**[First Quarter of 2005 Progress Report on the John Day RME pilot
project]{.underline}**

A Federal research, monitoring, and evaluation (RME) program for the
Columbia River Basin, has been called for under the US National Oceanic
and Atmospheric Administration Fisheries (NOAA-Fisheries) 2000 Federal
Columbia River Power System Biological Opinion (BiOp) and the Federal
Columbia River Salmon Recovery Strategy (All-H Strategy). Implementation
of this regionally coordinated, programmatic approach to the Tributary
Research, Monitoring, and Evaluation (RME) is being tested through pilot
projects in the Wenatchee, John Day, and Salmon subbasins, prior to
extending it to larger areas. This project seeks to develop the pilot
intensive RME program and an Intensively Monitored Watershed Study (IMW)
in the John Day basin. To aid in the coordination of the John Day RME
program and the IMW Study, four workgroups have been established; the
Freshwater Production Group, the Habitat Monitoring Group, and the GIS
Group, which are subgroups of the parent coordinating Analytical
Framework Group (AFG).

The AFG is charged with developing the overall analytical framework for
RME efforts in the John Day basin. The framework attempts: to organize
existing and future research activities to identify factors limiting
salmonid production; evaluate status and trends of salmonids and
habitat; coordinate project implementation and compliance monitoring;
assess reach-scale biological and physical impacts up to population
level salmonid productivity effects of restoration actions. In the first
quarter of 2005, the AFG has conceptually designed a program that
addresses these goals. The AFG will develop and test this program under
two broad approaches: development of IMWs and the development of a
basin-wide RME program.

**Development of Workgroups and Products**

Workgroups have been developed to help coordinate efforts to compile
information, summarize results from related projects, and design
projects for the IMW and the watershed assessments. Names in bold are
the workgroup leaders.

-   GIS workgroup -- **Kristin Swoboda**, Lanie Boler, Carol Volk, John
    Faustini, Francisco Madrinan, Russ Faux, Don Butcher, Steve
    Rentmeester, Nick Bouwes.

    -   Will compile data layers and coordinate distribution. Because
        there is overlap in the GIS layers needed for each project, this
        workgroup should determine the most efficient approach to gather
        this information. There is an opportunity here to divvy up work
        products that can be shared.

        -   Summarize/synthesize current activities

        -   Extract relevant information from above relative to needs
            for monitoring design process

    -   [Progress to date]{.underline}: inclusion of habitat and fish
        monitoring information into the Federal RME database and data
        dictionary

-   Habitat Monitoring - **Rick Henderson**, Shannon Hubler, Hiram Li,
    John Faustini, Jim Ruzycki, Nick Bouwes.

    -   Will develop work plan including, but not limited to data
        compilation, data assessment, indicator/protocol assessment, and
        performance metrics.

        -   Summarize/synthesize current activities

        -   Extract relevant information from above for monitoring
            design process

    -   [Progress to date]{.underline}: ODFW has completed 2004 annual
        report on habitat monitoring in the John Day. PIBO has completed
        a preliminary report on habitat monitoring in the Columbia River
        Basin for 2004. ODEQ is currently summarizing the past 5 yrs of
        monitoring. Some of this of information has been presented to
        the AFG.

-   Fish Monitoring - **Jim Ruzycki,** Peter Bayley, Charlie Paulsen,
    Nick Bouwes.

    -   Compile data and define performance metrics.

        -   Summarize/synthesize current activities

        -   Extract relevant information from above relative to needs
            for monitoring design process

    -   [Progress to date]{.underline}: Cooney provided an overview of
        the BRT work on the status and trends of steelhead and salmon in
        the John Day. ODFW has completed the draft 2004 annual report
        describing the fish monitoring over the past year.

**Designing the RME program for the John Day**

Because the pilot projects are being implemented as means to test and
learn about the development of a comprehensive effectiveness monitoring
program, the AFG has begun to develop a conceptual framework where we
identify where and how restoration actions should be implemented, and
how we determine the benefit of those actions with a high degree of
certainty and potential for learning. This framework is also the basic
premise of experimental management.

