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1 University of Washington School of Aquatic and Fishery Sciences
2 PC Trask and Associates
Landscape Planning Framework
Fish Habitat Catena Geodatabase Methodology
Mary Ramirez 1
Charles Simenstad1
Phil Trask2
Allan Whiting2
Alex McManus2
Funding provided by the Bonneville Power Administration
1
Contents
Figures .......................................................................................................................................................... 2
Tables ............................................................................................................................................................ 2
Glossary ........................................................................................................................................................ 3
Introduction ................................................................................................................................................... 5
Database Structure .................................................................................................................................... 6
Describing Habitat Availability ................................................................................................................ 7
Data Availability ....................................................................................................................................... 8
Data Development ........................................................................................................................................ 8
Direct Habitat ............................................................................................................................................ 8
Fish Habitat Catena ............................................................................................................................... 8
Indirect Habitat ....................................................................................................................................... 10
Wetland ............................................................................................................................................... 10
Drainage .............................................................................................................................................. 12
USACE 2-year Flood .......................................................................................................................... 14
Landscape Feature................................................................................................................................... 15
Confluence .......................................................................................................................................... 15
Potential Beaver Habitat ..................................................................................................................... 17
Head of Tide ....................................................................................................................................... 19
Additional Datasets ................................................................................................................................. 20
Isolated Lake ....................................................................................................................................... 20
Landscape Unit ................................................................................................................................... 21
Analysis and Application ............................................................................................................................ 22
Reach and Landscape Unit Statistics .................................................................................................. 22
Site and Landscape Unit Statistics ...................................................................................................... 26
User Manual Case Study ......................................................................................................................... 28
How To: Planning Case Study- Brix Bay | Deep River Confluence Restoration ............................... 28
Quantifying the Site and Landscape ................................................................................................... 30
Site Comparison .................................................................................................................................. 33
Characterizing Landscape Change ...................................................................................................... 34
Future Applications | Next Steps ................................................................................................................ 35
References ................................................................................................................................................... 37
Appendix ..................................................................................................................................................... 38
2
Figures
Figure 1. Location map showing the extent of the Columbia River estuary ................................................. 6
Figure 2. Schematic diagram illustrating the hierarchical structure of the LPF classification ..................... 7
Figure 3. Example illustration of fish habitat catenae ................................................................................... 9
Figure 4. Example illustration of surge plain tidal wetlands ...................................................................... 11
Figure 5. Example illustration of tidal and tidally impaired drainage area ................................................. 13
Figure 6. Example illustration of the 2-year flood extent ........................................................................... 14
Figure 7. Example illustration of channel confluences ............................................................................... 16
Figure 8. Example illustration of potential beaver habitat .......................................................................... 18
Figure 9. Tributary channel head of tide locations ..................................................................................... 19
Figure 10. Illustrative example of isolated lakes ........................................................................................ 20
Figure 11. Landscape units in the Columbia River estuary. ....................................................................... 21
Figure 12. Reach summaries of direct FHC and channel confluences........................................................ 24
Figure 13. Landscape summaries of direct FHC and channel confluences ................................................ 25
Figure 14. Map of surge plain wetlands in the Grays Bay Landscape ........................................................ 27
Figure 15. Scaling of tidal channel area and channel outlet count with wetland size ................................. 27
Figure 16. Map of the Brix Bay - Deep River Confluence restoration site................................................. 29
Figure 17. Map of the Deep River Confluence primary restoration actions ............................................... 29
Tables
Table 1. Fish habitat catena attribute table fields ........................................................................................ 10
Table 2. Wetland attribute table fields ........................................................................................................ 12
Table 3. Drainage attribute table fields ....................................................................................................... 13
Table 4. USACE 2-year flood attribute table fields .................................................................................... 15
Table 5. Confluence attribute table fields ................................................................................................... 17
Table 6. Potential beaver habitat attribute table fields ................................................................................ 18
Table 7. Head of tide attribute table fields .................................................................................................. 19
Table 8. Landscape unit attribute table fields ............................................................................................. 22
Table 9. Opportunity and capacity metrics used to characterize fish habitat .............................................. 23
Table 10. Queries used to isolate FHC features for site and landscape analysis ........................................ 31
Table 11. Summary statistics for the Deep River Confluence restoration case study ................................ 32
Table 12. Example site scale calculations of LPF metrics for case study ................................................... 33
Table 13. LPF metric change to the landscape from potential and project implementation ....................... 34
Table 14. Percent of the potential change realized from project implementation. ...................................... 34
3
Glossary
Adjacent wetlands: Herbaceous, scrub-shrub, and deciduous and coniferous forested wetlands that are
adjacent to aquatic/direct FHC.
*Backwater embayment: Shallow inundated areas connected to main channels but are not channelized
(CREEC ecosystem complex).
Biocatena: Descriptive name of the dominant land type within a geomorphic catena patch. Biocatena
classification is based on cluster analysis groupings of the proportion of landcover classes associated with
each catena class (CREEC geomorphic catena).
Channel bar: Periodically exposed channel deposits that have little to no vegetation; channel bars have
convex-up morphology, indicating formation by fluvial deposition, generally found along tributary
channels above significant tidal influence and in reaches of steeper channel gradient (CREEC geomorphic
catena).
Channel confluence: Confluences of dissimilar fish habitat catena channel types with a point centered on
the shared border of the two features.
*Channel shallows: Sparsely vegetated beaches and shallow water areas within channels.
Direct Fish Habitat: Areas of fish habitat catena that juvenile salmon may directly occupy.
Fish Habitat Catena: Aquatic habitat area that is believed to be beneficial to juvenile salmon based on
current scientific understanding of how juvenile salmon use estuarine habitat.
*Floodplain: Broad, relatively flat portion of tidal freshwater reaches periodically flooded by fluvial
discharge; in the Columbia River estuary, these features occur in Reaches D-H (CREEC ecosystem
complex).
*Floodplain channel: Channels that do not originate outside the flood plain and are not connected to a
primary channel at both ends (CREEC geomorphic catena).
Floodplain slough: A channel that is inundated seasonally with at least one point of entry.
Head of tide: Up-tributary extent (point) of tidal influence.
In-channel fill: Former channels that have been filled with human-placed materials.
Indirect Fish Habitat: Areas of fish habitat catena that juvenile salmon may not actively occupy, but
strongly influence the quality of direct fish habitat catena.
*Intermittently exposed: Frequently but not continuously inundated channel and backwater areas
between the low-water shoreline and the edge of floodplains or surge plains (CREEC geomorphic catena).
Isolated floodplain lakes: Isolated lakes in floodplains that appear not to have a channelized connection
to the larger estuary. These features may be located within the MHHW range of the estuary, but do not
provide direct fish habitat because of the lack of access.
Landscape units: A level of analysis between the scale of an ecosystem complex and hydrogeomorphic
reach. Landscape areas are based on complex boundaries and generally extend over a major tributary
channel floodplain.
4
*Minor tributary: Small channels that originate outside the floodplain or surge plain (CREEC
geomorphic catena).
Potential beaver habitat: Potential locations of American beaver habitat, based on specific small
tributary and vegetation criteria, which is known to benefit juvenile salmon in tidal wetlands (Hood
2012).
*Primary channel: Main channels of the estuary (CREEC ecosystem complex).
*Secondary channel: Channels that are connected to a Primary Channel at both ends at least seasonally
(CREEC ecosystem complex).
*Side channel: Channels connected to a Tributary Channel at both ends at least seasonally (CREEC
geomorphic catena).
Surge plain: Tidal floodplains; intertidal marshes and other wetlands that are dominated by tidal
flooding; estuarine floodplains occurring wholly within Reaches A-C (CREEC ecosystem complex).
Tertiary channel: Shallow, either permanently flooded or intermittently exposed channels within
floodplains or surge plains that have both ends connected to another channel (CREEC geomorphic
catena).
Tidal channel: Surge plain feature consisting of non-tributary channels (channels without sources outside
the estuary) strongly influenced by tides and connected to another channel at a single end (CREEC
geomorphic catena).
Tidal drainage: Areas below the estimated high water level and are subject to regular tidal influence.
Tie channel: Channels that connect floodplain lakes to the main channel (CREEC geomorphic catena).
*Tributary channel: Main channels of the major tributaries entering the estuary (CREEC ecosystem
complex).
Tributary confluence zone: Area of tributary confluences represented by a circle with a radius equal to
the width of the tributary channel at its mouth and centered on the midpoint of the line at the tributary
channel mouth.
Tributary delta: Intermittently exposed deposits within main channels but deposited from tributary
streams (CREEC geomorphic catena).
*Tributary secondary channel: Channel beginning in a tributary and connected to a larger channel at
the downstream end at least seasonally (CREEC ecosystem complex).
*Unknown depth: Channel or backwater areas lacking bathymetric data (CREEC geomorphic catena).
USACE 2-year flood: An estimate of the area inundated under the 2-year flood elevation (50% annual
exceedance probability) or extreme higher high water (mean highest monthly tide), whichever is higher.
*as defined in the Columbia River Estuary Ecosystem Classification Report Appendix A
5
Introduction
The Landscape Planning Framework (LPF) is a landscape ecology-based, geospatial approach to strategic
planning for restoration and preservation of specific species habitat (in this case, juvenile Pacific salmon
(Oncorhynchus spp.)) in the 233-rkm Columbia River estuary. This Bonneville Power Administration
supported project adapts the structure of the hierarchical Columbia River Estuary Ecosystem
Classification (hence, Classification; Simenstad et al. 2011, USGS 2012) to identify and compare
spatially-explicit sites that would most likely benefit unique, at-risk genetic stocks of Columbia River
salmon. This adaptation of the Classification could be applied to other species as well, including
shorebirds like plovers and sandpipers, wading birds like great blue heron and sandhill crane, amphibians
like Oregon spotted frog and western pond turtle, or mammals like the Columbian white-tailed deer or
American beaver. University of Washington and PC Trask & Associates delineated aquatic habitat area,
called fish habitat catena (FHC), based on the existing scientific data on estuarine habitat requirements of
juvenile Chinook salmon (Oncorhynchus tshawytsacha). The LPF is designed to address juvenile
Chinook habitat because their ocean-type life history forms tend to be the most dependent on estuarine
habitat and because their populations are depleted in the Columbia River basin to the point that five
Evolutionary Significant Units (ESU) are listed under the US Endangered Species Act (Bottom et al.
