Integrated Status & Effectiveness Monitoring Program

Project \# 2003-017-00

PI: Dr. Chris Jordan, NOAA Fisheries, NWFSC

Draft Annual Report

Performance Period: October 1, 2004 -- September 30, 2005

Reporting Period: January 1, 2004 -- September 30, 2005

**Abstract**

This project seeks to develop two novel monitoring and evaluation
programs: (i) subbasin-scale pilot status and trend monitoring efforts
for anadromous salmonids and their habitat in the Wenatchee, John Day
and Salmon River basins, and (ii) effectiveness monitoring for suites of
habitat restoration projects in selected watersheds within the three
target subbasins. Project progress in 2004 and 2005 has focused on the
development of standardized status monitoring designs and protocols
(Statement of Work (SOW), Task 1.1 and 1.2), effectiveness monitoring
designs and conceptual gap analyses for Intensively Monitored Watersheds
(IMWs) (SOW Task 1.2 and 1.3), inventory and compilation of existing
agency data and coordination efforts (SOW Task 1.3), and the development
of data management tools for agency and subbasin scale projects (SOW
Task 2). The overall technical and scientific coordination of the
project has been a responsibility of the project sponsor (NNMFS/NWFSC,
Dr. Chris Jordan). This report addresses the progress of three technical
coordination tasks: monitoring project design and data collation (SOW
Objective 1), data management oversight (SOW Objective 2), and
statistical support (SOW Objective 3).

The RME program seeks to design and implement both status and trend and
effectiveness monitoring programs within pilot basins. This monitoring
project addresses four objectives:

Status and Trend:

i)  To assess the status of adult and juvenile anadromous salmonid
    populations and

ii) To assess the status of adult and juvenile anadromous salmon
    population habitat, both at the scale of the subbasin.

Effectiveness:

iii) To determine the biological benefit to anadromous salmonid
     populations with respect to ongoing habitat restoration actions and

iv) To determine the distribution of physical/environmental habitat
    condition as a function of ongoing habitat restoration actions.

Implementing the subbasin scale intensive monitoring projects has
involved contracting with numerous individuals and agencies. A
coordination staff has been assembled for each subbasin BioAnalysts and
Terraqua (Wenatchee), Eco Logical Research and NMFS/NWFSC (John Day),
and Quantitative Consultants and NMFS/NWFSC (Salmon River). Project
coordination staff have been responsible for securing contracts with
agencies for project implementation, plan writing and productivity
monitoring component development, statistical design/analysis
development, and monitoring indicator development. For further
information regarding specific consulting tasks reference annual report
submittals and study plans from Terraqua and EcoLogical consultants.
Preliminary project design by Quantitative Consultants will not be
contracted until 2006.

RME progress within pilot basins has varied due to different resources
and project trajectories within basins. In 2004 - 2005, efforts within
the Wenatchee basin have focused on the development of spatial status
and effectiveness monitoring designs for the entire basin and Entiat
IMW, comparison of habitat and invertebrate field protocols and
evaluation of fish population distributions and field metrics (e.g. trap
efficiencies). In the John Day basin we have compiled a comprehensive
library of spatial and tabular data (historical and recent), compared
multiple in-stream habitat and sedimentation protocols, developed
conceptual IMWs and field studies for fish production (SF John Day IMW)
and sediment transport-incision (Bridge Creek IMW) projects and
collaborated with remote sensing and basin-wide sedimentation modeling
projects (University of Washington and Oregon State University). In the
Salmon basin, initial effectiveness monitoring strategies and sites for
channel reconnection restoration projects in association with the Lemhi
Habitat Conservation Plan have been discussed for full design and field
implementation in 2006.

Data management (Task 2) progress in 2004 - 2005 has included the
development of an Oracle database and adjacent Status and Trend
Monitoring internet data access page (Wenatchee pilot project), the
completion of a comprehensive Data Dictionary and Protocol Manager (John
Day pilot project), and spatial GIS data compilation and standardization
for both the John Day and Wentachee projects.

**Objective 1: Coordination of design and implementation of integrated
status and effectiveness monitoring project.**

Status monitoring and IMW effectiveness monitoring development has
focused on identifying the problems and effectiveness of associated
restoration projects limiting salmonid production in the RME pilot
basins. The primary product resulting from these discussions will be a
subbasin specific monitoring program implementation plan with identified
data collection efforts, funding and data management. Many subtasks will
continue to be handled through independent contracts and cooperative
agreements depending on external funding sources.

[]{.mark}

**Task 1.1. Oversee initiation of pilot projects in 3 Columbia River
subbasins**

The initiation of integrated status and effectiveness monitoring in the
pilot subbasins has taken very different forms in each basin. Each
subbasin is beginning the process of coordinated monitoring from a very
different place -- either based on current/historic monitoring programs
and investment or in the political/philosophical basis on which to build
a cooperative program focusing on data collection and management. As the
overall project coordinator, NWFSC and the PI have invested resources to
varying degrees and in varying manners in the Wenatchee, John Day and
Salmon basins. Also, due to varying degrees of existing coordination and
agency involvement prior to the RME program design, each basin has
piloted different subtasks of the pilot project according to the
immediate strengths and needs of the basin. As a coordinating entity,
the NWFSC and sponsoring PI have facilitated communication among
subbasin TOCs and coordinators that has resulted in the sharing of
piloted information. For example, the development of the John Day
Protocol Manager for data management was developed based on protocols
that are currently being field tested within the Wenatchee basin.
Similarly, the structure of the Status and Trend Monitoring Oracle
database designed by NWFSC for the Wenatchee basin has been shared with
the John Day basin coordinators to facilitate data collection and
storage within the John Day basin.

In the Wenatchee River basin, to initiate the pilot ISEMP, NWFSC and the
PI primarily lead discussions and design sessions with an existing
coordination entity, the Upper Columbia Salmon Recovery Board's Regional
Technical Team (RTT). The RTT is a long-standing chartered group that
functions to coordinate monitoring field work in the Upper Columbia,
serve as technical review for Salmon Recovery Funding Board project
proposals, and as a general coordination forum for salmon co-managers in
the Upper Columbia. The RTT was brought into the pilot project design
process informally during project initiation, and ultimately formally as
the official project Technical Oversight Committee for the Wenatchee
River basin pilot. As the official TOC, design and implementation issues
are discussed at the RTT, and overall project direction issues are
raised and discussed by the RTT. Final decisions on project goals and
progress is ultimately decided on by the Wenatchee coordinators
(Terraqua and BioAnalyst) and project sponsor (NWFSC/PI), but all issues
are raised for general guidance with the RTT. This process has been
highly successful as the RTT is an established group with good standing
with co-managers and related organizations.

In the John Day River basin no parallel organization to the Wenatchee
RTT currently exists, so project initiation has focused primarily on
generating on-the-ground support for the idea of an integrated status
and effectiveness monitoring program, and staffing the coordinator
position to keep the development effort moving forward. NWFSC and the
project PI have developed a collaborative forum (Analytical Framework
Group or AFG) with several large on-going monitoring data-collection
efforts in the John Day River basin to scope out the opportunities for
program development. The agencies involved have been Oregon Department
of Fish and Wildlife, Oregon Watershed Enhancement Board, Oregon
Department of Environmental Quality, US Forest Service (PIBO monitoring
group), US EPA (EMAP research group, WED-Corvallis), CTWSR Fish
biologists, US Bureau of Reclamation (ESA office PDX and BOI), and
Oregon State University. Staff from these agencies met regularly to
describe current monitoring programs, current efforts to establish
subbasin-wide approaches and standards for habitat and population
assessment, particular research and critical uncertainty work and needs,
and desires and needs for coordination and collaboration. Very little
progress on the latter was ever achieved outside of the meetings due to
the wide diversity of participants, varying agency mandates each
participant was trying to satisfy, and uncertain funding and long-term
planning on many fronts. However, the meetings did generate the raw
material upon which a coordinator could build when finally brought on
board. EcoLogical Research was contracted to begin coordination efforts
design and implementation of John Day River basin pilot project work
following up on initial scoping and design initiated by US Bureau of
Reclamation. The design and coordination work to date has focused on
maintaining an informal Technical Oversight Committee comprised of
agency staff who had participated in earlier scoping and planning
meetings, documenting current and historic monitoring efforts, and
designing Intensively Monitored Watershed experiments to complement
existing status monitoring and identified limiting factors.

In the Salmon River basin, project initiation focused on two major
issues -- which part of the geographically large and diverse basin
should be included in the pilot work, and how to balance status and
effectiveness components if they were not co-located. To date, progress
on these issues has resulted from regular meetings and discussions with
staff from Idaho Fish and Game, US Forest Service, Nez Perce and
Shoshone Bannock Tribes and Idaho Department of Environmental Quality.
The current discussions on location and design are focusing on the Lemhi
River and South Fork Salmon River as two locations in which differing
degrees of design and implementation effort will be applied. The Lemhi
River offers the opportunity, through the Lemhi River Habitat
Conservation Plan discussions to engage an existing forum that has done
considerable work in the area of large scale habitat restoration action
and limiting factor assessment. A major gap that the pilot project could
fill in the Lemhi would be monitoring the implementation of the Lemhi
HCP as an intensively monitored watershed to assess the population level
impact of the HCP on Chinook and Steelhead. In the South Fork Salmon
River, status monitoring for fish populations, in particular Chinook,
are well developed through the work of the Nez Perce and IDFG. There are
limited opportunities for effectiveness monitoring in the South Fork, at
least currently, but there are major gaps in the status monitoring
program in that little or no habitat data is collected in conjunction
with the fish data. Therefore, the Salmon River basin pilot project will
focus on the design of monitoring programs in the Lemhi River and South
Fork Salmon River that build off of current programs and plans,
specifically to address watershed scale effectiveness monitoring design
and implementation issues in the Lemhi and integrating habitat and fish
status monitoring in the South Fork Salmon. A coordinator for this work
has been identified, Quantitative Consultants, and agreed to by the
major co-managers for these basins (NPT, IDFG, S-BT). Quantitative
Consultants have begun scoping out the potential design consideration
for the Lemhi and South Fork Rivers, and will begin coordination in
earnest in FY2006.