The conceptual framework is illustrated in Figure 1. The diagram starts
with a goal statement. This statement should be concise as possible to
focus the RME process. In the John Day, the goal of the Federal Columbia
River Power System (FCRPS) BiOp, is to increase freshwater productivity
of salmonids. The AFG plans to help develop the Federal RME program to
identify, implement, and measure responses of mitigation strategies. The
goal statement is expected to be refined to a hypothesis as we develop
specific study designs in the IMWs.

Next, it is important to identify the problem or the factors limiting
salmonid production. Most restoration efforts fail because they have not
identified the problem, often a general packaged restoration plan is
implemented that may or may not be effective. This approach is not
likely to be cost effective in the long run. In addition, efforts should
be made to describe baseline or current conditions in which to describe
status and trends to compare to post mitigation responses. This will
require status and trends monitoring of fish and habitat, and research
directed to help understand the mechanisms limiting salmonid production.
This information has to be synthesized to identify the problem and to
refine broad questions into testable hypotheses. This will likely be an
iterative approach. These steps described thus far (open circles in the
above diagram) can be considered more exploratory in nature.

Hypotheses should be much more specific than goals (i.e. the presence of
fine sediments reduces the survival of steelhead eggs for a given
population, or temperatures are above optimal to maximize growth in
juvenile steelhead). We can then design an experiment to test this
hypothesis. This includes design of effectiveness monitoring and
directed research to document mechanisms of the response. The
restoration action is then implemented under this experimental design
and responses are measure over time. The results of this experiment can
be use to make decisions about the effectiveness of this restoration
approach and how to proceed with further actions. This may alter the
view of these original goals. These steps (shaded circles) are more
experimental in nature. Research to date coordinated by the AFG has been
exploratory. The goal of the AFG in 2005 is to expand on this
exploratory research and design the experimental components of the RME
program.

Figure 1: Diagram of the steps to experimental management necessary to
identify and test mitigation strategies.

The AFG agreed to attempt to lay out a process by which mitigation
strategies in the John Day Basin will be identified, implemented, and
their responses monitored. Our first task has been to synthesize current
research and monitoring efforts that are described in detail in the 2004
Analytical Framework document (Bouwes 2004). We will then begin to
develop experimental management approaches at two different scales and
ask the questions:

1\) **What are the steps necessary in developing and implementing an
experimental restoration program in a given watershed?** We refer to
this as the Intensively Monitored Watershed study.

2\) **What are the steps necessary in developing and prioritizing
restoration efforts, by watershed, and developing effectiveness
monitoring programs at the scale of the John Day Basin?** This will
initially be a large scale watershed assessment.

[Synthesis of research]{.underline}

Researchers are to summarizing current research to date so that
synthesis of this research can be used to design IMW and watershed
assessments. Progress has been made on research described in the 2004
AFG document. The AFG agreed to try to summarize 2004 research and
monitoring by the first quarter of 2005. The AFG will attempt to
synthesize this information to refine questions into testable hypotheses
for the IMWs. Things to consider:

-   Our original problem statement was summer low flow water
    temperatures and disrupted sediment deposition/transport strongly
    limits production and distribution of salmonids in the John Day
    River basin. Has the research to date changed these ideas?

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-   What is being measured, where in the John Day River basin?

-   What scale (time/space) does it represent?

-   What are the statistical properties(?) of the data?

-   Do we have the monitoring infrastructure in place to assess stream
    temperatures and sediment process status?

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-   Do we have salmonid population/productivity monitoring in place to
    assess status of populations?

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-   Do we have the monitoring infrastructure in place to assess change
    in stream temperature and sediment processes?

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-   Do we have the research and monitoring infrastructure in place to
    assess change in salmonid population processes that result from
    changes in stream temperature and sediment supply and transport?

-   

**SUMMARIZE WHAT HAS BEEN DONE TO DATE?**

[Models]{.underline}

Models can be a very useful tool in organizing monitoring and research
and designing experiments. The AFG has begun to consider and develop
some analytical models for these purposes. For example, the TMDL model
may allow us to play with "what if" scenarios in terms of our ability to
alter reach temperature regimes. If, say, under the best case scenario
our ability to restore riparian vegetation and hydraulic connectivity
will decrease stream temperatures by 1 °C, is it worth attempting to
decrease reach temperatures? The development of a fish bioenergetics
component to this model has been initiated to better understand the
influence of habitat characteristics impacts on temperature and
therefore growth of salmonids.