2005; Teel et al. 2014). During outmigration, these fish utilize the many distributary and dendritic
channels that provide areas of abundant feeding opportunities, subdued velocity, and low predation
pressure (Bottom et al. 2005). Estuarine wetlands provide the necessary backbone of these areas in the
form of drainage area and contributions to food web productivity.
The Columbia River is the second largest river in the United States, with a 660,480 km2 drainage basin
that includes seven states and two Canadian provinces (Simenstad et al. 2011). The LPF study area covers
the entire Columbia River estuary, defined as the stretch of the Columbia River between its mouth and the
Bonneville Dam (rkm 234), and the adjacent floodplain, including all areas historically inundated by tides
and river floods (Simenstad et al. 2011; Figure 1). Historically, selection of restoration and protection
projects in the Columbia River estuary has been based largely on near-term opportunities and limited
understanding of what constitutes high-value estuarine habitat for juvenile salmon, especially from a
landscape context. Noticeably lacking is a systematic method of (1) assessing where an action would be
most beneficial to at-risk stocks within the estuary landscape, and (2) measuring how habitat attributes
and availability change under various hydrologic conditions.
Recent policy initiatives highlight the need for additional scientific rigor in the identification and selection
of projects, to support strategic, long-term investment in estuary restoration and protection for the benefit
of ESA-listed salmon. The LPF is an approach for comparing possible estuary restoration and protection
scenarios for their potential to benefit juvenile salmon.
The LPF objectives are to:
1. use established and emerging science on juvenile salmon habitat requirements in estuaries to
identify landscape features that constitute restoration and conservation targets;
2. apply scientifically-based landscape metrics to quantify the structure, composition, and
distribution of FHC;
3. analyze characteristics of FHC that constitute beneficial estuarine habitat for juvenile salmon of
different ESU; and,
4. establish baseline metrics, from historical and current reference FHC, that strategically identify
the types and locations of habitats of priority for restoration and conservation.
6
Figure 1. Location map showing the extent of the Columbia River estuary from river mouth to the Bonneville Dam. The
eight Hydrogeomorphic Reaches divide the estuary according to distinct estuarine processes and conditions.
Database Structure
The LPF is designed as a Geographic Information System (GIS) framework to identify and compare areas
of the estuary that provide or could provide the most habitat benefit to diverse genetic stocks of salmon
migrating through and rearing in the estuary. The geodatabase is organized into nine datasets, each
described under the Data Development section (and Appendix). Direct fish habitat that is associated with
major ecosystem complexes from the Classification are delineated, as well as three levels of indirect fish
habitat: adjacent wetlands, tidal drainage, and USACE 2-year flood extent (Figure 2).
The database also defines three types of landscape features: channel confluences, potential locations of
American beaver (Castor Canadensis) habitat, and the head of tide in large tributaries to the estuary.
These features are attributes of direct fish habitat that suggest further benefits compared to other fish
habitat. Additional datasets provided are the isolated floodplain lakes, which were filtered out of the
direct FHC, and landscape units, which may provide a useful geographic scale for describing and
analyzing data.
7
Figure 2. Schematic diagram illustrating the hierarchical structure of the Landscape Planning Framework classification
of direct fish habitat catenae (blue), indirect habitat (green and pink), and landscape features (yellow) under major
Ecosystem Complexes (gray).
Describing Habitat Availability
Direct and indirect fish habitats are assembled into a geodatabase that can be analyzed, both for statistical
summarization of juvenile salmon habitats in the estuary, and for designing strategic restoration and
protection scenarios. The LPF can be applied at multiple spatial scales, from the reach or landscape level
to a user defined individual site level. Once the existing features have been characterized, their spatial
attributes, such as occurrence, size, distribution, and complexity, can be quantified. These attributes may
then be compared under various hydrologic conditions, such as restored and protected conditions at the
site level. The LPF allows users to quantify the expected increase in desirable attributes (habitat area and
complexity, etc.) in different locations. Results compare potential restoration or protection opportunities
to each other, to averaged values for the geographical area of interest, to reference sites, or to assigned
target values.
PRIMARY CHANNEL
SECONDARY CHANNEL
BACKWATER EMBAYMENT
CHANNEL SHALLOWS
INTERMITTENTLY EXPOSED
TRIBUTARY DELTA
CHANNEL BAR
ADJACENT WETLANDS
TIDAL DRAINAGE
USACE 2-YEAR FLOOD
LANDSCAPE FEATURE
CHANNEL CONFLUENCE
TRIBUTARY CHANNEL
TRIBUTARY SECONDARY
CHANNEL
CHANNEL SHALLOWS
INTERMITTENTLY EXPOSED
TRIBUTARY DELTA
CHANNEL BAR
SIDE CHANNEL
UNKNOWN DEPTH
TRIBUTARY CONFLUENCE ZONE
CHANNEL
ADJACENT WETLANDS
TIDAL DRAINAGE
USACE 2-YEAR FLOOD
LANDSCAPE FEATURE
CHANNEL CONFLUENCE
HEAD OF TIDE
FLOODPLAIN
CHANNELS
FLOODPLAIN SLOUGH
FLOODPLAIN CHANNEL
MINOR TRIBUTARY
SIDE CHANNEL
LAKES
LAKE/POND
TIE CHANNEL
ADJACENT WETLANDS
TIDAL DRAINAGE
USACE 2-YEAR FLOOD
LANDSCAPE FEATURE
CHANNEL CONFLUENCE
POTENTIAL BEAVER HABITAT
SURGE PLAIN
CHANNELS
TIDAL SLOUGH
TIDAL CHANNEL
TERTIARY CHANNEL
TRIBUTARY DELTA
CHANNEL BAR
MINOR TRIBUTARY
LAKES
LAKE/POND
ADJACENT WETLANDS
TIDAL DRAINAGE
USACE 2-YEAR FLOOD
LANDSCAPE FEATURE
CHANNEL CONFLUENCE
POTENTIAL BEAVER HABITAT
8
Data Availability
The FHC geodatabase, and associated metadata and methodology (as described here) are available for
public download through BPA’s cbfish database and the University of Washington’s Wetland Ecosystem
Team (depts.washington.edu/wet/lpf.html). Questions about these data and their use should be directed to
the WET lab at the University of Washington (wet@uw.edu).
Data Development
Each of the nine database elements is described below beginning with a general description, steps used in
processing the data, followed by descriptions of the fields from the attribute table. See Appendix A for the
full list of datasets included in the geodatabase.
Direct Habitat
Direct habitat references an area that juvenile salmon may directly occupy. The LPF classifies these
aquatic features as direct fish habitat catena.
Fish Habitat Catena Direct fish habitat catena (FHC) is a unique set of aquatic landscape features that describes opportunity
and capacity characteristics of valuable habitat for juvenile salmon. These aquatic catenae are areas that
juvenile salmon may directly occupy (Figure 3). The LPF selected aquatic geomorphic catenae from the
Classification that are believed to be beneficial to juvenile salmon, such as, large channel shallows
(intermittently exposed), backwater embayments, and floodplain and tidal channels, among others.
The Classification represents confluence zones of tributary channels as a circle with a radius equal to the
width of the tributary channel at its mouth, centered on the midpoint of the channel mouth. Deep water
catenae (permanently flooded and deep channel) that are within these confluence zones are included as
direct FHC.
Open FHC is identified as habitat that juvenile salmon can access without obstruction; however,
assumptions are not made about the seasonal accessibility of channels and lakes. Using the
Classification’s attribution of human cultural features, infrastructure, and modifications, altered FHC is
identified where natural tidal-fluvial flooding is regulated or isolated and thus has potential for future
restoration or enhancement. Lakes and ponds that appear to be naturally isolated from the larger
Columbia River system were removed from the direct FHC (see Isolated Lake below).
Data Processing The FHC were based primarily on aquatic geomorphic catenae from the Classification. After careful
inspection, it was determined that many significant channel features were not included in the original
dataset. Many of these missing channels occurred in diked (leveed) areas that are currently disconnected
from the mainstem, although the channel signature still exists. There were also many connected channels
that were not included, a majority of these located in very complex surge plain landscapes. Channel areas
and water features are the basis for fish habitat catena selection so the inclusion of these channels is very
important to the consistency of the dataset.
Referencing the LiDAR topography and aerial photos, all channels visible at the 1:500 scale were
digitized by reclassifying LiDAR and hand digitizing in areas lacking elevation data. All new channels
were quality checked using the LiDAR and aerial photos. Channels were then snapped to the geomorphic
catena polygons and fill areas were digitized using the cultural layer from the Classification as well
LiDAR and aerial photos. Tributary channels were also digitized using LiDAR and aerial photos,
regardless of the scale. These channels are important in identifying all tributary confluences zones.
9
From the revised geomorphic catenae, intermittently exposed areas of backwater embayments and large
channels (primary, secondary, and tributary) were selected as FHC. Areas attributed as unknown depth
where bathymetric data was lacking, were also selected from secondary and tributary channels.
Additionally, all moderate to small channels were selected, including: floodplain, minor tributary, side,
tertiary, tidal, and tie channels. Lake/pond and channel bar catenae as well as surge plain occurring within
a tributary confluence zone were also selected as FHC.