##### Table 1. Subbasin Coordination Summary 2004 - 2005. 

##### 

+---------------+-------------------+------+--------------------------+
|               | **Product         | **A  | **Annual report**        |
|               | delivery**        | ssoc |                          |
|               |                   | iati |                          |
|               |                   | on** |                          |
+---------------+-------------------+------+--------------------------+
| **John Day**  |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| EcoLogical    | John Day subbasin | Co   | EcoLogical-BPA 1st       |
|               | coordination and  | ntra | Quarter 2004-2005        |
|               | RME analytical    | ctor |                          |
|               | design            |      |                          |
+---------------+-------------------+------+--------------------------+
| NWFSC,        | Tabular and       |      | Directly incorporated    |
| N             | spatial data      |      | into BPA annual report   |
| OAA-Fisheries | collation,        |      |                          |
|               | storage, delivery |      |                          |
|               | and management    |      |                          |
+---------------+-------------------+------+--------------------------+
| NWFSC,        | Bridge Creek IMW  |      | Directly incorporated    |
| N             | monitoring design |      | into BPA annual report   |
| OAA-Fisheries | and restoration   |      |                          |
|               | plan              |      |                          |
+---------------+-------------------+------+--------------------------+
| EPA           | Habitat protocol  | Coll |                          |
|               | comparison and    | abor |                          |
|               | basin-wide        | ator |                          |
|               | sedimentation     |      |                          |
|               | model             |      |                          |
+---------------+-------------------+------+--------------------------+
| Oregon State  | SF John           | Coll | OSU- BoR Annual Report   |
| University    | Day-Murderer's    | abor | 2004-2005                |
|               | Creek IMW fish    | ator |                          |
|               | productivity      |      |                          |
|               | study and         |      |                          |
|               | effectiveness     |      |                          |
|               | monitoring design |      |                          |
+---------------+-------------------+------+--------------------------+
| BoR           | Data management,  | Coll |                          |
|               | protocol manager  | abor |                          |
|               | development       | ator |                          |
+---------------+-------------------+------+--------------------------+
| **Wenatchee** |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| TerrAqua      | Wenatchee         | Co   | Terraqua-BPA Annual      |
|               | subbasin          | ntra | Report 2004-2005         |
|               | coordination      | ctor | Terraqua                 |
|               |                   |      | -ISEMP_ImpStrat_Document |
|               |                   |      |                          |
|               |                   |      | Terraqu                  |
|               |                   |      | a-ISEMP_ImpStrat_Figures |
+---------------+-------------------+------+--------------------------+
| BioAnalyst    | Upper Columbia    | Co   | BioAnalyst-BPA Annual    |
|               | Monitoring        | ntra | Report 2004-2005         |
|               | Strategy          | ctor |                          |
|               | Development       |      |                          |
+---------------+-------------------+------+--------------------------+
| Chelan County | Water quality     | Co   |                          |
|               |                   | ntra |                          |
| Conservation  |                   | ctor |                          |
| District      |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| Washington    | Habitat surveys   | Co   | WDOE- BPA Annual Report  |
| Department    |                   | ntra | 2004-2005                |
|               |                   | ctor |                          |
| of Ecology    |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| US Fish and   | Smolt trapping,   | Co   | USFWS-BPA Annual Report  |
| Wildlife      | 2004 spawning     | ntra | 2004-2005                |
|               | surveys           | ctor |                          |
+---------------+-------------------+------+--------------------------+
| US Forest     | Snorkel surveys   | Co   | USFS-BiOp_2004           |
| Service       |                   | ntra |                          |
|               |                   | ctor | USFS- BPA Annual Report  |
| Wenat         |                   |      | 2004-2005_snork          |
| chee-Okanogan |                   |      |                          |
| NF            |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| US Forest     | Steelhead         | Co   | USFS-BiOp_2004           |
| Service       | spawning surveys  | ntra |                          |
|               |                   | ctor | USFS- BPA Annual Report  |
| Wenat         |                   |      | 2004-2005_steel          |
| chee-Okanogan |                   |      |                          |
| NF            |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| Yakama Nation | Smolt trapping    | Co   | Yakama-Nason\_ BPA       |
|               |                   | ntra | Annual Report 2004-2005  |
|               |                   | ctor |                          |
+---------------+-------------------+------+--------------------------+
| Washington    | Steelhead and     | Co   | WDFW_2004\_ BPA Annual   |
| DFW           | Chinook spawning  | ntra | Report 2004-2005         |
|               | surveys, smolt    | ctor |                          |
|               | trapping          |      |                          |
+---------------+-------------------+------+--------------------------+
| US Geological | Macroinvertebrate | Co   | USFS-Final Report 2005\_ |
| Survey        | status monitoring | ntra | BPA Annual Report        |
|               | collections and   | ctor | 2004-2005                |
| University of | protocol          |      |                          |
| Alaska        | comparisons       |      |                          |
|               |                   |      |                          |
| US Forest     |                   |      |                          |
| Service-      |                   |      |                          |
|               |                   |      |                          |
| Pacific       |                   |      |                          |
| Northwest     |                   |      |                          |
|               |                   |      |                          |
| Research      |                   |      |                          |
| Lab,Wenatchee |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| NWFSC,        | Spatial and       |      | Directly incorporated    |
| N             | tabular data      |      | into BPA annual report   |
| OAA-Fisheries | management and    |      |                          |
|               | delivery          |      |                          |
+---------------+-------------------+------+--------------------------+
| **Salmon**    |                   |      |                          |
+---------------+-------------------+------+--------------------------+
| Quantitative  | Monitoring study  | Co   |                          |
|               | analysis and      | ntra |                          |
| Consultants   | coordination      | ctor |                          |
+---------------+-------------------+------+--------------------------+
| NWFSC,        | GIS and tabular   |      | Directly incorporated    |
| N             | data collation    |      | into BPA annual report   |
| OAA-Fisheries | and storage       |      |                          |
+---------------+-------------------+------+--------------------------+

##### Task 1.2. Oversee design of subbasin specific monitoring programs

The overall goal of this project is to develop integrated status/trends
and effectiveness monitoring programs, watershed scale effectiveness
monitoring, and the rule sets that guide the design, implementation and
evaluation of these programs. However, achieving such large-scale
integrated program cannot follow a simple set of steps since it will be
so dependent on the particular setting that each subbasin presents. In
addition, coordinating the diversity of participants necessary to
implement a project of this scale will naturally introduce a new set of
constraints and variables due to participating program's personalities.
For a list of participants and their specific components, refer to Table
1 and the attached progress reports.

Target subbasin monitoring programs have been developed along
independent time and scope trajectories. For example, extensive
coordination of field support by basin coordinators has been necessary
in the Wenatchee basin while in the John Day basin far more of the
coordination effort has been focused on developing common objectives,
plans, methods and approaches across the myriad current and historic
monitoring data generators. As a result, each subbasin has presented
unique opportunities and challenges with correspondingly differing
levels and types of progress and products. These inherent differences in
the level of ongoing monitoring activity, coordination and support
forces this project to "pilot" a wide range of activities under the
common goal of overseeing design of monitoring programs. Below we
capture some of the progress and diversity of products and results
achieved under this task in 2004-2005.

*Integrated Status and Effectiveness Monitoring*

The basic goal of cost efficiency and data consistency drives the object
of establishing integrated status and effectiveness monitoring programs.
In its cleanest implementation, an integrated status and effectiveness
monitoring program would be one in which status/trends data collection
was designed to support subbasin to watershed statistical inference on
annual or trend based status assessments, but at the same time,
providing the control or spatial reference for mechanistic cause and
effect monitoring of particular management actions. Ideally then, for
such a concept to be realized, the status/trends monitoring would have
to be extremely generic, very comprehensive, or tuned to act as
reference for only a limited set of effectiveness monitoring programs.
Unfortunately there is a long list of design limitations that are
imposed by reality, however it is perhaps better that these situations
are being tackled by the pilot projects as they will then serve a useful
function of being real-life worked examples rather than perfect
unachievable textbook cases.

In the Wenatchee River basin the integrated Status/trend/effectiveness
monitoring of the steelhead and spring Chinook populations in the
Wenatchee subbasin has focuses primarily on supplementation programs
that differ between major watersheds within the basin (Nason, Peshastin,
Chiwawa, Little Wenatchee / White) and their efficacy in increasing the
number of naturally spawning adults. Since all major watersheds have
some type of supplementation the references or controls are confounded,
the differences that may emerge from the monitoring data will be
difficult to isolate to a single supplementation program rather than a
suite of common practices. This compromise design, while not ideal, is
imposed on the work in the Wenatchee due to ongoing programs, yet the
pilot monitoring project is the only way any assessments will be
possible due to the coordination, standardized data collection
approaches and inclusion of all watershed equally in the sampling design
for status/trends monitoring data collection.

Other design considerations that have been tackled in the Wenatchee
include the development of a standardized approach to lay out spatial
sampling using the random but spatially balanced frame from the EPA's
Generalized Random Tessellated Sampling. In particular, how does the
need to sample for both fish and habitat impose compromises on the
definition of sampling universe and choice of sample sites. TerrAqua and
NWFSC worked with United States Forest Service (USFS) and WA DEcy
personnel to generate a tool for site selection for random steelhead
spawning surveys and basin wide stream habitat surveys. This approach is
a potential advance in the location of sampling sites by incorporating
in-stream reach habitat data in conjunction with fish distribution data
to balance study monitoring study sites within the basin among
anadramous and non-anadromous streams. The merits of this approach are
being tested through its application in the Wenatchee pilot, with
results being expected in 2 -- 3 years.