[Intensively Monitored Watershed study]{.underline}

The plan is to implement the "ideal" experimental management action
within a given watershed as a means of testing the process of developing
an RME program. This includes: a process to identify the problem, such
as understanding the mechanisms limiting fish production and the
landscape context for these interactions; establishment of status and
trends of fish and their environment from associated monitoring
programs; defining specific hypotheses to test; designing the
experimental manipulation that achieves restoration goals while
maximizing learning, which include the experimental design (e.g. BACI
design), research design, the effectiveness monitoring program (e.g.
protocols, sample design, sample sizes, etc.); implementation of the
watershed restoration project, research and monitoring. This experiment
is expected to happen in one treatment watershed and one to several
control watersheds. Developing an RME program for a localized
experimental management project, will test the ability of the program to
meet the needs of large scale restoration efforts.

*IMW design considerations*

-   Statistical design: We need to determine the experimental design to
    maximize our ability to detect response. For example, a
    Before-After-Control-Impact (BACI; Green 1979, Stewart-Oaten et
    al. 1986) approach could be used, where a control and manipulated
    watershed would be compared pre- and post-manipulation over time.
    Underwood (1994) suggests that multiple control areas be used to
    account for different trajectories that naturally can occur between
    sites. There are other alternative approaches that may be explored.
    References will be put on the John Day website.

-   Monitoring design: Implementation monitoring (monitoring to
    determine if the manipulation is still in effect -- e.g. if logs
    were added to create pool, are the logs still there the next year)
    and effectiveness monitoring (monitoring of response variables to
    action) programs need to be developed. This includes evaluation of
    the multiple protocols already used in the John Day to monitor
    habitat and fish. An evaluation of different habitat monitoring
    protocols ability to distinguish signal from noise, and estimate the
    'truth' will occur this summer and may lead insight into design of a
    monitoring program. Also, an effectiveness sample design needs to be
    developed. This design will likely differ from status and trend
    monitoring in terms of selection and number of sample sites and
    response variables to measure. Other considerations include a
    cost:benefit analysis of the alternative approaches, covariates,
    consideration of variables with quick response times, surrogate
    measures and indices.

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-   Research: Currently there are several research projects occurring at
    multiple scales. The IMW is an incredible opportunity that we should
    take advantage of to develop research that can be done in
    contrasting conditions to elucidate mechanisms how fish interact
    with their environment, and how management might influence those
    interactions. We need to determine what research should be continued
    during an IMW, and what other projects should be added to address
    remaining critical uncertainties.

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-   Manipulation: There will be several things to consider when
    determine what manipulation we will test, beyond identifying the
    main limiting factors.

    -   Location-The location of where we can implement an IMW will
        likely be as important as anything else. By phrasing the
        question as in question 1, we can choose a watershed for
        manipulation based on practical considerations and go through
        the process of developing the best mitigation actions for that
        given basin (even though it may not be the most widespread
        problem in the John Day Basin). Practical considerations of
        where to conduct this study includes the availability of past
        and current research and monitoring to identifying the problem
        so that the exploratory steps to experimental management are
        largely completed, and the experimental component can proceed in
        the near future. Ownership of the land containing potential
        watersheds will also affect our ability to conduct an IMW.

    -   Logistics/feasibility: Obviously we have to give consideration
        to the feasibility of implementing a given restoration action.
        Constraints will be cost, time, and access. It is not clear, at
        this point, where the money will come from to implement a
        restoration program, although opportunities do exist. We will be
        more likely to obtain funding if we shop around with a well
        thought out plan in hand. We will have to estimate the cost
        associated with the planned activity and possibly alternatives.
        We also should consider the time it takes to see a response in
        determining the restoration action. The IMW has a minimum of 3
        years of funding. Future funding is uncertain so implementing a
        restoration project that requires 30 yrs to observe a response
        is not a likely option. We also have to consider the possible
        hurdles of obtaining the permits to implement a restoration
        activity such as time required to go through a NEPA process.

    -   Support: The effort required to conduct an IMW will be large and
        will require the input from several parties. We need to identify
        those parties and try to get them involved. Again, it might be
        best to have a working plan to generate the interest to join in
        this effort.