Fish habitat status was attributed based on each feature’s proximity to the larger Columbia River system.
Channels and lakes that form a continuous path to the primary channel were attributed as open. Lakes and
ponds that are not connected to a channel and are not adjacent to in-channel fill indicating natural
flooding has been modified were attributed as isolated and removed from the direct FHC. All other
features were attributed as altered and assumed to be inhibited by a structure (i.e. tidegate, culvert, dike,
etc.) or in-channel fill. Assumptions are not made regarding the exchange of water flow in or out of the
FHC.
Figure 3. Example illustration of fish habitat catenae. Tributary channel shallows (dark blue) and tidal channels (yellow)
are accessible to juvenile salmon, while a levee impedes access and natural flooding to altered floodplain channels (light
blue).
Attributes Five additional fields were created to attribute FHC (Table 1). All other fields are derived from the
Classification; please refer to the source metadata for descriptions of those derived fields.
10
Table 1. Fish habitat catena attribute table fields.
Field Description
FHC Unique ID Unique identifying number for each FHC feature. Altered features of
the same channel type that are disconnected by in-channel fill are
considered one unit and assigned the same ID number. The FHC ID
number is carried over to all indirect habitat associated with the
aquatic feature (i.e. adjacent wetlands). The "FHC_uniqueID" can be
queried across all feature classes within the geodatabase in order to
understand which features are associated with a unique FHC.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the identified fish habitat catena and the larger
Columbia River system. Value is either ‘Open’ or ‘Altered’.
Channel Type A descriptive or generalized channel type name that is primarily
derived from the associated ecosystem complex or geomorphic catena.
The channel type “small channel” was used to distinguish presumably
first order channels that may be at higher elevations with limited
flooding. These small channels are thought to provide little benefit to
juvenile salmon and may be filtered out for subsequent analyses.
FHC Area Acres The total area (acres) for a unique FHC feature as identified by the
FHC unique ID number.
Restoration Includes the project name and year. Used to note where FHC have
been updated as a result of the addition of a restored site since the
initial GIS selection of FHC. These updates can be as simple as
changing the status from ‘Altered’ to ‘Open’ (i.e. a tidegate removal)
or as complicated as the addition of entirely new direct and indirect
fish habitat (i.e. channel excavation). The associated
"FHC_uniqueID" can be queried across all feature classes within the
geodatabase in order to understand which features were enhanced by
the restoration effort. Detailed information is available for each
project, please visit http://www.cbfish.org/EstuaryAction.mvc/Actions.
Indirect Habitat
Indirect fish habitat are areas that juvenile salmon may not actively occupy, but strongly influence the
quality of direct FHC. These include adjacent wetlands and the surrounding extent of tidal drainage and
2-year flood inundation.
Wetland The indirect wetland dataset depicts herbaceous, scrub-shrub, and deciduous and coniferous forested
wetlands that are adjacent to aquatic/direct FHC (Figure 4). The vegetative structure and extent of
influence varies considerably by wetland type, so adjacency is defined for the wetland type as the
following: herbaceous wetland polygons are included within a 2-meter border of channel units; scrub-
shrub wetland polygons are included within a 5-meter border of channel units; and deciduous and
coniferous forested wetland polygons are included within a 20-meter border of channel units. These
border widths reflect the approximate height of mature forms of each associated wetland class, a rationale
typically applied in establishing forested riparian buffers. Wetlands were selected from the 2010 Lower
Columbia River estuary classified land cover data set provided by the Lower Columbia Estuary
Partnership. The land cover data set emphasizes estuarine and tidal freshwater vegetation types, and was
11
derived using high resolution image segmentation and an object-based classification process (LCEP
2010).
The vegetation types are classified under three inundation scenarios in the land cover (LCEP 2010). Tidal
wetland occurs below the estimated high water level and is subject to regular tidal influence. Diked
wetland occurs below the estimated high water level, but there is a human made barrier present partially
or completely inhibiting tidal influence. Non-tidal wetland occurs above the estimated high water level
and is not subject to tidal inundation. Water and mud land cover classes are also included in the indirect
wetland dataset.
Figure 4. Example illustration of surge plain tidal wetlands adjacent to a tidal channel (yellow) and tributary channel
(blue). Herbaceous wetland (pink) is delineated within 2 meters of a channel, scrub-shrub wetland (purple) within 5
meters, and deciduous (light green) and coniferous (dark green) forested wetland within 20 meters.
Data Processing To select wetlands adjacent to the FHC, three buffer polygons were created around open and altered
channel and lake features. A 2-meter buffer was used to clip all herbaceous wetlands as well as mud and
water land cover. Mud and water areas were retained because these areas in the dataset often represent
emergent habitats that bridge wetlands to the fish habitat catena. A 5-meter buffer was used to clip all
scrub-shrub wetlands and a 20-meter buffer was used to clip all deciduous and coniferous forested
wetlands. All of the clipped features were merged together into a single layer. To remove isolated
features, only wetlands contiguous to the fish habitat catena within 1 meter were retained.
In order to attribute wetlands and other indirect habitat as being associated with a distinct FHC, zones
around each unique aquatic feature were created. The zones were created using the ArcGIS Euclidean
allocation tool (Spatial Analyst) and are based on the unique ID number of the FHC. Channel bars, which
typically occur along or within a tributary channel, were not assigned a distinct zone. Rather, these active
12
features were merged with the adjacent channel to be included in the surrounding channel’s zone. The
Euclidean allocation output is a raster where each cell is assigned the value of the source (FHC unique
ID) to which it is closest according to Euclidean, or straight-line, distance. The raster was then converted
to polygon and zone boundaries were manually reviewed and revised. The intent was to create a general
area of influence around each FHC. Zones were modified where needed to better represent natural (e.g.
higher elevations) and artificial (e.g. levees) barriers that influence tidal inundation and flooding. Finally,
the adjacent wetlands are intersected with the unique zones to attribute wetlands with the associated FHC
values.
Attributes Wetland attributes include a descriptive name and values of the associated FHC (Table 2).
Table 2. Wetland attribute table fields.
Field Description
FHC Unique ID Unique identifying number of the associated FHC feature.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the associated fish habitat catena and the
larger Columbia River system. Value is either ‘Open’ or ‘Altered’ and
references the status of the associated channel or lake feature, not
necessarily the wetlands themselves.
Channel Type A descriptive or generalized channel type name of the associated
FHC.
Wetland Name A descriptive name, derived from the source land cover, of the
inundation scenario and wetland vegetation type (e.g. Non-tidal
Herbaceous Wetland; Diked Coniferous Forest Wetland).
Drainage The indirect drainage dataset provides an estimate of tidally influenced and tidally impaired floodplain
and surge plain areas adjacent to the FHC (Figure 5). The source data is derived from the 2010 land cover
hydrologic information for the Columbia River estuary prepared by the Lower Columbia Estuary
Partnership (LCEP 2010). The original delineation was done by comparing 2010 LiDAR elevation data to
an estimated mean higher high water (MHHW) level model for the estuary. Correction factors were also
applied based on actual water surface elevation data collected in 2009-2010 for 23 off channel sites,
which was provided by PNNL (LCEP 2010).
Tidal drainage areas occur below the estimated high water level and are subject to regular tidal influence.
Tidally impaired drainage areas occur below the estimated high water level, but there is a human made
barrier present partially or completely inhibiting tidal influence. Drainage polygons are associated with a
unique FHC aquatic feature and are attributed according to the values of the associated FHC.
Data Processing The LCEP (2010) hydrologic information was first joined to the direct FHC. The result was merged with
the land cover water class to fill any artificial gaps between the tidal dataset and delineated lakes and
channels. This data gap was most predominant in low elevation surge plain habitats. Non-tidal and fill
polygons were then deleted, retaining drainage areas below the estimated high water level. To remove
isolated features, tidal or tidally impaired polygons not contiguous to FHC were also deleted. Finally,
these areas were intersected with the unique FHC zones (as described above in Wetland Data Processing)
to attribute drainage areas with the associated FHC values.
13
Figure 5. Example illustration of tidal (green) and tidally impaired (brown) drainage area surrounding the fish habitat
catena (blue). Also shown are levees (red hatched) and fill (gray) from the Classification’s attribution of human cultural
features to illustrate how and where tidal inundation may be impeded.
Attributes Drainage polygons are attributed with the level of tidal inundation and values of the associated FHC
(Table 3).
Table 3. Drainage attribute table fields.
Field Description
FHC Unique ID Unique identifying number of the associated fish habitat catena feature.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the associated fish habitat catena and the larger
Columbia River system. Value is either ‘Open’ or ‘Altered’ and
references the status of the associated channel or lake feature, not
necessarily the drainage area.
Channel Type A descriptive or generalized channel type name of the associated fish
habitat catena.
Inundation Assessment of tidal impairment (tidal or tidally impaired), derived from
the source hydrologic information. Also identified are all areas covered
by the direct fish habitat catena and any water (land cover class)
occurring between direct fish habitat and tidal drainage.
14
USACE 2-year Flood The 2-year flood extent surrounding the FHC is derived from the 2011 modeled 50 percent Annual
Exceedance Probability (AEP) Stage Profile for Survival Benefit Unit for the Lower Columbia River
Estuary, dated 4 November, from the Army Corps of Engineers (USACE). This was done by determining
maximum water surface elevations along the reach annually for the period of complete main stem
regulation and performing statistics on the annual dataset to determine a 50 percent AEP stage. The
dataset represents an estimate of the area inundated under the 2-year flood elevation or extreme higher
high water (mean highest monthly tide), whichever is higher (Figure 6). Flood polygons are associated
with a unique FHC aquatic feature and are attributed according to the values of the associated FHC.