The project also aims to develop rules for the integration of a
watershed scale effectiveness monitoring program with status monitoring.
Again, in the ideal case, both programs could be based on a plan that
samples the same suite of reach scale physical / environmental
indicators at each project location as well as at random locations
across the basin. In this case, each project would contribute a sample
to the watershed status monitoring while the watershed status monitoring
would function as a control dataset for the reach scale projects;
however, because the project locations are not randomly distributed in
space these samples represent the population of projects, not the
background habitat condition. Effectiveness monitoring designs will be
explored to address the likelihood to detect change within the
restoration projects within the temporal scope of the project. In the
meantime, the project is trying to coordinate the implementation of
projects to minimize the "non-randomized" bias and to maximize the
effect size by maintaining "control" watersheds.

In the John Day basin the original problem statement from the
coordination group was that summer low flow water temperatures and
disrupted sediment deposition/transport strongly limits production and
distribution of salmonids at the basin scale. In this subbasin the
project is focusing its efforts to assess the status of stream
temperature and sediment processes within the basin and to assess
whether current monitoring plans effectively and accurately capture the
temperature and sediment regimes within the basin. We are also assessing
whether fish production and population assessments within the basin
provide enough response variable information to detect the effectiveness
of temperature and sediment regimes. In this case the integration of
status and effectiveness monitoring is being lead by the exploration of
historic monitoring data sets and the development of predictive models
against which current data collection can be compared and future data
collection efforts can be designs.

*Watershed Scale Effectiveness Monitoring*

Habitat restoration actions are generally implemented on a reach or
habitat unit scale and can be assessed for effectiveness at that scale.
However, when needing to determine the population level response to
restoration actions, the actions' cumulative impact must be assessed on
the scale of the demographic unit as a whole. Intensively Monitored
Watershed projects have been established to coordinate, focus, and
supplement existing research and monitoring projects that meet
basin-wide needs for fish population monitoring. These projects have
been developed to address common criticisms of habitat restoration work
-- that the scale of the restoration project is too small relative to
the scale of biological response variables such as population processes,
and that restoration projects are generally implemented without controls
or references so aren't properly designed experiments. Thus the
principles of the Intensively Monitored Watershed framework are to match
the scale of the restoration action to the biological response variable
and to do so in a treatment and control context to facilitate
statistically rigorous cause and effect evaluations.

A weak link in the implementation of large scale management actions is a
true understanding of what may be limiting population processes, and as
such, where large effect sizes will be realized upon implementing a
restoration strategy. Tools for the prioritization of watersheds for
restoration action and status monitoring development at the scale of the
subbasin are not well developed. The recent completion of the subbasin
has provided initial prioritizations of fifth field hydrologic units
according to attributing efforts of stream reaches within each basin for
the Ecosystem Diagnostic and Treatment model (EDT), but the validity of
these biological assessments and their sensitivity to the input data has
not been well established. Thus, in order to proceed with design and
implementation in the Wenatchee, John Day and Salmon River, part of the
coordination effort has been to develop monitoring programs around
hypothesized limiting factors and the programs designed to address them
(e.g., Lemhi HCP), to attempt to assemble a watershed scale restoration
project by combining existing or recent restoration projects (see Table
2 and Middle Fork John Day), or to begin from scratch with the limiting
factor, restoration action plan and the monitoring plan (e.g., Bridge
Ck).

*John Day IMW: South Fork John Day-Murderer's Creek*

A great deal of the monitoring and research coordinated by the AFG and
implemented by Oregon State University has occurred in the mainstem
South Fork John Day River and its tributaries: Black Canyon, Wind Creek,
Deer Creek, and Murderers Creek. This work includes: GIS analysis of how
landuse and landscape patterns impact habitat and fish distribution;
LiDAR and FLIR of the SF John Day and some these tributaries; TMDL model
development by Oregon Department of Environmental Quality on the
mainstem SF John Day; extensive continuous habitat surveys in the SF
John Day and these tributaries; PIT-tagging of fish in SF John Day
tributaries to track growth and survival of fish residing in each
watershed that differ in habitat and temperature regimes; radio-tagging
of fish to track movement patterns; screw trap monitoring on the
mainstem SF John Day; and extensive snorkel surveys. In 2005, Oregon
State University and EcoLogical Consultants drafted a comprehensive IMW
theoretical framework and study design for the SF John Day basin.

*John Day IMW: Bridge Creek*

Bridge Creek is a tributary to the lower mainstem of the John Day.
Research has been focused on the impacts of grazing on channel incision.
Large sections of Bridge Creek exhibit deep channel incision due to the
loss of vegetation through grazing and the mechanical disruption of the
stream bank from cattle. Stream elevation and gradient is altered
resulting in a lowering of the hyporheic water level. Further loss of
riparian vegetation occurs because root structures no longer have access
to the water table. Channel incision produces bank erosion and high
sediment inputs into the stream channel. Techniques exist to mitigate
for the effects of channel incision. This process can be jump started
through mechanical manipulation of the stream banks and floodplain
allowing for observable effects of restorations in the near term. A
Bridge Creek IMW plan is being drafted for the 2006 field season.

*John Day IMW: North Fork and Middle Fork John Day*

Several IMW restoration projects have been proposed for the North and
Middle Forks of the John Day. The development of an effectiveness
monitoring program for channel reconnections or widening (connect to old
meanders), mine tailing removal, or riparian fencing (stream buffering)
through several planned or existing restoration activities on TNC
(Dunstan Preserve) and CTWS (Oxbow) properties have been proposed after
communication with these agencies. The IMW study in the North or Middle
Forks would evaluate a combination of activities from multiple agencies
rather than impacts of individual actions. This IMW is still under
development as needs assessments and fish population evaluation needs
assessments are currently being conducted.

*Wenatchee-Entiat IMW; Entiat*

An effectiveness monitoring program for a channel complexity restoration
project in the Entiat basin has been proposed and will be included in
the 2006 study design plans and field season.

*Salmon IMW: Lemhi*

The Lemhi River is subject to a number of irrigation diversions that
have resulted in a substantial decrease in flow and alteration of the
historical hydrograph. Irrigation withdrawals in this subbasin routinely
result in dewatering of 29 out of the 31 major tributaries, thus
decreasing connectivity and habitat availability. The Lemhi River houses
a TRT identified population of spring/summer Chinook salmon
(*Oncorhynchus tshawytscha*) and steelhead trout (*Oncorhynchus mykiss*)
as well as bull trout (*Salvelinus confluentus*), all of which are
listed under the Endangered Species Act (ESA).

Recently, a multi-agency cooperative agreement with irrigators and
landowners in the Lemhi subbasin has allowed the opportunity to decrease
irrigation withdrawals. Increased in-stream water availability, although
unlikely to return historical quantities of water, will mimic the
historical hydrograph of the Lemhi River. In addition, a total of 10
tributaries will be reconnected with the mainstem Lemhi via modification
of diversion structures and increased in-stream flow, thereby increasing
habitat availability and population connectivity.

[]{.mark}

**Table 2. Inventory of habitat project types in the John Day basin from
the Pacific NW Salmon Habitat Project Tracking Database (NOAA-Fisheries,
NWFSC)**

  ------------------- --------------------------- ------------- ---------------
  **Project type**    **Project subtype**         **Earliest    **Most recently
                                                  documented    documented
                                                  project       project date**
                                                  date**        

  Barrier Removal     Culvert                     1998          2003
                      Improvements/Upgrade                      

                      Culvert Removal             1993          2003

                      Culvert Replacement         1998          2003

                      Dam Removal                 2002          2002

                      Log Jam/Debris Removal      2000          2000

                      Other                       1998          2003

                      Push-up Dam/Diversion Dam   1996          2002
                      Removal                                   

  Diversion Screens   Fish Screen Replacement     2003          2003

  Other               Fencing                     1995          1998

                      Water Development           1994          2001

  Restore Instream    Instream Water Rights       1996          2002
  Flow                                                          

                      Reduce/Regulate Water       2001          2003
                      Withdrawal                                

                      Water Quantity              2002          2002

  Restore Riparian    Bank Stabilization          2003          2003
  Function                                                      

                      Fencing                     1993          2005

                      Forestry Practices          1996          2003

                      Off-Channel Watering        1995          2002

                      Other                       1995          2005

                      Plant                       1993          2005
                      Installation/Revegetation                 

                      Plant Removal/Control       2000          2004

  Restore Stream      Boulders                    1996          2003
  Complexity -                                                  
  Instream Structure                                            

                      Deflector                   1996          2002

                      Large Woody Debris          1995          2002

                      Log Weir                    2002          2002

                      Other                       1998          2002

                      Rock Weir                   2002          2002

                      Rootwads                    2002          2003

                      Structure/Log Jam           1996          2005

                      Weir                        1996          2003

  Restore Stream      Bank Stabilization          1993          2003
  Complexity- Channel                                           
  Complexity                                                    

                      Channel Connectivity        2000          2002

                      Channel Reconfiguration     1999          1999

                      Off-Channel Habitat : Pond  1996          1996

                      Off-Channel Habitat : Side  1996          2001
                      Channel                                   

                      Other                       2001          2001

                      Wetland                     1998          2001
                      Improvements/Enhancement                  

                      Wetland Restoration         2001          2001

  Sediment Reduction  Erosion Control Structures  2001          2001

                      Other                       1991          2002

                      Road Closing/Abandonment    1993          2003

                      Road Drainage               1998          2003

                      Sediment Traps              2002          2002

  Upland Management   Erosion Structures          1997          2002

                      Fencing                     1993          2003

                      Invasive Plant Control      1993          2002

                      Livestock Management        1997          2002

                      Other                       1997          2003

                      Slope Stabilization         1996          2002

                      Vegetation Management       1995          2002

                      Water Development           1994          2002

  Water Quality       Other                       2001          2001
  Improvement                                                   
  ------------------- --------------------------- ------------- ---------------

[]{.mark}

###### []{.mark}

###### 

###### Task 1.3. Coordination of data collection to support monitoring design

###### NWFSC has been responsible for the comprehensive collation of both historical and recent GIS and tabular datasets. The assembly of existing data sources and locations allows the identification of both spatial and content gaps in current monitoring efforts and will provide a framework for designing supplemental monitoring projects within the basin. Inventories of the GIS data available for the John Day and Wenatchee have been assembled (ongoing) and initial datasets have been compiled and listed for the Salmon although the comprehensive list is not yet complete. An extensive collection of historical tabular datasets and current monitoring programs have been inventoried for the John Day Basin. Datasets supporting the conceptual plans of the John Day IMWs were the priority for collection efforts and assimilation into databases. In the Wenatchee, a pre-existing work group provided a base knowledge of available historical tabular datasets and the location and type of existing monitoring data have been noted and inventoried although data has not yet been compiled. Local agency knowledge and the Pacific NW Salmon Habitat Project Tracking Database (NOAA-Fisheries, NWFSC) have been the primary source of restoration project knowledge in the pilot basins. Extensive inventories of GIS, tabular, and restoration project data are available upon request. 