    -   We should review other working examples of IMWs and determine if
        there are tools or lessons learned from these studies that can
        be used in developing the IMW in the John Day.

*Potential IMW locations*

The AFG created a list of potential IMW projects that take the above
considerations into account. This information is summarized in Tables 1
through 3. The AFG has begun to develop IMW study designs on a subset of
these potential projects.

**The South Fork of the JDA**. The South Fork of the JDA provides an
excellent opportunity to conduct an IMW. A great deal of the monitoring
and research coordinated by the AFG occurs in the mainstem South Fork
John Day River and its tributaries: Black Canyon, Wind Creek, Deer
Creek, and Murderers Creek (see Figure 2). This work includes: GIS
analysis of how landuse and landscape patterns impact habitat and fish
distribution; LiDAR and FLIR of the SF JDA and some these tributaries;
TMDL model development on the mainstem SF; extensive continuous habitat
surveys SF JDA and these tributaries; PIT-tagging of fish in each
tributary (Figure 3) 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; and snorkel surveys. This information can serves as
baseline information as well as a means to identify the major limiting
factors in these watersheds.

Stream temperatures in the South Fork approach lethal levels for
juvenile steelhead. Juveniles attempt to find cold water refugia
throughout the system; however, upstream and downstream migration is
constrained by impassible push-up dams. Push-up dams are expected to be
removed in the summer of 2005 from the lower mainstem of the South Fork.
In addition, the lower portion of Murderers Creek is owned and managed
by the state of Oregon, and therefore, through partnership with ODFW,
may provide a feasible location to further test the removal of a water
diversion. The research in this area will allow for an evaluation of the
removal of these dams on habitat selection in the mainstem South Fork
and other tributaries. Development of an experimental design is
currently underway and is expected to be implemented in the summer of
2005.

![](media/image1.png){width="5.999305555555556in"
height="3.3041666666666667in"}

Figure 2. A map of the South Fork of the John Day (the SF flows North as
represented by the arrow) and its tributaries.

![](media/image2.png){width="5.999305555555556in" height="3.54375in"}

Figure 3. A map of the South Fork of the John Day and its tributaries,
showing the distribution of PIT tagged *O. mykiss* parr in 2004.

[Bridge Creek.]{.underline} 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. An IMW study could be designed to follow
this potential restoration action. Rock Creek also suffers from channel
incision and provide a control watershed in an experimental management
approach to this study. Coordination between research in the South Fork
John Day and Bridge Creek is underway to maximize sampling of fish
utilization and habitat information.

[Upper Middle Fork of John Day.]{.underline} This area might also
provide an opportunity for an IMW study as a fair amount of information
has been collected there and access to MF JDA is possible. Land holdings
include: The Nature Conservancy, Confederate Tribe of the Warm Springs
Reservation, Federal lands, and one private property, who might be
willing to work with us. In addition, several restoration activities
have been planned or are currently being implemented. Evaluating these
restoration actions that have already received funding may prove to be
cost effective. ODFW has recently finished complete habitat surveys of
the MF JDA on CTWSR land. In addition, there are chinook spawning
grounds surveys, snorkel surveys, and screw trap information to get some
information on chinook status. OSU has also conducted research in this
area in the past. FLIR surveys have also been collected on the Middle
Fork on three different years. Finally, a TMDL model will be available
for this reach.

Table 1: Potential Intensively Monitored Watershed studies in the South
Fork of the John Day River.

Table 1 (cont.): Potential Intensively Monitored Watershed studies in
the South Fork of the John Day River.