Figure 6. Example illustration of the 2-year flood extent (brown) above the fish habitat catena (blue). Flood polygons were
derived from the U.S. Army Corps of Engineers calculated 50% Annual Exceedance Probability (2011).
Data Processing To interpolate flood extent, the modeled 50 percent exceedance values were obtained from the USACE,
with points occurring every four to five miles. River cross sections were created at each modeled point as
perpendicular to the mainstem as possible without overlapping neighboring transects. Points were then
assigned along each transect with the same value as the base modeled point. The Topo to Raster tool was
used to interpolate linearly between the points, generating a 1-meter resolution raster from the point data.
The difference between the LiDAR elevation dataset and the generated raster was determined to identify
land that is below (<0) or above (>0) the 50 percent exceedance. The raster was converted to polygon and
everything above the 50 percent exceedance was deleted, leaving the estimated extent of the 2-year flood.
The resulting flood dataset was joined to the direct FHC. To remove isolated features, flood polygons not
contiguous to FHC were also deleted. Finally, these areas were intersected with the unique FHC zones (as
described above in Wetland Data Processing) to attribute flood areas with the associated FHC values.
15
Attributes Flood polygons are attributed with the values of the associated FHC (Table 4).
Table 4. USACE 2-year flood attribute table fields.
Field Description
FHC Unique ID Unique identifying number of the associated FHC feature.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the associated FHC and the larger Columbia
River system. Value is either ‘Open’ or ‘Altered’ and references the
status of the associated FHC channel or lake feature, not necessarily
the flood area.
Channel Type A descriptive or generalized channel type name of the associated
FHC.
Inundation Value is either ‘2-year Flood’ or ‘Direct fish habitat catena’.
Landscape Feature
Landscape features of importance to juvenile salmon include channel confluences, small channels where
beaver may potentially occur, and the head of tide in large tributaries.
Confluence This dataset represents confluences of dissimilar FHC channel types with a point centered on the shared
border of the two features (Figure 7). Confluences are attributed with FHC channel information for the
two contributing aquatic features as well as the confluence channel area (the upstream channel). The
confluence status is determined from the FHC habitat status of the contributing features. The confluence
is assigned the open status when both contributing FHC channels are open. Altered confluences have at
least one contributing altered FHC feature. A confluence is assigned the channel break status when the
channel type is (or would have been) the same for both features, but a modification is present that results
in a change in the FHC Status (e.g. tidal channel that is bisected by a levee).
Channel confluences provide an important indication of habitat opportunity for juvenile salmon. The
dataset maps active access points to surge plain and floodplain habitat, as well as identifies historical and
potentially restorable access points. With reference to the Classification’s attribution of human cultural
features and digital historical topographic survey maps (T-sheets; Burke 2010), a point was created where
a confluence most likely occurred.
16
Figure 7. Example illustration of open, altered, and channel break confluences. In the illustration, altered confluences
(yellow) are shown where a levee impedes access between the tributary and floodplain channels. Channel breaks (purple)
occur where branches of a floodplain channel are disconnected by a levee and road fill. Open channel confluences (blue)
are noted between the tributary channel and a floodplain, tidal, and side channel.
Data Processing To mark confluence points, the direct FHC was first augmented with deep water habitats and in-channel
fill from the Classification. In-channel fill was attributed with the adjacent altered channel type to bridge
the gap between disconnected channel units. Features were then dissolved on channel type and the dataset
was converted from polygon to line, storing polygon neighboring information. This identifies where a
shared boundary occurs (i.e. the confluence of different channel types). Selecting these shared lines, a
center point was created to represent the confluence. Each point was attributed with the associated FHC
values of both contributing channels.
Confluence points were manually reviewed and revised with reference to aerial photos, LiDAR
topography, mapped human modifications, and historic T-sheets from the lower Columbia River.
Attributes Confluence points are attributed with the FHC values of both contributing aquatic features. The two
features are distinguished in the attribute table as channel ‘a’ and channel ‘b’. This assignment is not
relevant to channel order. Based on the information of the contributing channels, the confluence status,
confluence (upstream) channel area, and confluence size were also characterized (Table 5).
17
Table 5. Confluence attribute table fields.
Field Description
Channel Type A descriptive or generalized channel type name of the associated
FHC. Channel type is listed for both channel 'a’ and channel ‘b’.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the associated FHC and the larger Columbia
River system. Value is either ‘Open’ or ‘Altered’ and references the
status of the associated FHC channel or lake feature, not necessarily
the confluence status. Fish habitat status is listed for both channel 'a’
and channel ‘b’.
FHC Unique ID Unique identifying number of the associated FHC feature. FHC
unique ID is listed for both channel 'a’ and channel ‘b’.
FHC Area Acres The total area (acres) for a unique FHC feature as identified by the
FHC unique ID number. FHC area is listed for both channel 'a’ and
channel ‘b’.
Confluence Channel Identifies the upstream channel. Value is either 'a’ or ‘b’.
Confluence Channel
Acres
The total area (acres) of the upstream channel.
Confluence Size Binary field based on the confluence channel area. Confluence size
where the channel area is less than 100 square meters (small channel)
is 0; all others are 1. These small channels are presumably first order
channels that may be at higher elevations with limited flooding. These
small channels are thought to provide little benefit to juvenile salmon
and may be filtered out for subsequent analyses.
Confluence Status An assessment of connectivity based on the fish habitat status and
channel type of both contributing FHC channels. Value ‘Open’ when
both contributing channels are open; ‘Altered’ when at least one
channel is altered; or ‘Channel Break’ when channel type is (or would
be) the same but fish habitat status is different.
Potential Beaver Habitat This dataset identifies potential locations of American beaver (Castor canadensis) channel habitat, which
is known to benefit juvenile salmon in tidal wetlands (Hood 2012; Figure 8). In a survey of tidal channels
in the Skagit River Delta (Puget Sound, Washington), Hood found beaver dams at densities equal to or
greater than in non-tidal rivers. These dams were found exclusively in small tidal channels within shrub
habitat. The considerable amount of sticks and logs in the dams indicated a dependence on woody
vegetation for construction material. Additionally, Hood surmised that beaver build dams in small tidal
channels to prevent them from draining completely at low tide, allowing for easier mobility. Large, deep
channels generally retain water at low tide, thus they remain accessible to beaver in the absence of a dam
(Hood 2012). GIS rules were developed to select FHC channels that met these criteria for beaver habitat.
Data Processing Potential beaver habitat includes small channels (approximately 1-3 meters wide) within wooded areas
with an upland connection. The Classification’s biocatena assessment was used to identify forested or
scrub-shrub wetland (including diked) ecosystems that were not on an island. Then any FHC tidal or
18
floodplain channels that intersected the wooded areas were selected. The perimeter-area ratio (channel
length (m) / channel area (m2)) was used as a proxy to identify narrow or small channels. Upon review of
the data, it was determined that channels with a perimeter-area ratio greater than 0.5 best reflect the size
criteria for potential beaver habitat.
Figure 8. Example illustration of potential beaver habitat (channels highlighted in yellow) selected from the fish habitat
catena (dark blue) based on size, channel type, and location in a wooded ecosystem (biocatena) criteria.
Attributes Potential beaver habitat features are attributed with their FHC values and the perimeter-area ratio (Table
6).
Table 6. Potential beaver habitat attribute table fields.
Field Description
Channel Type A descriptive or generalized channel type name of the FHC channel.
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the FHC channel and the larger Columbia
River system. Value is either ‘Open’ or ‘Altered’.
FHC Unique ID Unique identifying number of the FHC channel.
PARA Calculated field to divide channel length (edge) by channel area. To
select narrow channels, it was determined they needed to have a ratio
greater than 0.5.
Biocatena Ecosystem categorized on the basis of assemblages of primary cover
type, derived from the Classification.
19
Head of Tide The up-valley extent of channel mapping for tributary channels is defined by the Classification as
encompassing all areas of strong tidal influence. This limit was interpreted as the head of tide (Figure 9).
Figure 9. Tributary channel head of tide locations.
Data Processing A point was created at the up-valley extent of the 43 mapped tributary channels.
Attributes Head of tide points are attributed with the tributary channel’s name and FHC values (Table 7).
Table 7. Head of tide attribute table fields.
Field Description
Channel Name of the tributary channel.
Channel Type A descriptive or generalized channel type name of the FHC channel
(Tributary channel).
Fish Habitat Status An assessment of connectivity, based on human infrastructure and
modifications, between the tributary channel and the Columbia River
system. Value is either ‘Open’ or ‘Altered’.
FHC Unique ID Unique identifying number of the FHC tributary channel.
20
Additional Datasets
Additional datasets provided are the isolated floodplain lakes, which were filtered out of the direct FHC,
and landscape units, which may provide a useful geographic scale for describing and analyzing data.
Isolated Lake Isolated lakes appear not to have, or to have had, a regular, channelized connection to the larger Columbia
River system (Figure 10). These features may be located within the MHHW range of the estuary (as
mapped in the indirect drainage habitat), but do not provide direct fish habitat because of the lack of
suitable access. These features were excluded from the direct FHC because they may be highly variable
over time and do not consistently offer viable fish habitat. It is possible some isolated lakes would
provide temporary fish habitat (e.g. during flood events); however, they are precluded from the FHC in
order to be conservative in fish habitat selection.
Figure 10. Illustrative example of isolated lakes (yellow) with comparison to an open (blue) and altered (blue hatched)
lake. The area of tidal drainage (light green) surrounding the lakes is also shown.
Data Processing Refer to Data Processing for Direct Fish Habitat Catena for complete process steps. Lakes and ponds that
are not connected to a channel and are not adjacent to in-channel fill indicating natural flooding has been
modified, were attributed as isolated. These features were manually reviewed and revised with reference
to LiDAR topography, aerial photos, T-sheets, as well as local knowledge.
