tidal_wetlands_2011.shp for the Alsea estuary. Attribute tables contain all publicly

available data in the original site information tables, as well as updates from this project. 

Metadata are included with the shapefiles.
25

Table 7. Downloadable Wetland Shapefiles

[The projection for all GIS products is Oregon Lambert HARN (international feet), matching the projection of the LiDAR datasets used in the analysis.]

File Name Description Size Download Link

Yaquina_tidal_NWI_2011.zip Shapefile containing recommended revisions to the NWI 

classifications for Yaquina estuary. 1,658 KB http://pubs.usgs.gov/of/2012/1038/data/Yaquina_tidal_NWI_2011.zip

Alsea_tidal_NWI_2011.zip Shapefile containing recommended revisions to the NWI 

classifications for Alsea estuary. 631 KB http://pubs.usgs.gov/of/2012/1038/data/Alsea_tidal_NWI_2011.zip

Yaquina_tidal_wetlands_2011.zip

Shapefile containing prioritization sites identified in the 

1999 prioritization of tidal wetlands in the Yaquina 

estuary and updates from this project.

213 KB http://pubs.usgs.gov/of/2012/1038/data/

Yaquina_tidal_wetlands_2011.zip

Alsea_tidal_wetlands_2011.zip

Shapefile containing prioritization sites identified in the 

1999 prioritization of tidal wetlands in the Alsea estuary 

and updates from this project.

104 KB http://pubs.usgs.gov/of/2012/1038/data/

Alsea_tidal_wetlands_2011.zip

Acknowledgments

Special thanks to a former student contractor Meredith C. Payne for assistance with formatting the report into the U.S. 

Geological Survey (USGS) Open-File Report format, Patrick Clinton of the U.S Environmental Protection Agency (USEPA) for 

assistance with providing the original NWI layers to Greenpoint Consulting, and Christina L. Folger of USEPA for help with 

photograph selection and captions. This publication has been reviewed by personnel of the National Health and Environmental Effects 

Research Laboratory's Western Ecology Division of the USEPA and the Western Fisheries Research Center of the USGS. The 

information in this document has been funded in part by the USEPA. However, approval does not signify that the contents reflect the 

views of the USEPA.
26

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29

Appendix A: Landscapes and vegetation present across study areas in Yaquina 

and Alsea estuaries, Oregon.

Figure A1. Photograph of tidal marsh dominated by Deschampsia cespitosa (tufted hairgrass) at prioritization site 

A5, fig. 7 at Eckman Island in the Alsea estuary, Oregon. Photograph by Christopher Janousek, U.S.

Environmental Protection Agency, September 2010.
30

Figure A2. Photograph of Agrostis stolonifera (creeping bentgrass) at prioritization site A31 in figure 7 in the Alsea 

estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, September 2010.
31

Figure A3. Photograph of Hordeum jubatum (foxtail barley) at prioritization site Y1, fig. 6 in the Yaquina estuary, 

Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, August 2010.
32

Figure A4. Photograph of Juncus effusus (common rush) at prioritization site A24 in fig. 7 in the Alsea estuary, 

Oregon. This species tends to be found at high elevations in lower salinity tidal marshes. Photograph by 

Christopher Janousek, U.S. Environmental Protection Agency, November 2010.
33

Figure A5. Photograph of Juncus balticus ssp. ater (Baltic rush) at prioritization site Y1 in fig. 6 in the Yaquina 

estuary, Oregon. Several species of rushes are found in Oregon tidal wetlands. Baltic rush is the most frequently 

encountered species in high marsh. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, 

May 2010.
34

Figure A6. Photograph of Carex lyngbyei (Lyngybe’s sedge) at prioritization site Y40 in fig. 6 in Poole Slough, 

Yaquina estuary, Oregon. One of the most common tidal marsh species in the Pacific Northwest, Lyngybe’s sedge 

grows in both low and high marsh. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, 