[]{.mark}

*Tabular Data*

Data compilation efforts in the John Day and Wenatchee basins were
prioritized according to IMW and monitoring design data needs. Datatypes
of interest included water quality (temperature, DOC, turbidity, and
nutrients), habitat, fish (redd, juvenile, and adult counts),
macroinvertebrates, stream gages, cross sections, and vegetation. In
2004 and 2005 a comprehensive collection effort of historical tabular
data was compiled for both the John Day and Wenatchee basin (see Table
3.). For the John Day basin over 20 years of water temperature data,
ODFW index reach redd counts (since 1960's), and USFS in-stream habitat
survey data (early 1990's) have been assimilated. The priority has been
to collect and standardize existing data in the Wenatchee and Salmon
basins has been of secondary importance until data storage and
standardization methods have been developed for the John Day basin.

NOAA-Fisheries has assimilated a list of available GIS datasets for both
the John Day and Wenatchee basins. The master inventory includes data
from agencies with specific objectives (e.g. US Forest Service harvest
records) as well as datasets from regional projects (e.g. ICBEMP).
Supplemental GIS datasets created by NOAA-Fisheries, UW, and BoR have
also been accounted for in the inventory. In the Wenatchee basin,
contracts with PBI and Earth Systems Inc. (TRIAD) have also provided GIS
data resources.

An associated imagery project supported by the Bureau of Reclamation,
the University of Washington, and NOAA-Fisheries is concurrently being
piloted in the John Day, Wentachee, and Salmon basins. Remote sensing
data derived from the landsat 5 Thematic Mapper sensor and IKONOS high
resolution multispectral imager are being employed to assess
relationships between land cover and fish habitat throughout the
Columbia River Basin. Using a time series of satellite imagery from
1984-2000, this research is quantifying change in land cover and
vegetation patterns over six main subbasins of the CRB, including the
John Day, Wenatchee, Willamette, Ykima, Salmon and Grande Ronde.
Temporal variabliilty in vegetation cover, as well as spatial metrics of
patch compostion and structural heterogeneity are calculated from the
time series of spectral data to evaluate the relative intensity of
vegetation cover and the connectivity between land cover types in
relation to knonwn indicators of fish habitat. Designed to improve
modeling efforts for predicting suitable and sustainable fish habitat,
this research offers a new perspective on the analysis of land cover in
providing a temporatl dataset that defines not only the variability in
thematic cover types, but the indices and spatial pattern metrics of
land cover that may more directly influence habitat distribution.

[John Day data collection]{.underline}

In 2005, three workgroups were created to facilitate the coordination of
the John Day RME program. These included the Freshwater Production
Group, the Habitat Monitoring Group, and the GIS Group, which are
subgroups of the parent coordinating Analytical Framework Group (AFG)
established in 2004. The AFG has been developing the overall analytical
framework for RME efforts in the John Day basin. The framework attempts
to: i) organize existing and future research activities to identify
factors limiting salmonid production; ii) evaluate status and trends of
salmonids and habitat; iii) coordinate project implementation and
compliance monitoring; and iv) assess reach-scale biological and
physical impacts up to population level salmonid productivity effects of
restoration actions. The GIS workgroup has been responsible for the
compilation of data layers and coordination of spatial data
distribution. The habitat monitoring group has been largely responsible
for data needs assessments as established within IMWs and the associated
work plans, protocol assessments, and performance metrics. The fish
monitoring workgroup has been establishing baseline performance metrics
for fish within IMW projects.

In an effort to establish a working base of status monitoring sites,
NOAA-Fisheries compiled a comprehensive collection of historical
monitoring sites utilized in the past 20 years. Data have been
categorized and inventoried according to type: fish, macroinvertebrates,
fish habitat, vegetation, water quality, and water flow (gage).
Collation efforts have also been coordinated with the Pacific NW Salmon
Habitat Project Tracking Database (NOAA-Fisheries, NWFSC) and the Middle
and North Fork John Day Watershed Council to inventory existing
restoration projects within the John Day basin.

Tabular records of water temperature, habitat cross sections,
macroinvertebrates, and fish have been targeted as the priority for data
collation efforts in the basin. Multiple agencies are responsible for
the collection of these data types and limited communication among
groups has resulted in non-standardized data storage methods and limited
data sharing capacities. To facilitate the data sharing and use process,
these existing data have been collected directly from agencies and
stored in SQL databases until incorporation into the Oracle database
created for the Salmon watershed. Specifically, water temperature data
from more than 800 unique sites and 3,2000 monitoring events across 10
agencies have been collected and stored for the basin. Over 60 cross
section and macroinvertebrate monitoring sites have been recorded
although data collation for these types is still in process. Recent fish
data collected by the Oregon Department of Fish and Wildlife (since
2000) along with the 2004 construction of a MS ACCESS database
containing historical Steelhead redd spawning surveys have been the
initial products of the fish data collation process. Additional fish
data from Oregon State University and ODFW (Corvallis, OR) have been
identified but are not currently housed in NOAA-Fisheries databases.
Data collection and the inventory process is ongoing but has been
simplified with the establishment of working databases for each
datatype.

Data assimilation efforts have also facilitated the coordination of
local agencies and their monitoring designs and current data storage
methods. Current agencies participating in data standardization and
monitoring designs include both local, state, and federal agencies, such
as Oregon Department of Environmental Quality (ODEQ), Environmenetal
Protection Agency, Bureau of Land Management, U.S. Forest Service,
Oregon Department of Fish and Wildlife, U.S. Geological Service, Soil
and Water Conservation Distrctis, Confederated Tribes of the Warm
Springs, Oregon Water Resources Division, University of Washington,
Oregon State University, National Oceanic and Atmospheric Administration
(NOAA-Fisheries), and U.S. Bureau of Reclamation. A basin-wide meeting
in May 2005 of 10 agencies concluded that there is a need for basin-wide
coordination of monitoring efforts and increased communication between
agencies. We proposed an annual winter monitoring meeting to discuss
upcoming summer monitoring and restoration projects and continue working
towards standardizing data collection and storage methods.

The assembly of GIS datasets for the John Day basin has included the
collection of agency-produced layers from the US Forest Service, Pacific
NW Research Science lab (US Forest Service), Umatilla National Forest
(harvest and water quality records), Malheur National Forest (harvest
and fire regime records), Wallawa-Whitman National Forest (harvest and
fire regime records), Oregon State University (fish habitat, fish use,
and temperature) and University of Washington (remote sensing imagery).
Additional datasets from the internet or at a regional scale have also
been assembled from the internet and the Biological Opinion 2000
Technical Recovery Team (BiOp TRT) (see Table 4).

[Wenatchee data collection]{.underline}

In 2005, field data collection of water chemistry, habitat,
macroinvertebrates, juvenile salmonids, and adult salmonids was
continued according to the initial monitoring design implemented in 2004
and following slightly modified EMAP protocols (Upper Columbia
Monitoring Strategy). In 2004 and 2005, data collections were contracted
to multiple agencies and individual efforts have been summarized for
reporting purposes.

The Chelan County Conservation District was contracted to collect water
quality data at five sites in the Wenatchee River basin. Hourly
temperature, pH, conductivity, dissolved oxygen, and turbidity readings
were collected and data loggers were calibrated and maintained on a
biweekly schedule. Field sampling precision assessments were conducted
by collecting replicate samples at one site (20% replication rate)
during each sampling session.

The USGS and US Forest Service Pacific Northwest Research Lab were
contracted to sample 60 stream sites within the Wenatchee subbasin to
determine invertebrate productivity and investigate invertebrate-fish
relationships. The study was designed to compare macroinvertebrate
community composition and production in Ecological Sub-Region (ESR) 4
(dry ecoregion) and ESR 11 (wet ecoregion). In both ecoregions, 15 low
impact (little past logging and presence of roads) and high impact
(recent logging and roads) sites were sampled in 2004 and 2005.

The WDFW and Yakama Nation were contracted to 1) estimate the total
number of steelhead *Oncorhynchus mykiss* redds in selected streams
(Nason, Chiwawa, Peshastin and upper Wenatchee) within the Wenatchee
subbasin by conducting index spawning ground counts and assess their
accuracy and precision for the Wenatchee subbasin; 2) estimate the smolt
production of spring Chinook *O. tshawytscha* salmon and steelhead for
the Wenatchee subbasin and 3) describe the temporal variability of
outmigrating spring Chinook and steelhead within Nason Creek. The
average trapping efficiency for the season was 21.4% and 15.7% for
spring Chinook and steelhead/rainbow trout juveniles, respectively.
Wenatchee River basin co-managers estimated that 66,395 (±20,147 95%CI)
sub-yearling (age 0) Chinook and 16,082 (±3,982 95%CI) steelhead/rainbow
trout, representing three age-classes, emigrated from Peshastin Creek
during the 2004 sampling period. Steelhead/rainbow trout age-0, age-1,
age-2 are estimated to represent 52% (8,419), 42% (6,770), and 6% (893)
of the population estimate, respectively. A production estimate for
Chinook spring salmon could not be generated due to a low capture of
individuals.