<table style="width:100%;">
<colgroup>
<col style="width: 7%" />
<col style="width: 8%" />
<col style="width: 9%" />
<col style="width: 11%" />
<col style="width: 8%" />
<col style="width: 9%" />
<col style="width: 10%" />
<col style="width: 7%" />
<col style="width: 6%" />
<col style="width: 9%" />
<col style="width: 9%" />
</colgroup>
<tbody>
<tr class="odd">
<td>subbasin</td>
<td>location</td>
<td>controls</td>
<td>biological response metric</td>
<td>potential for response</td>
<td>physical response metric</td>
<td>representative</td>
<td>ESA</td>
<td>TMDL ?</td>
<td>cooperators</td>
<td>lead</td>
</tr>
<tr class="even">
<td>South Fork</td>
<td>Mainstem SF</td>
<td>Black Canyon, Deer Canyon, Wind Creek, SF mainstem</td>
<td><p>fish movement (Hughes and Grand), fish growth, fat,
production?</p>
<p>Secondary production (maybe difficult), ppr</p></td>
<td>quick, effect size?</td>
<td>Increase connectivity, decrease barriers.</td>
<td>yes</td>
<td>yes, steelhead</td>
<td>yes</td>
<td>AFG</td>
<td>Hiram, Jim, Tim</td>
</tr>
<tr class="odd">
<td></td>
<td>Murderers Creek</td>
<td>Black Canyon, Deer Canyon, Wind Creek, SF mainstem</td>
<td><p>fish movement (Hughes and Grand), fish growth, fat,
production?</p>
<p>Secondary production (maybe difficult), ppr</p></td>
<td>quick, effect size?</td>
<td>Increase connectivity, decrease barriers</td>
<td>yes</td>
<td>yes, steelhead</td>
<td>yes</td>
<td>AFG</td>
<td>Hiram, Jim, Tim</td>
</tr>
<tr class="even">
<td></td>
<td>Black Canyon</td>
<td>May require comparisons with other similar watersheds with different
fire histories in NFJD, MFJD, and upper mainstem, e.g., Tower fire, Mt.
Baldy fire.</td>
<td>Patterns of habitat use and fish density. Relative distribution and
extent of redds. Standardize for watershed area, habitat size, stream
gradient, valley type, mean annual ppt. and elevation.</td>
<td>Substitute space for time.</td>
<td>Examine factors influenced by fire (e.g., sediment, stream
temperature, large wood distribution, retention time &amp; length of
nutrient spirals)</td>
<td>With careful selection of other sites, may compare how fire policy
can influence habitat restoration.</td>
<td>yes, steelhead</td>
<td>yes</td>
<td>AFG</td>
<td>Hiram, Jim, Tim</td>
</tr>
</tbody>
</table>

Table 2: Potential Intensively Monitored Watershed studies in the Middle
Fork of the John Day River.