April 2011.
35

Figure A7. Photograph of Carex obnupta (slough sedge) at prioritization site A17 in fig. 7 in the Alsea estuary, 

Oregon. Slough sedge grows in the upper marsh in less saline regions of the estuaries and can also be found in 

freshwater wetlands. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, September 

2010.
36

Figure A8. Photograph of Triglochin maritimum (seaside arrowgrass) at prioritization site Y40 in fig. 6 in Poole 

Slough, Yaquina estuary, Oregon. Seaside arrowgrass is a succulent perennial forb commonly found in low tidal 

marsh. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, May 2010.
37

Figure A9. Photograph of Picea sitchensis (Sitka spruce) at the edge of a marsh along Drift Creek at prioritization 

site A28 in fig. 7 in the Alsea estuary, Oregon. Sitka spruce is the principal foundation species of brackish tidal 

swamps in Oregon. It can also be found growing on nurse logs in estuarine marshes. Photograph by Christopher 

Janousek, U.S. Environmental Protection Agency, December 2011.
38

Figure A10. Photograph of black twinberry (Lonicera involucrata) growing on the bank of a tidal channel in tidal 

swamp at prioritization site Y28 in fig. 6 in the Yaquina estuary, Oregon. Trees in the background are Sitka spruce, 

also growing on the tidal channel banks. Summer surface water salinity at this site is in the mesohaline range (8–

9). Photograph by Laura Brophy, Green Point Consulting, September 2006.
39

Figure A11. Photograph of salt-stressed black twinberry (Lonicera involucrata) with epiphytic lichens and mosses 

in emergent tidal marsh along the main stem of the Alsea River, Oregon at prioritization site A17 in fig. 7. The 

stressed condition of the specimen may be due to high salinity. Photograph by Christopher Janousek, U.S. 

Environmental Protection Agency, September 2010.
40

Figure A12. Photograph of scrub shrub tidal wetland at prioritization site Y40 in fig. 6 in upper Poole Slough, 

Yaquina estuary, Oregon. Dominant shrubs are black twinberry (Lonicera involucrata) and Pacific crabapple (Malus 

fusca). Photograph by Christopher Janousek, U.S. Environmental Protection Agency, September 2010.
41

Figure A13. Photograph of low marsh and algal-dominated mudflats at prioritization site Y34 in fig. 6 near the 

mouth of McCaffery Slough in the Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. 

Environmental Protection Agency, August 2010.
42

Figure A14. Photograph of tidal marsh at prioritization site Y30 in fig. 6 in the upper Yaquina estuary with Phalaris 

arundinacea (reed canarygrass) growing above other emergent vegetation (e.g., Carex, Potentilla). Photograph by 

Christopher Janousek, U.S. Environmental Protection Agency, July 2010.
43

Figure A15. Photograph of red alder (Alnus rubra) on the margin of tidal marsh at prioritization site A27 in fig. 7 in 

the Alsea River estuary, Oregon. Grass in the foreground is Pacific reedgrass (Calamagrostis nutkaensis), typical 

of the ecotone between brackish tidal marsh and brackish tidal swamp. Photograph by Laura Brophy, Green Point 

Consulting, July 2005.
44

Figure A16. Photograph of red alder (Alnus rubra) growing from a nurse log at prioritization site Y1 in fig. 6 in the 

lower Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency,

November 2010.
45

Figure A17. Photograph of low marsh vegetation in a saline marsh at prioritization site Y1 in fig. 6 in the lower 

Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, August 

2010.
46

Figure A18. Photograph of Achillea millefolium (common yarrow) flowers in foreground with Symphyotrichum 

subspicatum (Douglas aster) and Grindelia stricta (coastal gumweed) in background found at prioritization site Y1

in fig. 6 in the Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection 

Agency, August 2010.
47

Figure A19. Photograph of high marsh dominated by Carex lyngbyei and Agrostis stolonifera at prioritization site 

Y30 in fig. 6 in the Yaquina estuary, Oregon. Photograph by Laura Brophy, Green Point Consulting, September 

2006. 
48

Figure A20. Photographs of Potentilla anserina (Pacific silverweed) at (a) prioritization site Y13a in fig. 6 Critesers 

Marsh in the Yaquina estuary, Oregon and (b) prioritization site A30 in fig. 7 in the Alsea estuary, Oregon. A 

member of the rose family, Pacific silverweed is a common species in high tidal marsh from Alaska to California. 