In 2004, smolt production monitoring began in Peshastin Creek by the
USFWS, Mid-Columbia River Fisheries Resource Office (MCRFRO). The
initial purpose of this monitoring by MCRFRO was to evaluate the
productivity and progeny characteristics of outplanted spring Chinook
hatchery adults from Leavenworth NFH. This type of monitoring was
quickly recognized as critical in implementing the 2000 NMFS FCRPS
Biological Opinion RPA Actions which seeks to develop basin-scale
monitoring and evaluation programs for the Wenatchee, John Day, and
Upper Salmon River basins. Subsequently, the Peshastin Smolt Monitoring
Program was expanded in a joint effort to meet both the requirements set
forth in the Leavenworth NFH and the NMFS FCRPS BiOp's. Results from
2004 Wenatchee fish survey information indicated steelhead spawning
counts are feasiblble and have reasonable accuracy at the basin scale.
It was determined that further studies are needed to address basin-wide
temperature patterns and steelhead distribution relationships.
Information gathered from spawning ground surveys indicates several
valuable pinpoint areas (lower mainstem) that require additional
investigation as to preservation and influential factors in the area due
to their importance as spawning ground to Chinook and steelhead
populations.

The Wenatchee National Forest found distinct differences in species
assemblages and species/habitat relationships between Steelhead spawning
sites. The beta-test involved sampling at a subset of these 50 sites:
the anadromous-accessible sites in Peshastin, Nason, and Chiwawa
watersheds (13 sites). In 2004 strong habitat and temporal relationships
were found, suggesting that these factors should be addressed when
extrapolating from sampled sites to larger areas (e.g. basin-wide).

The Wenatchee National Forest was also responsible for snorkeling
surveys and methodological comparisons according to Hillman 2004. Day
snorkels, night snorkels, and three pass electrofish sampling were
conducted and two types of results are presented: biological and
methodological. Biological analysis considers stream size, channel type,
and habitat type relative to: 1) fish abundance per wetted area and 2)
species richness. We also consider diurnal patterns of fish abundance.
Methodology issues addressed include: 1) identification of species, and
categorization of a species into adult/juvenile based on length; 2)
variability across the season of snorkel data collection; 3)
quantification of rare species by this and alternative protocols; and 4)
applying partnered habitat data (collected by DOE) to fish population
data.

*Spatial Data*

Two comprehensive and complementary GIS datasets were developed for the
Upper Columbia Basin. The Terrain Inventory and Analysis Database
(TRIAD) developed by Earth Systems Institute, draws on digital elevation
data to describe landscape scale processes. Pacific Biodiversity
Institute's classification of habitat in the Upper Columbia Basin draws
together ecoregional, drainage basin, valley, and reach scale
classifications with detailed mapping of riparian vegetation and land
use from satellite and airborne imagery.

The Terrain Inventory and Analysis Database (TRIAD) maps and classifies
ecological attributes of landscapes based on current scientific
foundations in geomorphology and riverine ecology. The analysis draws on
digital elevation data to describe relationships between watersheds and
their river networks at landscape and larger scales. Products in the
database include high resolution digital grids that predict gradients in
surfaces processes and attributed features that represent watersheds,
stream reaches, and tributary junctions.

Pacific Biodiversity Institute's work in the Upper Columbia provides a
suite of GIS layers necessary for sub-basin planning efforts. These
layers include ecoregional classification, geology, land ownership, a
road density index, Naiman valley segment and Rosgen reach
classifications, and stream habitat attributes. Additional, extensive
work was undertaken to classify and map riparian vegetation and land use
from LANDSAT and ASTER satellite imagery. The mapping of riparian areas
was further cleaned and verified by detail comparison with airborne
imagery.

[Salmon Pilot Basin]{.underline}

In 2005 NOAA-Fisheries and Quantitative Consultants began outlining
study site selection by assimilating GIS datasets necessary pertinent to
the site selection process. A GIS layer depicting riparian land use and
stream area has been produced to support decision making efforts in
selecting tributaries for reconnection. Land use composition within
riparian buffers was summarized in the Lemhi basin to allow the
comparison of habitat availability and current land use in the 31 major
tributaries. The output files will assist Quantitative Consultants in
assessing suitability of the major tributaries in the Lemhi for
modification of diversion structures and increasing in-stream flows.

[Watershed classification]{.underline}

In conjunction with the development RME monitoring program within the
target basins, NOAA-Fisheries staff have initiated a watershed
classification project to group similar 6^th^ field watersheds
(Hydrologic Unit Code 6, HUC 6) in the Pacific Northwest according to
watershed characteristics. MCLUST software will be used to classify
spatially continuous GIS data such as precipitation, temperature,
watershed topography, geology, and hydrography metrics into discrete
classes. This regionally continuous classification of watersheds can be
used to determine if the selected Intensively Monitored Watersheds
equally represent the landscape diversity. Additionally, the
classification effort will be useful in determining where RME IMW pilot
basin production outcomes and restoration effectiveness monitoring
designs and protocols will be most applicable and effective.