Attributes Isolated lake features are attributed with Channel Type (Lake/pond) and Fish Habitat Status (Isolated).
All other fields are derived from the Classification; please refer to the source metadata for descriptions of
those derived fields.
21
Landscape Unit A landscape unit represents a level of analysis between the scale of an ecosystem complex and
hydrogeomorphic reach (Figure 11). Landscape areas are based on complex (delineated in the
Classification) boundaries and generally extend over a major tributary channel floodplain. The Columbia
River complex landscape is divided by reach boundaries.
Figure 11. Landscape units in the Columbia River estuary.
Data Processing To delineate landscape boundaries, features were initially dissolved on the channel field in the
Classification’s ecosystem complex dataset. Unnamed polygons were then merged with the adjacent
channel unit. Surge plain and floodplain islands combine with the adjacent secondary channel to form an
island sub-landscape. The island sub-landscape combines with the adjacent surge plain or floodplain to
form the total landscape area. Small complexes that are not connected to a large landscape area are
attributed as a shoreline sub-landscape and combine with the Columbia River sub-landscape to form the
Columbia River landscape. Landscape areas may carry across reach boundaries (see the Cowlitz
landscape in reach C), but sub-landscapes do not.
Attributes Landscape units are attributed with a descriptive name and include nested sub-landscape units (Table 8).
22
Table 8. Landscape unit attribute table fields.
Field Description
Landscape Name A descriptive name of the landscape usually based on the major
tributary name. Where there is no major tributary, the name is
culturally based. Landscapes should be compared to other landscapes.
Sub-Landscape Name A descriptive name of the smaller landscape that is nested within the
landscape unit. Sub-landscapes should be compared to other sub-
landscapes.
Acres Total area (acres) of the sub-landscape unit.
Analysis and Application
The Landscape Planning Framework allows users to examine patterns in available and potential fish
habitat at multiple scales. The scale at which one applies the LPF depends on the objective. Genetic stock
identification has provided information on variability in the temporal and spatial distributions of specific
populations of juvenile Chinook salmon at the hydrogeomorphic reach scale (Teel et al. 2014). With this
improved understanding of stock-specific estuary-wide habitat use, summaries of large scale patterns of
habitat opportunity and capacity provide important information to identify areas where discrepancies
between fish use and habitat availability occur, therefore enabling a strategic approach to restoration
planning.
If the objective is to examine patterns at a local scale, restoration site design for instance, evaluating the
site within the context of its landscape is more appropriate. Ecological patterns are sensitive to the
surrounding landscape processes, and the LPF database provides a tool for comparing landform scaling
relationships between multiple sites within a landscape relative to the characteristics and distributions of
fish habitat catena in natural, reference regions of the local landscape. This approach analyzes site-
specific deviations from scaling relationships and as Hood (2007a) states, provides a “linkage between
restoration guidelines for tidal channel form and ecological restoration goals”.
Reach and Landscape Unit Statistics The LPF database maps over 45,000 acres of open FHC, and over 7,500 acres of altered FHC throughout
the Columbia River estuary. Major channel types that contribute to the assemblage of open fish habitat
include intermittently exposed areas of primary and secondary channels, as well as tidal channels/sloughs
and tributary channels. Together, these channel types account for over 80 percent of the open fish habitat
in each reach, except reach F where lakes/ponds comprise half of the total open FHC. In comparison,
altered fish habitat is dominated by floodplain channels/sloughs in the lower three reaches (these are
typically altered forms of tidal channels), and a mix of lakes/ponds and floodplain channels/sloughs in
reaches D through H.
When open and altered habitats are combined, direct FHC ranges from 8.6 percent (reach E) to 18.1
percent (reach F) of the total reach area. Over 5,500 acres of wetland habitat are mapped in association
with open FHC features, and over 2,300 acres in association with altered FHC features. Additionally, the
database maps approximately 3,100 open channel confluence points, with an additional 563 altered
confluence points. Spatial metrics are generated by GIS-based (ArcGIS) rules to qualify the FHC (Table
9).
23
Table 9. Opportunity and capacity metrics used to characterize fish habitat.
Opportunity Metrics Description
Channel Type
Occurrence
The count of distinct FHC summarized by channel type. This provides
information about the occurrence and location of individual features, such
as backwater embayments which provide juvenile salmon protected areas
buffered from strong currents.
Confluence Density Confluence Density is a measure of the number of confluence points
divided by the analysis area. Confluences are important to juvenile
salmonids as entry points into discrete habitat patches.
Confluence Nearest-
Neighbor
The shortest distance from one confluence to another. The mean nearest-
neighbor distance of all confluences within a landscape provides
information about the relative isolation of habitat patches.
Surge Plain/Floodplain
Connectivity
Surge or floodplain connectivity may be summarized as the proportion of
primary or tributary channel length to adjacent levee or developed land.
Capacity Metrics Description
Area The amount of all or distinct types of direct habitat juvenile salmon may
access or indirect habitat that may influence the quality of the FHC. Size
may be summarized for an individual patch, an entire class, or as a percent
of the landscape.
Edge The perimeter length of FHC channel or lake features. Edge Density is a
measure of the length of FHC perimeter divided by the analysis area
(landscape), and provides information about the amount of edge habitat
relative to the size of the landscape.
Perimeter-Area Ratio The perimeter-area ratio is a simple measure of shape complexity for a
given channel or lake feature. The ratio is dependent on the size of the
feature: holding shape constant, an increase in channel size will cause a
decrease in the perimeter-area ratio (McGarigal et al. 2012).
SHAPE Index Measures the complexity of a given channel or lake feature compared to a
standard shape (square) of the same size (McGarigal et al. 2012). When a
patch is a square, the index will equal 1. As the patch becomes more
irregular, the index will increase. SHAPE equals patch perimeter (m)
divided by the square root of patch area (m2), adjusted by a constant to
adjust for a square standard:
𝑆𝐻𝐴𝑃𝐸 =0.25 ∗ 𝑝𝑒𝑟𝑖𝑚𝑒𝑡𝑒𝑟
√𝑎𝑟𝑒𝑎
Adjacent Wetland
Length
The length of FHC with contiguous wetland. Wetlands provide a number of
services to adjacent aquatic features (e.g. prey resource input, temperature
regulation, temper and filter floodplain drainage); knowing the proportion
of length with wetland coverage can indicate information about the quality
of the FHC feature.
Adjacent Wetland Class The composition of wetland adjacent to the FHC, which may provide
information about water temperature regulation or prey resource input.
24
Preliminary results from the LPF provide some insight into the framework’s utility for conservation and
restoration planning in estuarine settings. For example, LPF allows the user to compare the relative gain
in the opportunity and capacity of direct fish habitat and confluence density that would accrue with
restoring tidal-fluvial flooding to existing altered FHC features among the eight reaches (Figure 12).
Initial analyses indicate that proportional increases in direct FHC would be greatest in the mid- to upper
reaches E, F, and G. Similarly, proportional increases in confluence density would be greatest in reach A,
as well as E through G. Surveys to sample and identify the genetic stock composition of juvenile Chinook
salmon in the estuary found stock diversity was greatest in reaches A and E through G (Teel et al. 2014).
These results imply the need for multiple conservation strategies that would provide different benefits to
different stocks.
Analyses of fish habitat among landscape units are highly variable and demonstrate the complexity and
patchiness of accessible ecosystems as juvenile salmon move through the estuarine gradient (Figure 13).
There are a number of landscapes between reaches D and F that have a high proportion of altered habitat
(seen in Figure 13 as a high percent change in FHC area and confluence density with full restoration).
This would suggest that this stretch of the estuary may represent a deficiency, or gap, in sufficient habitat
for fish as they migrate downriver.
Figure 12. (A) Total area in acres of open FHC (blue) and altered FHC (yellow) by reach. Percent change (dashed line) in
FHC by reach that would accrue if all altered habitat were restored to natural tidal-fluvial flooding is shown on the
second axis. (B) Count of all open confluences (blue) and altered confluences (yellow) by reach. Percent change (dashed
line) in confluence density by reach that would accrue if all altered confluences were restored to natural tidal-fluvial
flooding is shown on the second axis.
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25
Figure 13. (A) Total area in acres of open FHC (blue) and altered FHC (yellow) by landscape unit. Percent change
(dashed line) in FHC by landscape unit that would accrue if all altered habitat were restored to natural tidal-fluvial
flooding is shown on the second axis. (B) Count of all open confluences (blue) and altered confluences (yellow) by
landscape unit. Percent change (dashed line) in confluence density by landscape unit that would accrue if all altered
confluences were restored to natural tidal-fluvial flooding is shown on the second axis.
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26
Site and Landscape Unit Statistics Through the concept of landscape allometry and its application in restoration ecology, Hood describes the
correlation of landscape form and ecological processes (Hood 2002, 2007a, 2007b, 2014, 2015). Working
in Puget Sound deltas and the lower Columbia River estuary, Hood has documented patterns between
marsh surface area and various metrics of the tidal channels that drain the marshes. By accounting for
marsh size, relationships generated from a large number of active reference marshes can be used as a
standard for comparison of restoration sites, improving upon restoration design and monitoring (Hood
2007b, 2014, 2015). For example, when designing dike breaching in tidal marsh restoration, managers
can cite the number of channel outlets in reference marshes throughout the landscape to determine how
many breaches should be made at the restoration site (Hood 2015).
Following these principles, the Landscape Planning Framework was used to examine the scaling
relationship of tidal channel surface area and channel outlet count with total wetland surface area. In the
following example, individual surge plain (active and isolated) wetlands were identified in the Grays Bay
Landscape using the Ecosystem Complex designation from CREEC and dike locations (Figure 14).