+-----+-----+----------+--------+-------+------+--------+-----+-------+
| su  | lo  | hy       | manipu | land  | ac   | pre    | sca | scale |
| bba | cat | pothesis | lation | owne  | cess | -infor | le- | -size |
| sin | ion | (        |        | rship |      | mation | te  |       |
|     |     | problem) |        |       |      |        | mpo |       |
|     |     |          |        |       |      |        | ral |       |
|     |     |          |        |       |      |        | re  |       |
|     |     |          |        |       |      |        | spo |       |
|     |     |          |        |       |      |        | nse |       |
+-----+-----+----------+--------+-------+------+--------+-----+-------+
| Mid | Ma  | loss of  | e      | Warm  | ac   | See    | 15+ | Large |
| dle | ins | riparian | xclude | Spr   | cess | Powe   | ye  | water |
| F   | tem | habitat  | cattle | ings, | to   | rpoint | ars | shed. |
| ork | MF  | has lead | from 5 | TNC,  | w    | S      |     | Many  |
|     |     | to       | miles  | Fo    | hole | lide\" |     | Subb  |
|     |     | disfu    | ri     | rrest | s    | OSU    |     | asins |
|     |     | nctional | parian | R     | tudy | S      |     | are   |
|     |     | stream   | area,  | anch, | area | patial |     | large |
|     |     | system   | Oregon | Oxbow | (but | D      |     | (e.g. |
|     |     | (loss of | Water  | R     | some | ata\", |     | Big   |
|     |     | pools,   | Trust  | anch, | rea  | recent |     | C     |
|     |     | increase | may    |       | ches | ODFW   |     | reek, |
|     |     | temp     | still  | pote  | are  | h      |     | Grani |
|     |     | erature, | have a | ntial | s    | abitat |     | te-Bo |
|     |     | high     | lease  | for   | till | inv    |     | ulder |
|     |     | se       | on     | an    | in   | entory |     | C     |
|     |     | diment). | water  | other | pri  | on     |     | reek, |
|     |     | Grazing, | rights | ranch | vate | entire |     | Camp  |
|     |     | fire     | in a   | to    | ha   | CTWSR  |     | C     |
|     |     | distu    | key    | pa    | nds) |        |     | reek, |
|     |     | rbances, | reach  | rtici |      |        |     | Clear |
|     |     | logging  | in the | pate, |      |        |     | C     |
|     |     | on south | Austin | Pa    |      |        |     | reek, |
|     |     | flowing  | Ju     | ckett |      |        |     | Big   |
|     |     | wa       | nction | pro   |      |        |     | Bou   |
|     |     | tersheds | vic    | perty |      |        |     | lder) |
|     |     |          | inity. | downs |      |        |     |       |
|     |     |          | Steven | tream |      |        |     |       |
|     |     |          | P      |       |      |        |     |       |
|     |     |          | arrett |       |      |        |     |       |
|     |     |          | is     |       |      |        |     |       |
|     |     |          | c      |       |      |        |     |       |
|     |     |          | ontact |       |      |        |     |       |
|     |     |          | at     |       |      |        |     |       |
|     |     |          | Oregon |       |      |        |     |       |
|     |     |          | Water  |       |      |        |     |       |
|     |     |          | Trust. |       |      |        |     |       |
|     |     |          | Po     |       |      |        |     |       |
|     |     |          | ssible |       |      |        |     |       |
|     |     |          | water  |       |      |        |     |       |
|     |     |          | div    |       |      |        |     |       |
|     |     |          | ersion |       |      |        |     |       |
|     |     |          | manipu |       |      |        |     |       |
|     |     |          | lation |       |      |        |     |       |
|     |     |          | on old |       |      |        |     |       |
|     |     |          | V      |       |      |        |     |       |
|     |     |          | idondo |       |      |        |     |       |
|     |     |          | Ranch. |       |      |        |     |       |
+-----+-----+----------+--------+-------+------+--------+-----+-------+
|     | Bri | Removal  | small  | ranch | li   | sp     | 1+  | wate  |
|     | dge | of       | dam    | and   | kely | awning | ye  | rshed |
|     | Cr  | r        | r      | pu    |      | ground | ars | for   |
|     | eek | eservoir | emoval | blic, |      | su     |     | mov   |
|     | to  | would    |        | USFS, |      | rveys, |     | ement |
|     | ma  | increase |        | above |      | BLM    |     |       |
|     | ins | fish     |        |       |      | Prin   |     | reach |
|     | tem | access   |        |       |      | eville |     | for   |
|     | MF  | decrease |        |       |      | Fish   |     | t     |
|     |     | water    |        |       |      | Inve   |     | emper |
|     |     | temp     |        |       |      | ntory, |     | ature |
|     |     | eratures |        |       |      | late   |     |       |
|     |     |          |        |       |      | 1      |     |       |
|     |     |          |        |       |      | 980\'s |     |       |
+-----+-----+----------+--------+-------+------+--------+-----+-------+

Table 2 (cont.): Potential Intensively Monitored Watershed studies in
the Middle Fork of the John Day River.

  ---------- ---------- ------------- ----------------------- ----------- ------------- ----------------- ------------ ------- ------------- ------
  subbasin   location   controls      biological response     potential   physical      representative    ESA          TMDL?   cooperators   lead
                                      metric                  for         response                                                           
                                                              response    metric                                                             

  Middle     Mainstem   upstream/     juvenile                long term   temperature   Must be careful   yes,         yes     CTWSR, TNC,   Alex
  Fork       MF         downstream-   abundance/production,               and increase  to avoid          steelhead,           private land  
                        distance      spawner abundance                   in habitat    confounding       bull trout           owners        
                                                                                        effects,                                             
                                                                                        (rrigation,                                          
                                                                                        grazing, timber                                      
                                                                                        harvest,                                             
                                                                                        channelization,                                      
                                                                                        road                                                 
                                                                                        construction,                                        
                                                                                        mining impacts,                                      
                                                                                        wild fire, water                                     
                                                                                        donations,                                           
                                                                                        passive and                                          
                                                                                        active                                               
                                                                                        restoration,                                         
                                                                                        installation of                                      
                                                                                        instream                                             
                                                                                        structures,                                          
                                                                                        fencing), but                                        
                                                                                        basin is large                                       
                                                                                        and appropriate                                      
                                                                                        contrasts may be                                     
                                                                                        possible within                                      
                                                                                        drainages.                                           