**Table 3. Inventory of tabular data in the John Day and Wenatchee**

+-------------+--------+-----+--------+--------+---------+-----------+
| **Data      | **Data | **Y | **Ag   | **     | **      | **Data    |
| type**      | d      | ear | ency** | Collec | Basin** | l         |
|             | escrip | s** |        | tion** |         | ocation** |
|             | tion** |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| cross       |        | 2   | MNF    |        | John    | MNF       |
| sections    |        | 004 |        |        | Day     |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| cross       |        |     | PIB    |        | John    | PIBO-USFS |
| sections    |        |     | O-USFS |        | Day     |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| cross       |        | 200 | EMA    |        | John    | EMAP-ODEQ |
| sections    |        | 0-2 | P-ODEQ |        | Day     |           |
|             |        | 004 |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| cross       |        |     | EPA    |        | John    | EPA       |
| sections    |        |     |        |        | Day     |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | C      | 199 | ODFW   | scale  | John    | ODFW,     |
|             | hinook | 9-2 |        | card   | Day     |           |
|             |        | 003 |        | data   |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | redd   | John    | ODFW,     |
|             | inook, | 9-2 |        | c      | Day     |           |
|             | Ste    | 003 |        | ounts, |         | NOAA-     |
|             | elhead |     |        | live   |         | Fisheries |
|             |        |     |        | fish   |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 2   | ODFW   | trap   | John    | ODFW,     |
|             | inook, | 002 |        |        | Day     | NOAA-     |
|             | Ste    |     |        |        |         | Fisheries |
|             | elhead |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 200 | ODFW   | s      | John    | ODFW,     |
|             | inook, | 0-2 |        | eining | Day     |           |
|             | Ste    | 004 |        |        |         | NOAA-     |
|             | elhead |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 2   | ODFW   | s      | John    | ODFW,     |
|             | inook, | 000 |        | norkel | Day     |           |
|             | Ste    |     |        |        |         | NOAA-     |
|             | elhead |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 2   | ODFW   | s      | John    | ODFW,     |
|             | inook, | 001 |        | norkel | Day     |           |
|             | Ste    |     |        |        |         | NOAA-     |
|             | elhead |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 2   | ODFW   | trap   | John    | ODFW,     |
|             | inook, | 001 |        |        | Day     |           |
|             | Ste    | and |        |        |         | NOAA-     |
|             | elhead | 2   |        |        |         | Fisheries |
|             |        | 003 |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 2   | ODFW   | hook   | John    | ODFW,     |
|             | inook, | 003 |        | and    | Day     |           |
|             | Ste    |     |        | line   |         | NOAA-     |
|             | elhead |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | redd   | John    | ODFW,     |
|             | inook, | 9-2 |        | c      | Day     |           |
|             | Ste    | 003 |        | ounts, |         | NOAA-     |
|             | elhead |     |        | live   |         | Fisheries |
|             |        |     |        | fish   |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | s      | John    | ODFW,     |
|             | inook, | 9-1 |        | pawner | Day     |           |
|             | Ste    | 995 |        | coun   |         | NOAA-     |
|             | elhead |     |        | ts/est |         | Fisheries |
|             |        |     |        | imates |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | est    | John    | ODFW,     |
|             | inook, | 6-1 |        | imated | Day     |           |
|             | Ste    | 999 |        | h      |         | NOAA-     |
|             | elhead |     |        | arvest |         | Fisheries |
|             |        |     |        | counts |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | redd   | John    | ODFW,     |
|             | inook, | 9-2 |        | c      | Day     |           |
|             | Ste    | 001 |        | ounts, |         | NOAA-     |
|             | elhead |     |        | live   |         | Fisheries |
|             |        |     |        | fish   |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | s      | John    | ODFW,     |
|             | inook, | 9-1 |        | pawner | Day     |           |
|             | Ste    | 995 |        | coun   |         | NOAA-     |
|             | elhead |     |        | ts/est |         | Fisheries |
|             |        |     |        | imates |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | Ch     | 195 | ODFW   | est    | John    | ODFW,     |
|             | inook, | 6-1 |        | imated | Day     |           |
|             | Ste    | 993 |        | h      |         | NOAA-     |
|             | elhead |     |        | arvest |         | Fisheries |
|             |        |     |        | counts |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | r      | 1   | OSU    | s      | John    | OSU       |
|             | edband | 990 |        | norkel | Day     |           |
|             | trout, | s-p |        |        |         |           |
|             | stee   | res |        |        |         |           |
|             | lhead, | ent |        |        |         |           |
|             | c      |     |        |        |         |           |
|             | hinook |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        | 19  | ODFW   |        | John    | www.stre  |
|             |        | 90s |        |        | Day     | amnet.org |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        | 200 | ODFW   |        | John    | C         |
|             |        | 0-2 | Re     |        | Day     | orvallis, |
|             |        | 002 | search |        |         | OR        |
|             |        |     | Lab,   |        |         |           |
|             |        |     | Cor    |        |         |           |
|             |        |     | vallis |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        | 19  | UNF    |        | John    | USFS      |
|             |        | 90s |        |        | Day     |           |
|             |        |     |        |        |         | NRIS      |
|             |        |     |        |        |         | database  |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        | 19  | MNF    |        | John    | USFS      |
|             |        | 90s |        |        | Day     |           |
|             |        |     |        |        |         | NRIS      |
|             |        |     |        |        |         | database  |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        | 19  | ONF    |        | John    | USFS      |
|             |        | 90s |        |        | Day     |           |
|             |        |     |        |        |         | NRIS      |
|             |        |     |        |        |         | database  |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     |        |     | CTWS   |        | John    | CTW       |
|             |        |     |        |        | Day     | S-Prairie |
|             |        |     |        |        |         | City, OR  |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        | l   | OSU    |        | John    | OSU       |
| vertebrates |        | ate |        |        | Day     |           |
|             |        | 19  |        |        |         |           |
|             |        | 90s |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        |     | Upper  |        | John    | Upper     |
| vertebrates |        |     | SFJD   |        | Day     | SFJD      |
|             |        |     | Wat    |        |         | Watershed |
|             |        |     | ershed |        |         | Council   |
|             |        |     | C      |        |         |           |
|             |        |     | ouncil |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        | 2   | Eco    |        | John    | EcoLog    |
| vertebrates |        | 005 | Logica |        | Day     | ical-Utah |
|             |        |     | l-Utah |        |         | State     |
|             |        |     | State  |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        | 2   | OWRD   |        | John    | OWRD      |
| vertebrates |        | 005 |        |        | Day     |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        |     | TNC    |        | John    | TNC       |
| vertebrates |        |     |        |        | Day     |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| **Data      | **Data | **Y | **Ag   | **     | **      | **Data    |
| type**      | d      | ear | ency** | Collec | Basin** | l         |
|             | escrip | s** |        | tion** |         | ocation** |
|             | tion** |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| vegetation  | moni   |     | TNC    |        | John    | TNC       |
|             | toring |     |        |        | Day     |           |
|             | plots  |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| vegetation  | moni   |     | CTWS   |        | John    | CTWS      |
|             | toring |     |        |        | Day     |           |
|             | plots  |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | water  |     |        |        | John    | STORET    |
| quality     | and    |     |        |        | Day     |           |
|             | air    |     |        |        |         |           |
|             | temper |     |        |        |         |           |
|             | ature, |     |        |        |         |           |
|             | nut    |     |        |        |         |           |
|             | rients |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | ODFW   | cont   | John    | S         |
| quality     | une-Oc | 1-1 |        | inuous | Day     | treamnet, |
| (temp)      | tober, | 997 |        | l      |         | NOAA-     |
|             | 1995   |     |        | oggers |         | Fisheries |
|             | (42    |     |        |        |         |           |
|             | sites, |     |        |        |         |           |
|             | sep    |     |        |        |         |           |
|             | t-oct) |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | MNF    | cont   | John    | MNF,      |
| quality     | une-Oc | 8-2 |        | inuous | Day     |           |
| (temp)      | tober, | 003 |        | l      |         | NOAA-     |
|             | some   |     |        | oggers |         | Fisheries |
|             | May,   |     |        |        |         |           |
|             | some   |     |        |        |         |           |
|             | w      |     |        |        |         |           |
|             | inter, |     |        |        |         |           |
|             | 1-6    |     |        |        |         |           |
|             | sites  |     |        |        |         |           |
|             | per    |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | TNC    | cont   | John    | TNC,      |
| quality     | une-Oc | 3-2 |        | inuous | Day     |           |
| (temp)      | tober, | 003 |        | l      |         | NOAA-     |
|             | 1-2    |     |        | oggers |         | Fisheries |
|             | sites/ |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | 1-4    | 199 | Baker  | cont   | John    | ONF,      |
| quality     | sites/ | 3-2 | RD,    | inuous | Day     |           |
| (temp)      | stream | 004 | ONF    | l      |         | NOAA-     |
|             |        |     |        | oggers |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | Blue   | cont   | John    | ONF,      |
| quality     | une-Oc | 3-2 | Mt RD, | inuous | Day     |           |
| (temp)      | tober, | 004 | ONF    | l      |         | NOAA-     |
|             | some   |     |        | oggers |         | Fisheries |
|             | May,   |     |        |        |         |           |
|             | 1-3    |     |        |        |         |           |
|             | sites/ |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | Warm   | cont   | John    | CTWS,     |
| quality     | une-Oc | 7-2 | S      | inuous | Day     |           |
| (temp)      | tober, | 004 | prings | l      |         | NOAA-     |
|             | some   |     |        | oggers |         | Fisheries |
|             | w      |     |        |        |         |           |
|             | inter, |     |        |        |         |           |
|             | 1-6    |     |        |        |         |           |
|             | sites/ |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | J      | 199 | MSWCD  | cont   | John    | MSWCD,    |
| quality     | une-Oc | 9-2 |        | inuous | Day     |           |
| (temp)      | tober, | 004 |        | l      |         | NOAA-     |
|             | 1-4    |     |        | oggers |         | Fisheries |
|             | sites/ |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | 1-13   | 200 | PIBO   | cont   | John    | PIBO      |
| quality     | sites/ | 0-2 |        | inuous | Day     |           |
| (temp)      | stream | 004 |        | l      |         |           |
|             |        |     |        | oggers |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       |        | 200 | ODFW   | cont   | John    | ODFW,     |
| quality     |        | 0-2 | Bull   | inuous | Day     |           |
| (temp)      |        | 002 | trout  | l      |         | NOAA-     |
|             |        |     |        | oggers |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | full   | 200 | ODFW   | cont   | John    | ODFW,     |
| quality     | years  | 1-2 |        | inuous | Day     |           |
| (temp)      | 1-6    | 002 |        | l      |         | NOAA-     |
|             | sites/ |     |        | oggers |         | Fisheries |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | Ma     | 198 | UNF    | cont   | John    | UNF,      |
| quality     | y-Nov, | 8-2 |        | inuous | Day     |           |
| (temp)      | some   | 004 |        | l      |         | NOAA      |
|             | w      |     |        | oggers |         | -Fisheris |
|             | inter, |     |        |        |         |           |
|             | 2-19   |     |        |        |         |           |
|             | sites/ |     |        |        |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       |        | 199 | OSU    | FLIR   | John    | OSU       |
| quality     |        | 3-2 |        | and    | Day     |           |
| (temp)      |        | 004 |        | cont   |         |           |
|             |        |     |        | inuous |         |           |
|             |        |     |        | l      |         |           |
|             |        |     |        | oggers |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       |        | 198 | BLM    | cont   | John    | BLM,      |
| quality     |        | 5-2 |        | inuous | Day     |           |
| (temp)      |        | 003 |        | l      |         | NOAA-     |
|             |        |     |        | oggers |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       |        | 198 | EPA    | cont   | John    | STORET,   |
| quality     |        | 0-2 |        | inuous | Day     | DEQ,      |
| (temp)      |        | 003 |        | l      |         | NOAA-     |
|             |        |     |        | oggers |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | Ju     | 200 | ODEQ   | cont   | John    | NOAA-     |
| quality     | ne-Dec | 0-2 |        | inuous | Day     | Fisheries |
| (temp)      | 1-2    | 002 |        | l      |         |           |
|             | sites/ |     |        | oggers |         |           |
|             | stream |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | s      |     |        |        | We      | USFS-     |
|             | norkel |     |        |        | natchee | Wenatchee |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | misc   | 199 |        |        | We      | USFS-     |
|             | sn     | 2-2 |        |        | natchee | Wenatchee |
|             | orkel, | 003 |        |        |         |           |
|             | redd,  |     |        |        |         |           |
|             | fish   |     |        |        |         |           |
|             | counts |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | DART   |     |        |        | We      | <         |
|             | data   |     |        |        | natchee | http://ww |
|             | st     |     |        |        |         | w.cbr.was |
|             | orage. |     |        |        |         | hington.e |
|             | CRB    |     |        |        |         | du/dart/d |
|             | fish   |     |        |        |         | art.html> |
|             | data   |     |        |        |         |           |
|             | s      |     |        |        |         |           |
|             | torage |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | smolt  |     | Yakama |        | We      | Yakama    |
|             | traps  |     | Nation |        | natchee | Nation,   |
|             |        |     |        |        |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        | smolt  |     |        |        | We      | Yakama    |
|             | traps  |     |        |        | natchee | Nation    |
+-------------+--------+-----+--------+--------+---------+-----------+
| fish        |        |     | WDFW   |        | We      | WDFW,     |
|             |        |     |        |        | natchee |           |
|             |        |     |        |        |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| **Data      | **Data | **Y | **Ag   | **     | **      | **Data    |
| type**      | d      | ear | ency** | Collec | Basin** | l         |
|             | escrip | s** |        | tion** |         | ocation** |
|             | tion** |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| habitat     | In-    |     | WDOE   |        | We      | WDOE,     |
|             | stream |     |        |        | natchee |           |
|             |        |     |        |        |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
|             |        |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        |     | WDOE   |        | We      | WDOE,     |
| vertebrates |        |     |        |        | natchee |           |
|             |        |     |        |        |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| macroin     |        |     | USGS   |        | We      | US        |
| vertebrates |        |     | -USFSL |        | natchee | GS-USFSL, |
|             |        |     |        |        |         | NOAA-     |
|             |        |     |        |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| sediment    |        |     | US     |        | We      | USFS-     |
|             |        |     | FS-Wen |        | natchee | Wenatchee |
|             |        |     | atchee |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | water  |     | EPA    |        | We      | STORET    |
| quality     | and    |     |        |        | natchee |           |
|             | air    |     |        |        |         |           |
|             | temper |     |        |        |         |           |
|             | ature, |     |        |        |         |           |
|             | nut    |     |        |        |         |           |
|             | rients |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       |        |     | Chelan |        | We      | Chelan Co |
| quality     |        |     | Co     |        | natchee | Con       |
|             |        |     | Conser |        |         | servation |
|             |        |     | vation |        |         | District, |
|             |        |     | Di     |        |         | NOAA-     |
|             |        |     | strict |        |         | Fisheries |
+-------------+--------+-----+--------+--------+---------+-----------+
| water       | water  |     | US     |        | We      | USFS-     |
| quality     | and    |     | FS-Wen |        | natchee | Wenatchee |
|             | air    |     | atchee |        |         |           |
|             | tempe  |     |        |        |         |           |
|             | rature |     |        |        |         |           |
+-------------+--------+-----+--------+--------+---------+-----------+