Photographs by Christopher Janousek, U.S. Environmental Protection Agency, (a) taken in April 2010 and (b) 

taken in October 2010.

a.

b.
49

Figure A21. Photograph of Heracleum lanatum (cow parsnip) at prioritization site Y13a in fig. 6 in Critesers Marsh

in the Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, May 

2010.
50

Figure A22. Photograph of a small tributary in estuarine emergent marsh at prioritization site Y40 in fig. 6 in upper 

Poole Slough in the Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental 

Protection Agency, August 2010.
51

Figure A23. Photograph of estuarine emergent marsh, including a small patch of tall Schoenoplectus sp(p)., at 

prioritization site Y26 in fig. 6 at Mill Creek in the Yaquina estuary, Oregon. This wetland was formerly designated 

by the National Wetlands Inventory as palustrine marsh. Photograph by Christopher Janousek, U.S. Environmental 

Protection Agency, August 2010.
52

Figure A24. Photograph of cattail (Typha latifolia) marsh at prioritization site Y27 in fig. 6 in the upper Yaquina 

River, Oregon. This is a restored tidal wetland, formerly diked; it was previously classified in the National Wetlands 

Inventory as a seasonally-flooded palustrine marsh with no diking modifier. Photograph by Christopher Janousek, 

U.S. Environmental Protection Agency, September 2010.
53

Figure A25. Photograph of Oenanthe sarmentosa (water parsley) submerged at high tide at prioritization site Y28

in fig. 6 in the Yaquina estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection 

Agency, November 2010.
54

Figure A26. Photograph of Eleocharis palustris (common spike rush) near prioritization site Y29 in fig. 6 growing 

at the edge of the river in the upper part of the Yaquina estuary, Oregon. This species is found in lower salinity 

wetlands. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, August 2010.
55

Figure A27. Photograph of low marsh at prioritization site A32 in fig. 7 in the saline portion of the Alsea estuary, 

Oregon (mouth of Lint Slough). Photograph by Laura Brophy, Green Point Consulting, September 2003.
56

Figure A28. Photograph of Sarcocornia perennis (pickleweed) at prioritization site A30 in fig. 7 in the Alsea 

estuary, Oregon. Pickleweed is commonly found in saline low marsh habitat but can also occur at higher tidal 

elevations in brackish parts of Oregon’s estuaries. Photograph by Christopher Janousek, U.S. Environmental 

Protection Agency, October 2010.
57

Figure A29. Photograph of tidal marsh and channel banks covered with diatoms and green algae at prioritization 

site A31 in fig. 7 in the Alsea estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental 

Protection Agency, September 2010.
58

Figure A30. Photograph of tidal freshwater zone near prioritization site A39 in fig. 7 in Drift Creek, a tidallyinfluenced palustrine system in the Alsea River Estuary, Oregon. Photograph by Laura Brophy, Green Point 

Consulting, August 2005.
59

Figure A31. Photograph of Drift Creek and adjoining tidal marshes at prioritization site A26 in fig. 7 in the Alsea 

estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency, November 2010.
60

Figure A32. Photograph of Angelica lucida (seawatch angelica) at prioritization site A36 in fig. 7 close to Eckman 

Lake in the Alsea estuary, Oregon. Photograph by Christopher Janousek, U.S. Environmental Protection Agency,

October 2010.