             Bridge     Clear Creek,  movement and            quick,      temperature   somewhat unique   yes,         yes in                
             Creek to   Vincent,      productivity , juvenile effect      and increase  but gets at       steelhead    MF                    
             mainstem   others?       density in reach below  size?,      in habitat    passage and                                          
             MF                       dam, redds/mile         large below               temperature                                          
                                                              dam                       impacts                                              
  ---------- ---------- ------------- ----------------------- ----------- ------------- ----------------- ------------ ------- ------------- ------

Table 3: Potential Intensively Monitored Watershed studies in the North
Fork and Mainstem of the John Day River.

  ---------- ------------ -------------- -------------- -------------- ---------- ----------------- --------------- -----------
  subbasin   location     hypothesis     manipulation   land ownership access     pre-information   scale- temporal scale -size
                          (problem)                                                                 response        

  North Fork Granite      increase in    level mine     FS, private    likely     OSU Spatial Data, 15+             watershed
             Creek to NF  channel        tailings                      high       EMAP site, FLIR                   
                          complexity and                                                                            
                          flood plain                                                                               
                          connectivity                                                                              
                          to increase                                                                               
                          spawing                                                                                   
                          habitat                                                                                   

             Upper        fire and clear natural        FS             likely     OSU Spatial Data, happen 10 yrs   large
             NF/Trail     leads to an    restoration                   high       EMAP site, FLIR   ago, 10+ yrs    watershed
             Creek        increase in                                             1998                              
                          temperature                                                                               
                          for large                                                                                 
                          section of the                                                                            
                          NF                                                                                        

             Desolation   Installation   Evaluate       USFS & private Likely     OSU Research      Depends on type Large
                          of instream    impact of      in-holdings.   high       1989, but sketchy of study.       watershed
                          structures to  brook trout on                           stuff. I          Removal of      
                          increase       bull trout and                           snapshot.         exotics on the  
                          pools, role of red band                                                   production on   
                          which not      trout? What is                                             survival and    
                          evaluated.     the                                                        the degree of   
                                         distribution                                               hybridization   
                                         and abundance                                              of brookies     
                                         of natural vs.                                             with bull trout 
                                         man-made pools                                             may take less   
                                         (too few to                                                than 5 years.   
                                         make a                                                                     
                                         difference).                                                               
                                         Compare                                                                    
                                         functions and                                                              
                                         fish densities                                                             
                                         of natural vs.                                                             
                                         man-made                                                                   
                                         pools? This                                                                
                                         gets hairy.                                                                

  Lower      Bridge Creek channel        sediment traps Park Service   sampling   little to no data 10+ years       reach -
  Mainstem   to MS        inciscion                     and BLM,       access                                       10km??
                          results in                    private                                                     
                          loss of                                                                                   
                          rearing                                                                                   
                          habitat,                                                                                  
                          spawing                                                                                   
                          habitat                                                                                   
                          increase temp                                                                             

             Pine Creek   channel                       Warm Springs,             Wayne Bowers and                  
             to Lower     inciscion                     ranch                     Tim Unterwegner                   
             MS????       results in                                              may have some                     
                          loss of                                                 data as they                      
                          rearing                                                 worked on                         
                          habitat,                                                projects with                     
                          spawning                                                OMSI in that                      
                          habitat                                                 region.                           
                          increase temp                                                                             
  ---------- ------------ -------------- -------------- -------------- ---------- ----------------- --------------- -----------

Table 3 (cont.) : Potential Intensively Monitored Watershed studies in
the North Fork and Mainstem of the John Day River.