**Table 4. Inventory of spatial data assembled to date for project**

**Basins**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

CRB_US.shp Columbia River Shapefile-polygon 1:24k NOAA-Fisheries

HUC1_Region_reo.shp OR, WA, CA Shapefile-polygon 1:24k NOAA-Fisheries

HUC1_Region_streamnet.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

HUC2_SubRegion_reo.shp OR, WA, CA Shapefile-polygon 1:24k NOAA-Fisheries

HUC2_SubRegion_streamnet.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

HUC3_Basin_reo.shp OR, WA, CA Shapefile-polygon 1:24k NOAA-Fisheries

HUC3_Basin_streamnet.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

HUC4_SubBasin_reo.shp OR, WA, CA Shapefile-polygon 1:24k NOAA-Fisheries

HUC4_SubBasin_streamnet.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

HUC5_Watershed_reo.shp OR, WA, CA Shapefile-polygon 1:24k NOAA-Fisheries

HUC6_sr OR, WA, CA ESRI-Grid 30m NOAA-Fisheries

HUC6_SubWatershed_reo.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

HUC6_SubWatershed_sr.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

IMW_Total.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

JohnDay_Basin.shp John Day Basin Shapefile-polygon 1:24k NOAA-Fisheries

JohnDay_HUC6.shp John Day Basin Shapefile-polygon 1:24k NOAA-Fisheries

NHD_Catchments PNW ESRI-Grid 30m NOAA-Fisheries

Salmon_Basin.shp Salmon Basin Shapefile-polygon 1:24k NOAA-Fisheries

Salmon_HUC6.shp Salmon Basin Shapefile-polygon 1:24k NOAA-Fisheries

Skagit_Sauk_Basin.shp Skagit and Sauk Shapefile-polygon 1:24k
NOAA-Fisheries

StudyArea.shp PNW Shapefile-polygon 1:24k NOAA-Fisheries

UpperColumbia Upper Columbia Shapefile-polygon 1:24k NOAA-Fisheries

Wenatchee_HUC6.shp Wenatchee Shapefile-polygon 1:24k NOAA-Fisheries

Wenatchee_Watershed Wenatchee Shapefile-polygon 1:24k NOAA-Fisheries

**Boundaries**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Idaho.shp Idaho Shapefile-polygon 1:200k NOAA-Fisheries

Land Ownership PNW Shapefile-polygon USBR

Malheur National Forest Malheur National Shapefile-polygon

Oregon.shp Oregon Shapefile-polygon 1:200k NOAA-Fisheries

Township/Range Grid Umatilla National Shapefile-polygon

Washington.shp Washington Shapefile-polygon 1:200k NOAA-Fisheries

**Climate**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

GrowingDegreeDay PNW ESRI-Grid 2km NOAA-Fisheries

Precip_MeanAnnual PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanApr PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanAug PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanDec PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanFeb PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanJan PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanJul PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanJun PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanMar PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanMay PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanNov PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanOct PNW ESRI-Grid 4km NOAA-Fisheries

Precip_MeanSep PNW ESRI-Grid 4km NOAA-Fisheries

Tempature_Max PNW ESRI-Grid 4km NOAA-Fisheries

Temperature_Min PNW ESRI-Grid 4km NOAA-Fisheries

**DEMs**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

10m_DEM Continental US ESRI-Grid 10m NOAA-Fisheries

30m_DEM PNW ESRI-Grid 30m NOAA-Fisheries

90m_DEM Continental US ESRI-Grid 90m NOAA-Fisheries

90m_SRTM PNW ESRI-Grid 90m NOAA-Fisheries

**Fish Distribution**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Anadromous Distribution-Entiat Entiat Watershed Shapefile-line 1:100k
NOAA-Fisheries

Anadromous Distribution-Wenatchee Wenatchee Shapefile-line 1:100k
NOAA-Fisheries

Barriers-Anthropogenic Interior Columbia Shapefile-point NOAA-Fisheries

Barriers-Natural Interior Columbia Shapefile-point NOAA-Fisheries

Barriers-ODFW Oregon Shapefile-point

Bull Trout Distribution John Day Basin Shapefile-line 1:24k Streamnet

Bull Trout Distribution Oregon Shapefile-line 1:100k Streamnet

Chinook Scale Card Data Bull Run, Clear, Shapefile-line

Chinook-Fall Distribution PNW Shapefile-line 1:100k Streamnet

Chinook-Spring Distribution PNW Shapefile-line 1:100k Streamnet

Chinook-Summer Distribution PNW Shapefile-line 1:100k Streamnet

Chum Distribution PNW Shapefile-line 1:100k Streamnet

Coho Distribution PNW Shapefile-line 1:100k Streamnet

Fish Screens John Day Basin Shapefile-line 1:12k USBR

Last Fish-Wentachee Wenatchee ESRI-Grid 10m NOAA-Fisheries

Pink Distribution PNW Shapefile-line 1:100k Streamnet

Rainbow Trout Distribution Oregon Shapefile-line 1:100k Streamnet

Resident Distribution-Entiat Entiat Watershed Shapefile-line 1:100k
NOAA-Fisheries

Resident Distribution-Wenatchee Wenatchee Shapefile-line 1:100k
NOAA-Fisheries

Sockeye Distribution PNW Shapefile-line 1:100k Streamnet

SSHIAP Fish Distribution Washington Shapefile-line 1:24k NOAA-Fisheries

Steelhead Distribution Oregon Shapefile-line 1:24k Streamnet

Steelhead-Summer Distribution PNW Shapefile-line 1:100k Streamnet

Steelhead-Winter Distribution PNW Shapefile-line 1:100k Streamnet

**Geology**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

ID_Geology Idaho Shapefile-polygon 1:500k NOAA-Fisheries

OR_Geology Oregon Shapefile-polygon 1:500k NOAA-Fisheries

PNW_Geology OR, WA, ID Shapefile-polygon 1:500k NOAA-Fisheries

WA_Geology Washington Shapefile-polygon 1:500k NOAA-Fisheries

Soils - SSURGO Oregon Shapefile-polygon 1:24k NOAA-Fisheries

Soils - STATSGO Oregon Shapefile-polygon 1:250k NOAA-Fisheries

**Habitat**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Aquatic Habitat Inventory John Day-Middle coverage

Aquatic Habitat Inventory John Day-North coverage

Aquatic Habitat Inventory John Day-South Shapefile-line

Aquatic Habitat Inventory John Day-Upper coverage

BPI_Basins Upper Columbia Shapefile-polygon 1:24k NOAA-Fisheries

BPI_Reaches Upper Columbia Shapefile-line 1:24k NOAA-Fisheries

BPI_RiparianLandUse Upper Columbia Shapefile-polygon 1:24k
NOAA-Fisheries

Chinook and Steelhead Redd Counts John Day Basin Shapefile-line

EMAP Reference Sites PNW Shapefile-point

Habitat Survey John Day Basin Shapefile-line 1:24k

ICB_200mReaches Interior Columbia Shapefile-line 1:100k NOAA-Fisheries

Salmon and Steelhead Habitat Oregon coverage 1:100k

TMDL Oregon Shapefile-line

TRIAD_Basins Upper Columbia Shapefile-polygon 1:12k NOAA-Fisheries

TRIAD_Reaches Upper Columbia Shapefile-line 1:12k NOAA-Fisheries

TRIAD_TributaryJunctions Upper Columbia Shapefile-point 1:12k
NOAA-Fisheries

**Human Impact**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Census Oregon Shapefile-polygon

Cities PNW Shapefile-point

Constructed Features Umatilla NF Umatilla National coverage

Culverts John Day Basin Shapefile-point

Diversions John Day Basin Shapefile-point 1:12k USBR

Grazing Allotments OR, WA Shapefile-polygon BLM OR/WA

Historic Roads Umatilla National coverage

John Day Basin Water Rights John Day Basin Shapefile-line USBR/OWRD

Major Highways John Day Basin Shapefile-line

Major Towns Umatilla National coverage

Mines PNW Shapefile-point

Pumps John Day Basin Shapefile-point 1:12k USBR

Roads_GTRN John Day Basin Shapefile-line 1:24k USBR

Water Rights Oregon Shapefile-line

**Hydrography**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Banks John Day-South Shapefile-line

Listed 303d Streams Oregon Shapefile-line 1:100k

NHD_HighResolution PNW Shapefile-line 1:24k NOAA-Fisheries

NHDPlus PNW Shapefile-line 1:100k NOAA-Fisheries

ReachFileVersion3 PNW Coverage 1:100k NOAA-Fisheries

SSHIAP Washington Coverage 1:24k NOAA-Fisheries

**Imagery**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Aerial Photo Imagery John Day Basin ESRI-Grid 1:12k USBR

LANDSAT5: TM data John Day Basin ESRI-Grid 35m USBR

Over 70 LANDSAT images Columbia River ESRI-Grid 30m NOAA-Fisheries

USGS DOQ John Day Basin ESRI-Grid USGS

**Landscape**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Ecoregions PNW coverage

Erosion Potential Upper Columbia Shapefile-polygon

Erosion Potential-Agricultural Interior Columbia Shapefile-polygon
NOAA-Fisheries