Restored surge plain wetlands were identified where dike breaching has allowed reconnection of tidal
channels with the tributary channel; however, dikes were not fully removed. These site were historically
wetland before being leveed and converted to agriculture. The proposed Brix Bay – Deep River
Confluence restoration site was also identified for comparison with active reference wetlands (see the
following section for more information on this project). Within each wetland, the number of channel
outlets (tidal channel confluences) was counted and tidal channel surface area was summed. The wetland
surface area was also calculated, excluding the channel area. Wetland area was plotted against the
dependent metrics (channel area and channel outlet count) for all reference wetlands. All variables were
log transformed for regression analysis to fit power functions (Hood 2014). The slope of the log-linear
regression trendline is equal to the exponent of the power function and describes how the dependent
metric changes in relation to wetland area (Hood 2014). Restoration sites were then plotted to examine
deviation from the reference wetland regression relationship.
Tidal channel area and wetland area in reference surge plain habitats of the Grays Bay Landscape was
highly correlated (Figure 15A). The data indicate channel area increased at a slightly more rapid rate than
wetland area (scaling exponent equals 1.27). The channel area to wetland area relationship in restored
wetlands and the Brix Bay – Deep River restoration site was nearly identical to reference wetlands. This
suggests an appropriate amount of total channel habitat in restored wetlands compared to reference
habitats.
The number of channel outlets also scaled with wetland area in reference surge plain habitats, though
outlets increased more slowly than wetland area (scaling exponent equals 0.37; Figure 15B). A previous
study that looked at the relationship between channel outlet count and marsh area in surge plain islands of
the Columbia River Estuary found much higher densities of channel outlets than those reported here
(Hood 2015). This difference emphasizes the heterogeneous distribution of fish habitat and the
importance of examining relationships within the context of the surrounding landscape. In the Grays Bay
landscape, the number of channel outlets in restored wetlands and at the restoration site was consistently
lower than surrounding reference wetlands, with all data points falling below the reference trendline. This
agrees with results from Hood’s (2015) study where completed and proposed tidal marsh restoration
projects had on average 5 times fewer channel outlets than reference marshes.
In addition, the average channel size per outlet was significantly greater in restored wetlands than in
reference wetlands in the Grays Bay Landscape (p<0.001). Average channel area in restored wetlands
(including the restoration site) was 2.17 acres, compared to an average channel area of 0.42 in reference
wetlands. Such discrepancies in the size of channels and the number of access points may have
consequences in the restored habitat’s ability to effectively support rearing juvenile salmon.
27
Figure 14. Map of surge plain wetlands in the Grays Bay Landscape. Active surge plain is distinguished from isolated
surge plain, as well as wetlands with restored tidal channels.
Active Wetland Restored Wetland Restoration Site
Figure 15. Scaling of tidal channel (FHC) area (A) and channel outlet count (B) with wetland size in the Grays Bay
Landscape. The trendline and equation shows the power function of active wetland data points.
y = 0.0087x1.2735 R² = 0.9486
0.01
0.1
1
10
100
1 10 100 1000
FH
C A
rea (
acre
s)
Wetland Area (acres)
A y = 1.1099x0.3682 R² = 0.765
1
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Channel O
utlet
Count
Wetland Area (acres)
B
28
User Manual Case Study
The Landscape Planning Framework allows users to evaluate the effects of restoration to juvenile salmon
habitat. Once the existing features, or proposed in the case of restoration planning, have been
characterized, their spatial attributes can be quantified and compared to a reference site, other restored
sites, other restoration scenarios, or pre-restoration conditions. Discrete project areas and their proposed
features can also be assessed for their contribution of open FHC to larger landscapes. This allows the LPF
user to quantify the change a project provides to broader landscapes (in terms of open habitat versus
potential habitat).
The following restoration planning case study will illustrate how to quantify the landscape, calculate LPF
metrics, and interpret those metrics to tell a compelling story about the effects of restoration to juvenile
salmon habitat. The following case study is just an example, and does not calculate every single LPF
metric. However, a new user should be able to replicate the processes outlined below and establish a
foundation for using the LPF.
To perform the LPF restoration evaluation, the following software is needed:
a spreadsheet program (Microsoft Excel, Apache OpenOffice Spreadsheet, Google Sheets) for
organizing your landscape values, LPF metrics, and change percentages;
a geographic information system (GIS) (ArcGIS, QuantumGIS) for displaying, selecting (using
feature attributes and location), geoprocessing FHC features, and quantifying landscape values.
All screenshots and directions are written with the use of Microsoft Excel and ESRI ArcMap for
Windows desktop. Users performing the LPF restoration evaluation with different software should be able
to follow along, but may need to alter some steps slightly to fit within the constructs of different software
packages.
How To: Planning Case Study- Brix Bay | Deep River Confluence Restoration The Brix Bay – Deep River Confluence site is located in a transition zone for migrating juvenile
salmonids in freshwater tidal rearing habitats before transitioning to the broader Columbia River estuary
(Figure 16). The project site, directly adjacent to Deep River, Brix Bay, and Grays Bay, historically
provided important rearing habitat within a broader freshwater tidal swamp complex. The project is also
very close to the North Channel of the Columbia River estuary. North Channel is a semi-diffused
distributary channel off the mainstem that begins upriver from Rice Island and meanders closely to Gray
Bay area. Fish tagging studies completed by Pacific Northwest National Laboratory (PNNL) in 2010
show a high proportion (87%) of subyearling Chinook migrating across shallows surrounding North
Channel (McMichael et al. 2011).
The 175-acre project site was historically connected to the Deep River by three large tidal channel
systems, providing access to a complex network of tidal meanders and a diverse mosaic of Sitka spruce
surge plain wetlands. Today, the site is constrained by a road levee with three tidegates at the historical
tidal channel confluences that control minimal juvenile salmonid ingress/egress into the site. The project
goal map (Figure 17) characterizes primary restoration actions planned for the Brix Bay – Deep River
Confluence site. The goal of the project is to re-establish tidal hydrology by removing the tidegates and
replacing them with bridge structures that will allow full tidal volume exchange, reshaping and restoring
diverse and complex estuarine habitat over time.
29
Figure 16. Map of the Brix Bay - Deep River Confluence restoration site.
Figure 17. Map of the Deep River Confluence primary restoration actions.
30
Quantifying the Site and Landscape The first step in using the LPF is choosing the scales of analysis. For the Brix Bay – Deep River
Confluence restoration project, the Grays Bay Landscape and Deep River Sub-landscape were chosen to
highlight contributions of the project in the context of these larger landscapes (see Figure 16). This
approach provides a nested landscape consideration to understand the contributions of the project to the
Deep River system and the Grays Bay Landscape as a whole. These local landscapes all reside within
Reach B, a reach situated near the freshwater tidal – oligohaline transition within the estuary. Habitat
transitions in the estuary near the ocean are considered relevant to rearing and migrating juvenile
salmonids, as this transition involves dramatic shifts in prey and predators (Simenstad, Cordell 2000).
At the site scale, the Brix Bay – Deep River Confluence project site is compared to an upstream wetland
that was breached 12 years ago on the Deep River. The site was historically wetland before being leveed
and converted to agriculture. The site underwent restoration in 2004 and has had twelve years of tidal and
fluvial inundation and propagation of native wetland vegetation, primarily characterized as tidal
coniferous forest. As the restored site has responded to the reintroduction of increased hydrologic
volumes, coniferous forest die-off and shrub scrub propagation has been observed. It could be expected
that the project site will evolve on a similar trajectory. The project site is also compared to two
undeveloped surge plain sites of approximately the same size located within the Grays Bay Landscape.
Reference Site A is located along Grays River and is primarily characterized as a mixed coniferous-
deciduous forested tidal wetland; Reference Site B is a mixed tidal and non-tidal coniferous forested
wetland located along Crooked Creek. These sites serve as references for wetland conditions where
development has not impeded the geomorphic structure of the habitat and are suggestive of an endpoint
target for the project site as hydrologic processes are restored.
Once the scales of analysis are selected, the user must define which LPF metrics to calculate (see Table 9
in the Data Summary section above). In this example, Confluence Density (CD), Direct FHC Percent
Landscape (PLAND), Direct FHC Edge Density (ED), and SHAPE Index were chosen. Confluence
Density is a measure of the number of confluence points divided by the analysis area (acres), multiplied
by 100 (to convert to confluence count per 100 acres). Confluences are important opportunities for
juvenile salmonids as entry points into discrete habitat patches. Percent Landscape is a measure of FHC
area divided by landscape area, multiplied by 100 (to convert to a percentage). Understanding the percent
of the landscape that is made up of direct FHC can inform the user of the relative amount of habitat within
a defined landscape that is regularly available to juvenile salmonids. Edge Density is a measure of the
length of FHC perimeter divided by the analysis area, and provides information about the complexity and
foraging interface of the FHC relative to the total landscape area. SHAPE Index is calculated at the site
scale for the largest tidal channel in each of the selected wetlands and equals the channel perimeter
divided by the square root of the channel area, adjusted by a constant to adjust for a square standard
(McGarigal et al. 2012). The index equals 1 when the feature is square and increases as the shape
becomes more irregular. The largest channel represents a significant portion of the available fish habitat
(ranging from 33 to 80 percent in the selected wetlands) and this index provides a representative measure
of channel irregularity, or complexity, which can be compared among sites.
The site is a marsh located in the surge plain (although it is currently isolated from tidal influence) with
floodplain channels as the main hydrologic feature. Since these features are the focus of the restoration,
they will also be the focus of the analysis. In the selection process (below), only surge plain and surge
plain isolated complexes will be included for the marsh area and only floodplain and tidal channels will
be included for the confluences, Direct FHC area, and Direct FHC edge. For this analysis, small channels
(where total channel area is less than 100 square meters; Confluence Size = 0) will also be omitted.