  ---------- ------------ ------------- --------------- ----------- -------------- ---------------- ------------ ------- ------------- ---------
  subbasin   location     controls      biological      potential   physical       representative   ESA          TMDL?   cooperators   lead
                                        response metric for         response                                                           
                                                        response    metric                                                             

  North Fork Granite      Bull Run,     increase        large       channel        toxins unique,   bulltrout,   maybe   FS, ODFW      Jeff
             Creek to NF  other?        redds/mile,                 complexity,    mining           steelhead                          Neal,
                                                                    temperature    broadscale                                          ODFW

             Upper NF/    timeseries    productivity    large       temperature    large scale      steelhead    Yes     FS ODEQ       Don
             Trail Creek  appoarch,     and redds/mile              and increase   restoration      and                                
                          Baldy or                                  in habitat                      bulltrout                          
                          Crane                                                                                                        

             Desolation   Pre-post      degree of       Quick?      natural vs.                                                        Michael
                          study.        hybridization               man-made                                                           Pollock
                          Possibility   and relative                pools. Pool                                                        
                          of using      composition of              complexity?                                                        
                          upper         pure vs. hybrid             Additional                                                         
                          mainstem      bull trout?                 pool volume                                                        
                          sites to      Compare                     and habitat                                                        
                          examine the   productivity of             for entire                                                         
                          influence on  natural vs.                 watershed?                                                         
                          brook trout   man-made pools                                                                                 
                          on bull       (must                                                                                          
                          trout,        understand                                                                                     
                          redbands, but patterns of                                                                                    
                          upper         movement for                                                                                   
                          mainstem also this to provide                                                                                
                          has westslope dividends)                                                                                     
                          cutthroat                                                                                                    
                          trout. Might                                                                                                 
                          be able to                                                                                                   
                          use Cable                                                                                                    
                          Creek, a                                                                                                     
                          tributary to                                                                                                 
                          Camas Creek                                                                                                  
                          as a control.                                                                                                

  Lower      Bridge Creek Rock Creek,   fish                        flow,          yes              yes,         no      Park Service, Michael
  Mainstem   to MS        others?       productivity                temperature,                    steelhead            BLM           Pollock
                                                                    sediments,                                                         
                                                                    riparian                                                           
                                                                    habitat,                                                           
                                                                    channel                                                            
                                                                    complexity,                                                        
                                                                    etc.                                                               

             Pine Creek                                                                                                                Michael
             to Lower                                                                                                                  Pollock
             Mainstem                                                                                                                  
  ---------- ------------ ------------- --------------- ----------- -------------- ---------------- ------------ ------- ------------- ---------

[Basin-wide RME program]{.underline}

The IMW can potentially be implemented in the near term. However, there
is a need to develop and RME program with the goal to identify
mitigation opportunities at the scale of the John Day Basin. While this
will be much more difficult, the AFG has begun to outline how progress
can be on this while implementing an IMW. The AFG plans to conduct
watershed assessments to identify limiting factors, evaluate current
restoration activities, prioritize future restoration activities, and
develop effectiveness monitoring strategies to compare control and
treatment watersheds. A limiting factors analysis will be conducted for
all watersheds. This is where the AFG can tie in with other efforts that
have been working towards this goal such as subbasin planning, which has
used the Ecosystem Diagnostic and Treatment model (EDT) throughout the
John Day to identify limiting factors. Other processes will also feed
into this larger efforts such as the TRT and watershed and recovery
plans. The current exploratory studies coordinated under the AFG will
also be useful in this process, especially projects describing how
landscape patterns and land use practices relate to habitat and fish
distribution at the reach and watershed scale, because these studies
occur throughout the John Day Basin (see 2004 AFG document). Some of
these studies include the landscape changes and patterns study that will
classify watersheds and describe historical data, the TMDL studies, and
FLIR surveys that have been collected throughout much of the JDA.

Next, the AFG will prioritize restoration efforts by watershed defined
as potential importance for aiding in the recovery of focal species,
potential for improvement (perhaps determined from historic to current
condition), practicality of implementation (e.g. private landowners,
expense, etc.), and the likelihood to detect change given what we
learned from the ability of monitoring programs to distinguish signals
from noise. These steps are largely exploratory in nature. Multiple
restoration projects throughout the JDA will likely be done in
cooperation of several interested parties. Lessons learned in the IMW
study will be useful in setting these projects in an experimental
management approach and developing RME programs to determine benefits
from these activities. The larger scale of the John Day may provide
opportunities for greater spatial comparisons, higher replicates of
treatments and controls, and greater universe of restoration types for
extrapolation to other basins.

There may also be opportunities to evaluate existing restoration
activities retrospectively. The AFG will need to map out restoration
efforts to date throughout the JDA. Much of this information has already
been complied NMFS. The AFG will design an effectiveness monitoring
program around these restoration projects.