Erosion Potential-Forested Interior Columbia Shapefile-polygon
NOAA-Fisheries

Land Use Land Cover PNW ESRI-Grid

National Land Cover Dataset 1992 PNW ESRI-Grid 1:24k

Sediment Production-Agricultural John Day Basin Shapefile-line
NOAA-Fisheries

Sediment Production-Forested John Day Basin Shapefile-line
NOAA-Fisheries

**Vegetation**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

Current Vegetation Umatilla National coverage

Current-Historic Fuels Comparison Umatilla National coverage

Fire Frequency/Severity-Current OR, WA, ID ESRI-Grid

Fire History Ochoco National coverage

Fire History Umatilla National coverage

Fire Management Zones Umatilla National coverage

Harvest Malheur National coverage

Harvest Ochoco National coverage

Harvest Umatilla National coverage

Historic Timber Types Umatilla National coverage

Old Growth Stand Umatilla National coverage

Permanent Ecology Plots Blue Mountain coverage

Potential Vegetation Umatilla National coverage

Reforested Lands Ochoco National coverage

Timber Lands Umatilla National coverage

Timber Sales Ochoco National coverage

**Water Quality**

**Dataset** **Spatial Extent** **Data Type** **Scale** **Location**

FLIR 1998, 2002, 2003, 2004 John Day Basin ESRI-Grid ODEQ

John Day Temperature Gages John Day Basin Shapefile-point 1:100k

USGS Stream Gages PNW Shapefile-point 1:100k

Water Quality Station Umatilla National Coverage 1:24k

**Objective 2: Coordination of data management needs assessment, scoping
and design for integrated status and effectiveness monitoring project.**

###### Task 2.1. Coordination of data management needs assessment, scoping and design

Data management in the Wenatchee and John Day basins has been piloted by
three efforts: 1) development of the Status and Trend Monitoring Oracle
database and GIS interface by the Northwest Fisheries Science Center
data management group and Bureau of Reclamation; 2) development of
interim storage and MS ACCESS databases for individual data types (e.g.
water temperature and geomorphic cross sections) and IMW projects; and
3) development of standard GIS datasets in geodatabase space. Both
status and effectiveness monitoring data (IMW) will be housed in the
Status and Trend Monitoring database and will conceptually and
structurally be standardized to the Data Dictionary and Protocol
Manager.

*Database dictionary and protocol manager.* The Bureau of Reclamation
has established a working Database dictionary and they are currently
developing a "Protocol Manager" which will house data collection
protocols used to collect data within the John Day Basin. The Protocol
Manager will be useful in describing which collection characteristics
and methods pertain to specific attributes and indicators used within
the various protocols, such as EMAP and PIBO.

*Wenatchee Status and Trend Monitoring database.* The NOAA-Fisheries
Scientific Data Management Team (SDM Team) has developed a database
structure, data migration tools, and preliminary application interfaces
for Status-and-Trend monitoring data from the Wenatchee pilot basin. The
intention was to create a shared data repository in a web-accessible
Oracle environment. Database development to date includes the successful
migration of 2004 field data and the prototype web interface development
for water quality and habitat data. These data are internally accessible
by NOAA-Fisheries for testing and further query development. There is
ongoing refinement of the protocol builder associations developed by
Bureau of Reclamation. Database architecture was assembled to allow
growth in functionality and datatype expansion as needed for future data
collection efforts. Development of this database for the Wentachee basin
has been conducted in close coordination with the John Day Pilot project
and the associated Monitoring Data Dictionary. In 2004-2005, six joint
meetings involving the Wenatchee SDM database development team and the
BoR John Day data management team have facilitated communication between
groups. Further development of the Oracle database web interface is
projected to include increased tabular and spatial query power.

[]{.mark}

NOAA-Fisheries developed MS ACCESS and SQL databases to facilitate
interim tabular data manipulation and storage until data incorporation
to the Status and Trend Monitoring Database. These interim databases are
also being developed for use by agency, IMW, and subbasin project teams
to ensure data standardization and future incorporation into the STM
database. Database development is being limited to data management needs
that are not currently addressed within agency monitoring programs or
housing projects. For example, within the John Day basin, communication
with local data collection agency personnel identified a need for a
water temperature database for agency storage of data. The designed
interim water temperature database structure is consistent with the
Status and Trend Monitoring database and facilitates data loading and
storage at the agency level. Such databases will facilitate the future
incorporation of data from local agencies into IMW and status monitoring
research databanks.

NOAA-Fisheries has also addressed data management needs for spatially
continuous GIS data. GIS datalayers have been compiled and standardized
into MS ACCESS-ESRI software geodatabases. NOAA-Fisheries is currently
maintaining geodatabases for the Wentachee and John Day basins and will
develop a geodatabase for the Lemhi-Salmon as data is collected.
Preservation of GIS data within standard geodatabases according to a
standard, referenced, hydrography layer (National Hydrography
Dataset-Plus, August 2005) will facilitate spatial analyses and
cross-referencing among data types. A NHD-networked geodatabase is also
being customized for each IMW to facilitate data sharing among multiple
users and with tabular data. These geodatabases are currently housed at
the NWFSC in Seattle.

**Objective 3: Statistical analysis for monitoring and experimental
design, as well as preliminary data analysis.**

The pilot projects aim to address questions of design considerations for
monitoring status and trend of populations and habitat as well as the
aggregate impact of habitat restoration projects on population
condition. To formalize the assessment of design issues for these
programs requires posing the questions in terms of data quality and
quantity requirements. This framework should parallel the monitoring
program design and coordination process. To accomplish this, the pilot
projects are developing analysis tools as necessary to meet ongoing
design questions, and in advance of the data analysis phase with data
from outside the project. Overall, considerable work will be required
under this objective, dominating the NWFSC component of this project in
the next 2-3 years. At present, several preliminary analyses are
complete and are outlined below.

One of the major future objectives will be a mock data analysis
exercise. It will be a "mock" data analysis exercise since we will begin
"analyzing" data prior to complete data collection; however, the
analysis will support monitoring program design decisions, as well as
form the basis for program assessment and evaluation.

*Analysis of sampling schemes*

Precise, unbiased estimates of population size are an essential tool for
fisheries management. Redd counts are commonly used to monitor annual
trends in abundance for a wide variety of native salmonid fishes. In
most situations population estimates are developed by inference from a
sample of the population. Using a dataset that consisted of
georeferenced censuses of Chinook salmon redds from a large wilderness
basin in central Idaho, we evaluated six common sampling strategies for
estimating the total abundance of redds. The dataset was a nine-year
time series of redd population data with a range of 20 to 2,271 redds
per year. We evaluated two sampling-unit sizes (200-, and 1000-meter
reaches), three sample proportions (0.05, 0.10, and 0.29), and six
sampling strategies (index sampling, simple random sampling, systematic
sampling, stratified sampling, adaptive cluster sampling, and a
spatially balanced design). We evaluated the strategies based on their
accuracy (confidence interval coverage), precision (relative standard
error), and cost (cost function based on travel time). Model-based
methods for estimating the number of redds from the non-probability
index strategy are biased. None of the other strategies were always
accurate, but accuracy increased with increasing number of redds,
increasing sample size, and smaller sampling units. The total number of
redds in the watershed and budgetary constraints will influence which
strategies are most precise and effective. For years with very few redds
(0.15 redds/km) a stratified sampling strategy was most precise whereas
for years with more redds (0.15 to 2.9 redds/km) either of two
systematic strategies were most precise. We also found with a simple
cost function that inexpensive strategies were best for years with very
few redds and the expensive but precise strategies for years with medium
to many redds in the watershed.

*Sampling location selection tool*

EPA's methodology was used to select a spatially balanced sample of
stream resources for the Wenatchee and Entiat basins. Sampling efforts
were stratified according to Strahler stream order and fish usage
(anadromous streams versus resident streams). GIS layers representing
EPA sample points, fish distribution, Strahler stream order, and stream
gradient were assembled for the two basins. Extent of resident fish
distribution in the Wenatchee basin were predicted by a statistical
model developed under the Forest Practice Water Typing project at the
Washington State Department of Natural Resources. The model predicted
the last upstream point that resident fish were expected to be observed.
Those points were transferred to the 1:100k NHD stream network and all
downstream sections of stream were designated as having resident fish
usage. Anadromous distribution in the Wenatchee was determined by
interviewing USFS and local biologists. Fish distribution in the Entiat
also was determined through interviews with local biologists. Strahler
stream order and stream gradient were calculated in ArcView 3.2. The
length of the stream network in each Strahler order and fish usage
category were summed and sample sites were partitioned to strata
relative the proportion of the network in each strata.

To test the spatial balance of the sample sites, NOAA-Fisheries compared
the cumulative frequency distribution (cdf) of pairwise distances
between points within our sample sites relative to that of the master
list of all possible sample sites. The master list was developed as a
spatially balanced sample by EPA. Pairwise distances of all points were
calculated in the master sample, ranked according to distance and
plotted as a cdf. Fifty sites were iteratively randomly selected
according to code and conforming to the set stratification rules.
Pairwise distances of sites within the random samples were rank and plot
for comparison against the cdf for the master sample. Sites within 500
meters of one another along the stream network we removed from the
sample site location set.