To populate the metrics table with values, FHC must be selected with a combination of selection tools
within GIS: select by location, select by attribute, and manual selection. Try selecting features from the
31
FHC based on their location (completely within, intersect, etc.) relative to your scale of analysis polygon
(site, sub-landscape, landscape). Be careful when using select by location with polygons that do not
originate from the FHC layers (project site or reference site polygons) because they may not share the
same boundaries as the FHC polygons. It may help to alter your project site or reference site polygon (if
possible) to better fit within the FHC polygon boundaries. This is a good time to zoom in and make sure
all the FHC features on your site have been selected, and no external features are included. If the selection
needs to be adjusted, use the manual selection tool to add or subtract features from the selection. After
using the select by location tool, isolate just open or just altered FHC using the select by attribute tool
(and selecting from the current selection). Repeat the selection process until the table has all the necessary
values. Alternatively, instead of using the selection tools within GIS, geoprocessing tools like intersect
and union also isolate features for analysis using the scale of analysis polygon (project site, sub-
landscape, landscape) and an FHC layer as inputs to the tools. Table 10 lists the queries used to isolate the
target features. With the scales of analysis and LPF metrics chosen, the user can quantify the features to
calculate metrics. For the four metrics mentioned above (CD, PLAND, ED, SHAPE) the values needed
for each scale of analysis calculation are listed in Table 11.
Table 10. Select by attribute queries used to isolate FHC features for site and landscape analysis.
Target Feature Select by Attribute Query
Open Floodplain and Tidal
Channel Confluence
(("ChannelType_a" = 'Floodplain channel' OR
"ChannelType_a" = 'Tidal channel') OR
("ChannelType_b" = 'Floodplain channel' OR
"ChannelType_b" = 'Tidal channel')) AND
("ConfluenceSize" = 1 AND
"ConfluenceStatus" = 'Open')
Altered Floodplain and Tidal
Channel Confluence
(("ChannelType_a" = 'Floodplain channel' OR
"ChannelType_a" = 'Tidal channel') OR
("ChannelType_b" = 'Floodplain channel' OR
"ChannelType_b" = 'Tidal channel')) AND
("ConfluenceSize" = 1 AND
"ConfluenceStatus" = 'Altered')
Open Floodplain and Tidal
Channel Direct FHC
("ChannelType" = 'Floodplain channel' OR
"ChannelType" = 'Tidal channel') AND
("Complex" = 'Surge plain' OR
"Complex" = 'Isolated surge plain') AND
"FishHabitatStatus" = 'Open'
Altered Floodplain and Tidal
Channel Direct FHC
("ChannelType" = 'Floodplain channel' OR
"ChannelType" = 'Tidal channel') AND
("Complex" = 'Surge plain' OR
"Complex" = 'Isolated surge plain') AND
"FishHabitatStatus" = 'Altered'
Complex Selection "Complex" = 'Surge plain' OR
"Complex" = 'Surge plain (isolated)'
32
Table 11. Summary statistics used to quantify landscape metrics at each scale of analysis for the Deep River Confluence restoration case study.
Confluence
(Count)
Direct FHC Area
(Acres)
Direct FHC
Length
(1,000 Feet)
Largest
Channel
Area
(Acres)
Largest
Channel
Length
(1,000
Feet)
Surge
Plain
(Acres)
Isolated
Surge
Plain
(Acres)
Total
Complex
(Acres) Scale Open Altered Open Altered Open Altered
Grays Bay
Landscape 89 31 64.45 94.90 211.55 228.87 -- -- 1,887.05 1,716.32 3,603.37
Deep River
Sub-landscape 13 13 4.75 57.22 8.20 122.88 -- -- 291.93 1,024.31 1,316.24
Reference Site A 10 -- 4.89 -- 15.45 -- 1.63 5.00 131.70 -- 131.70
Reference Site B 5 -- 5.66 -- 17.07 -- 4.52 12.55 192.66 -- 192.66
Restored Site 3 -- 5.67 -- 14.38 -- 4.47 10.30 142.12 -- 142.12
Project Site -- 3 -- 12.69 -- 29.96 5.77 15.48 -- 175.69 175.69
33
Site Comparison Many of the LPF metrics are densities or percentages (as is the case for the metrics in this example),
which allows for comparing among landscapes of varying sizes. Using the values quantified through the
selection process described above, the formulas for CD, PLAND, ED, and SHAPE can be calculated and
used for comparison and evaluation of site scale change (Table 12).
Table 12. Example site scale calculations of LPF metrics for the Deep River Confluence restoration case study. Open
habitat is summarized for the Reference and Restored Sites, and potential habitat (altered) is summarized for the Project
Site.
Scale
Confluence
Density
(Count per 100
acres)
Direct FHC %
Landscape
Direct FHC
Edge Density
(Feet per
landscape acre) SHAPE Index1
Reference Site A 7.59 3.71 117.29 4.68
Reference Site B 2.60 2.94 88.60 7.08
Restored Site 2.11 3.99 101.20 5.84
Project Site 1.71 7.22 170.51 7.72 1SHAPE Index is calculated for the largest channel in the wetland.
Confluence Density is a measure of the number of confluence points per 100 acres of analysis area.
Confluences are important opportunities for juvenile salmonids as entry points into discrete habitat
patches. The CD of open confluences at the restored site is 2.11 compared to 1.71 for the potential open
confluences at the project site. Both sites have three confluences, but the project site is approximately 30
acres larger, decreasing the CD score. When compared to reference marshes, both the project site and the
restored site have lower confluence densities. From a purely ecological perspective, this could suggest
that the restoration approaches at both the project site and restored site are conservative in the number of
breaches planned, and the sites could benefit from additional levee breaches or complete levee removal. A
more aggressive breaching or levee removal plan could provide more opportunity for channel (and thus
confluence) development, higher confluence densities, and a more natural marsh development trajectory,
mimicking reference marshes nearby.
Direct FHC Percent Landscape (PLAND) is a measure of FHC area divided by complex area and
represents the capacity of a site or landscape. Understanding the percent of the landscape that is made up
of direct FHC can inform the user of the amount of habitat that is regularly available to juvenile
salmonids. The project site potential PLAND is almost twice that of the restored site. This discrepancy in
PLAND scores can be attributed to more area of direct FHC on the project site than on the restored site.
In this case, there is the same number of channel features (three) for both sites, but the project site
channels are larger. When compared to reference marshes, the Direct FHC PLAND values for the project
site and restored site were similar or higher. The number of channel features on the project site and
restored site were fewer and larger than the relatively smaller and more numerous channels on reference
sites.
Edge Density is a measure of the length of FHC perimeter divided by the analysis area and provides
information about the complexity and extent of foraging interface of the FHC. In this example, the project
site has the greatest density of edge habitat compared to both the reference and restored sites.
Additionally, the SHAPE Index for the largest channel in each of the wetlands was greatest at the project
34
site, suggesting this channel had a relatively irregular shape. High irregularity in channel shape
demonstrates a potential for a particularly sinuous and complex channel habitat. Greater sinuosity and
complexity of channel features offers a better foraging interface for juveniles to interact with adjacent
wetland vegetation.
Overall, the project site differs from reference sites primarily in terms of confluence density and channel
size, and compares similarly with the restored site. The project proposes to open the same number of
confluences as the restored site while providing a greater density and complexity of direct FHC. The
comparison to the restored site, along with the project sites adjacency to the confluence of Deep River and
Grays Bay/Mainstem Columbia River make it a strong candidate for restoration in the future.
Characterizing Landscape Change To demonstrate the change a project provides to the landscape, it is important to understand the FHC that
is currently open versus the FHC that is altered and has potential for restoration. By adding the altered
FHC from the project site, which will be restored to open, to the open values that already exist in the
Deep River and Grays Bay landscapes, the user can see how the LPF metrics change with the
implementation of the project (Table 13). These values are relative to size and unit of measurement and
do not always convey change clearly. However, if you quantify the project’s proportional change of the
total potential change for the landscape, a more intuitive picture comes into focus. Percent of potential
change is calculated as:
% 𝐶ℎ𝑎𝑛𝑔𝑒 = 𝑂𝑝𝑒𝑛 𝑤𝑖𝑡ℎ 𝑃𝑟𝑜𝑗𝑒𝑐𝑡 − 𝑂𝑝𝑒𝑛
𝑃𝑜𝑡𝑒𝑛𝑡𝑖𝑎𝑙 − 𝑂𝑝𝑒𝑛∗ 100
Table 13. LPF metric change to the landscape from potential (open + altered) and project implementation.
Landscape
Confluence Density
(Count per 100 acres) Direct FHC % Landscape
Direct FHC Edge Density
(Feet per acre)
Open Potential Open Potential Open Potential
Grays Bay 4.72 3.33 3.42 4.42 112.11 122.23
Deep River 4.45 1.98 1.63 4.71 28.08 99.59
Open Open w/ Project Open Open w/ Project Open Open w/ Project
Grays Bay 4.72 4.46 3.42 3.74 112.11 117.08
Deep River 4.45 3.42 1.63 3.73 28.08 81.59
By describing the project’s change relative to the potential change for the landscape, you convey the
proportion of potential change capitalized with the envisioned project (Table 14).
Table 14. Percent of the potential change for the entire landscape realized from project implementation.
Landscape Confluence Density Direct FHC % Landscape Direct FHC Edge Density
Grays Bay 18.49 32.21 49.16
Deep River 41.63 68.23 74.83
Grays Bay and Deep River fish habitat availability would increase from the proposed restoration. These
landscapes, Reach B, and the Columbia River estuary would derive benefit, as would the salmonid stocks
35
that utilize the estuary. The Grays Bay landscape and Deep River sub-landscape CD scores decrease with
project implementation. The CD metric decreases for the landscape and sub-landscape because the project
opens a large acreage of surge plain habitat with relatively few confluences that provide access to the site
(see Table 11 CD values). When compared to reference marshes, the project site’s confluence density is
much lower. Re-introducing a site with low confluence density lowers the landscape and sub-landscape
confluence densities that include both restored and reference sites. This illustrates an argument for more
breach locations for planned restoration, as argued by Hood (2015). The Grays Bay landscape would
realize 18.49 percent of its CD change from restoration, while Deep River would realize 41.63 percent of
its CD change. The metric of Direct FHC PLAND realizes approximately 32 percent and nearly 70
percent of the potential for Grays Bay and Deep River, respectively. The ED metric also sees a dramatic
increase with almost 50 percent and almost 75 percent realized potential lift for the Landscape and Sub-
landscape. As mentioned previously, the channels in altered marshes are larger and fewer in number than
open reference marshes, which exhibit numerous smaller channels as a result of exposure to tidal and
riverine flows. These open reference marshes could provide a template for restoration design,
recommending not only to reconnect the larger channels seen in altered marshes, but to create additional
smaller channels to increase opportunity and capacity of restoration sites. There is more restoration
potential in Deep River and Grays Bay. Much of the surge plain wetland habitat has been isolated by
levees and water control structures. With the implementation of the Brix Bay – Deep River Confluence
restoration project, a large piece of habitat will be restored and accessible to juvenile salmonids. The
changes from this project will have significant impacts to Deep River and the Grays Bay landscape as a
whole, making a major stride towards restoring FHC in the landscape.
Future Applications | Next Steps
The Landscape Planning Framework (LPF) is a landscape ecology-based, geospatial approach to identify
and compare spatially-explicit sites that would most likely benefit unique, at-risk genetic stocks of
Columbia River salmon. The LPF is designed to address juvenile Chinook habitat because their ocean-
type life history forms tend to be the most dependent on estuarine habitat and because their populations
are depleted in the Columbia River basin to the point that five Evolutionary Significant Units (ESU) are
listed under the US Endangered Species Act (Bottom et al. 2005; Teel et al. 2014). While the framework
has been highly specialized to date, its versatility transcends species and geography.
The LPF process of developing guiding principles, identifying habitat requirements, and applying those
tools to create a spatial database classifying habitat is pertinent to any species of concern in any estuary.
For researchers in the Columbia River estuary, the spatial database framework is already in place with the
Columbia River Estuary Ecosystem Classification (Simenstad et al. 2011 and USGS 2012). In the
Columbia River estuary, the LPF approach could be applied to other species including other salmonids
like Coho or steelhead, shorebirds like plovers and sandpipers, wading birds like great blue heron and
sandhill crane, amphibians like Oregon spotted frog and western pond turtle, or mammals like Columbian
white-tailed deer or American beaver. These species inhabit a variety of estuary habitat types that are
covered in detail by the Classification.
In other estuaries, a robust ecosystem classification is the first step to developing the LPF. Some
estuaries, like the Sacramento River, are already poised to develop the LPF approach on top of an existing
classification system. Undoubtedly, there are a large number of estuarine researchers with a firm grasp on
species habitat requirements and guiding principles. These individual pieces are important, but realize
their true potential when combined into the Landscape Planning Framework.
Currently, the LPF would not be well positioned for species that primarily utilize subtidal habitats such as
sturgeon or lamprey. The Classification that serves as the basis for LPF is considerably underdeveloped
36
for subtidal ecosystems. An effort to classify those ecosystems would be valuable in the application of
LPF for species that utilize those habitats.
The LPF is a powerful tool for understanding the spatial distribution of species specific habitats in estuary
ecosystems. The LPF can be used to quantify landscapes and individual sites, which can inform
restoration and conservation planning. LPF has the versatility and scientific rigor for a variety of
applications. Whether the application is setting habitat restoration and conservation targets, informing a
strategy to identify the priority types and locations of habitats for restoration and conservation, or
understanding how a site contributes to the landscape, LPF has the tools and metrics to provide those
insights. Moving forward, the LPF team is exploring further analysis and intuitive metrics for
understanding landscapes and telling compelling stories of restoration and conservation.
37
References
Bottom, D. L., Simenstad, C. A., Burke, J. L., Baptista, A. M., Jay, D. A., Jones, K. K., Casillas, E., and
Schiewe, M. H. 2005. Salmon at river’s end: The role of the estuary in the decline and recovery
of Columbia River salmon. U.S. Department of Commerce, NOAA Technical Memorandum.
Burke, J. L. 2010. Georeferenced historical topographic survey maps of the Columbia River estuary.
School of Aquatic and Fishery Sciences, University of Washington, Seattle, Wa.
Hood, W. G. 2015. Predicting the number, orientation and spacing of dike breaches for tidal marsh
restoration. Ecological Engineering 83: 319-327.
Hood, W. G. 2014. Differences in tidal channel network geometry between reference marshes and
marshes restored by historical dike breaching. Ecological Engineering 71:563-573.
Hood, W. G. 2012. Beaver in tidal marshes: Dam effects on low-tide channel pools and fish use of
estuarine habitat. Wetlands 32: 401-410.
Hood, W.G. 2007a. Landscape Allometry and Prediction in Estuarine Ecology: Linking Landform
Scaling to Ecological Patterns and Processes. Estuaries and Coasts 30: 895-900.
Hood, W. G. 2007b. Scaling tidal channel geometry with marsh island area: a tool for habitat restoration,
linked to channel formation process. Water Resources Research 43, W03409. Doi:
http://dx.doi.org/10.1029/2006WR005083.
Hood, W. G. 2002. Application of landscape allometry to restoration ecology. Restoration Ecology 10:
213-222.Lower Columbia Estuary Partnership. 2011. High Resolution Land Cover Mapping in
the Lower Columbia River Estuary. Prepared by Sanborn Map Company.
McGarigal, K., S. A. Cushman, and E. Ene. 2012. FRAGSTATS v4: Spatial Pattern Analysis Program for
Categorical and Continuous Maps. Computer software program produced by the authors at the
University of Massachusetts, Amherst. Available at the following web site:
http://www.umass.edu/landeco/research/fragstats/fragstats.html
McMichael, G. A., R. A. Harnish, J. R. Skalski, K. A. Deters, K. D. Ham, R. L. Townsend, P. S. Titzler,
M. S. Hughes, J. Kim, and D. M. Trott. 2011. Migratory behavior and survival of juvenile
salmonids in the lower Columbia River, estuary, and plume in 2010. PNNL-20443, Pacific
Northwest National Laboratory, Richland, Washington.
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.
Simenstad, C.A., Cordell, J.R. 2000. Ecological assessment criteria for restoring anadromous salmonid
habitat in Pacific Northwest estuaries. Ecological Engineering. 15: 283-302.
Teel, D. J., Bottom, D. L., Hinton, S. A., Kuligowski, D. R., McCabe, G. T., McNatt, R., Roegner, G. C.,
Stamatiou, L. A., and Simenstad, C. A. 2014. Genetic identification of Chinook salmon in the
Columbia River estuary: Stock-specific distributions of juveniles in shallow tidal freshwater
habitats. North American Journal of Fisheries Management. 34: 621-641.
U.S. Geological Survey. 2012. Columbia River Estuary Ecosystem Classification. Vector digital data.
38
Appendix
Appendix A. Datasets and descriptions included in the Fish Habitat Catena geodatabase (FHCv1_FINAL.gdb).
Dataset Description Data Sources Analysis Metric(s)
Direct_fish_habitat_ catena
Polygon; categorized as open or altered habitat that may be directly utilized by juvenile salmon
CREEC Catena (2012) CREEC Cultural Features
(2012) OR NAIP (2009) WA NAIP (2009) LiDAR/Columbia River Terrain
Model (1930-2010) T-sheets (1868-1901)
Capacity area edge
Opportunity channel type diversity tributary
confluence connectivity
Indirect_wetland Polygon; adjacent wetlands occurring within 2 meters (herbaceous), 5 meters (scrub-shrub), or 20 meters (forested) of fish habitat catena
Lower Columbia River Estuary Land Cover (2010)
Capacity wetland type area channel
connectivity
Indirect_drainage Polygon; estimate of tidally influenced and tidally impaired areas around the fish habitat catena
Lower Columbia River Estuary Land Cover Hydrologic Information (2010)
Lower Columbia River Estuary Land Cover (2010)
Capacity area
Indirect_USACE_ 2y_flood
Polygon; estimate of area inundated under the 2-year flood elevation around the fish habitat catena
USACE 50% AEP Stage for Columbia River Estuary (2011)
LiDAR/Columbia River Terrain Model (1930-2010)
Capacity area
LandscapeFeature_ confluence
Point; channel confluence point where dissimilar FHC aquatic features converge
CREEC Catena (2012) CREEC Cultural Features
(2012) OR NAIP (2009) WA NAIP (2009) LiDAR/Columbia River Terrain
Model (1930-2010) T-sheets (1868-1901)
Opportunity occurrence nearest neighbor
LandscapeFeature_ potential_beaver_ habitat
Polygon; potential locations of American beaver habitat selected from the fish habitat catena based on size, channel type, and location in a wooded ecosystem criteria
CREEC Catena (2012) Opportunity occurrence
LandscapeFeature_ head_of_tide
Point; up-valley extent of strong tidal influence, defined by the Classification
CREEC Catena (2012) Opportunity occurrence
Isolated_lake Polygon; naturally isolated lakes with no channelized connection to the Columbia River system
CREEC Catena (2012) CREEC Cultural Features
(2012) OR NAIP (2009) WA NAIP (2009) LiDAR/Columbia River Terrain
Model (1930-2010) T-sheets (1868-1901)
Landscape_unit Polygon; level of analysis between the scale of an ecosystem complex and hydrogeomorphic reach
CREEC Complex (2012) Scale of analysis
Recommended