Yankee Fork Dredge Tailings Restoration Project
(BPA project # 2002-059-00)
Shoshone Bannock Tribes
Preface
The Shoshone-Bannock Tribes (Tribes) have been working under contract with the Bonneville
Power Administration (BPA) since 2005 on the Yankee Fork of the Salmon River Dredge Tailings
Restoration Project (Project # 2002-059-00). The Tribes submitted to BPA in May 2008 a
proposal for the Yankee Fork Floodplain Restoration Project Implementation Plan 2008-2018
(2008 Implementation Plan (Attachment A)). The 2008 Implementation Plan identified multiple
activities located throughout the dredged segment of the Yankee Fork to be implemented over
a ten-year time frame.
BPA referred the proposal to the Northwest Power and Conservation Council (Council) for a
funding recommendation. Due to the significant scale and costs of the proposal, the Council
recommended that the proposal be subject to the Council’s Three-Step Review Process and
requested in July 2008 a review by the Independent Scientific Review Panel (ISRP). The ISRP
responded in September 2008 with a determination that the proposal did not satisfy the
requirements of Step 1 and identified three areas of critical deficiency that needed to be
addressed before the proposal could proceed to Step 2 (Attachment B).
After receiving the ISRP review comments, the Tribes recognized that the 2008 Implementation
Plan was likely too ambitious and lacked watershed scale context. Since 2008, the Tribes have
participated in and worked collaboratively with the Yankee Fork Interdisciplinary Team (IDT) to
identify and address data gaps to provide the watershed-scale context for the 2008
Implementation Plan. In addition, the Tribes, U.S. Bureau of Reclamation (Reclamation), BPA,
JR Simplot Company (Simplot), the U.S. Forest Service (USFS), and Trout Unlimited (TU) are
working together to implement habitat improvement activities on the Yankee Fork. Habitat
improvement activities are selected, developed and implemented through collaborative efforts
of the IDT to support the goals of the Yankee Fork Salmon River Dredge Tailings Restoration
Project (Project # 2002-059-00).
Reclamation and BPA contribute to the implementation of habitat improvement projects in the
upper Salmon subbasin (Hydrologic Unit Code HUC 17060201) to help meet commitments
contained in the 2010 Supplemental Federal Columbia River Power System (FCRPS) Biological
Opinion (BiOp) (NOAA Fisheries 2010). The BiOp includes a Reasonable and Prudent Alternative
(RPA), or a suite of actions, to protect listed salmon and steelhead across their life cycle.
Habitat improvement activities in various Columbia River tributaries are one aspect of this RPA.
Reclamation provides technical assistance to states, tribes, federal agencies, and other local
partners for identification, design, and construction of stream habitat improvement activities
that primarily address stream flow, access, entrainment, and channel complexity.
Reclamation has adopted a tributary-reach based approach to help meet commitments in the
BiOp. This approach uses an IDT process involving technical specialists and stakeholders. With
Reclamation in the lead, the IDT has completed a watershed-scale physical and ecological
evaluation or tributary assessment of the lower and middle subwatersheds of the Yankee Fork
(HUC 1706020105). The Yankee Fork Tributary Assessment (Attachment C) is a first step to
evaluate physical and ecological processes occurring at the tributary-scale. The intent of the
Yankee Fork Tributary Assessment is to enable the focus of recovery efforts toward the most
appropriate spatial scales (i.e., reach or project area) that have the greatest potential to benefit
ESA-listed fish species. Subsequent steps may include reach assessments to further evaluate
how physical and ecological processes are affected at the reach-scale or alternatives evaluation
leading to design and construction at the site-scale.
The Yankee Fork Tributary Assessment identified the historically dredged segment of the
Yankee Fork (Reaches 2 and 3) as having the highest potential for habitat improvement. Reach
3 is the upper half of the dredged area from river mile (RM) 9 to RM 7. This reach is more
complex physically and has been recommended for more detailed assessment. A reach-scale
assessment is currently underway in Reach 3 with completion scheduled for September 2012.
The Yankee Fork Tributary Assessment found that there is sufficient knowledge about physical
and ecological characteristics in Reach 2 from RM 7 to RM 3 to identify and develop individual
activities. Two proposed habitat improvement activities have been identified in Reach 2 and
are in the design and permitting process. Other reaches have also been identified for further
assessment and alternative development, but with less potential and, therefore, lower priority
than reaches 2 and 3. It is envisioned that future activities will occur on these other reaches
once actions have been implemented in the dredged segment.
Introduction
Findings from the 2008 ISRP review found three major areas of critical deficiency that needed
to be addressed before the 2008 Implementation Plan could proceed to Step 2. The three
major areas of critical deficiency were the following:
(1) Completion of missing proposal components – the project sponsors should provide
study results on fish populations and fish habitats; establish and justify quantitative
biological objectives; outline M&E sufficient for Step 1; and address mercury and
selenium contamination. (Additionally the ISRP included “consideration of the
project’s role in the larger watershed” as a missing component elsewhere in their
document).
If any elements above cannot be established at this stage because of inadequate
information, then that information should be gathered, analyzed, and incorporated
in the next Project Implementation Plan submittal.
(2) Resolution of land access and conservation easement issues.
(3) A benefits analysis demonstrating the proposed alternatives are favorable to fish and
wildlife resources.
To assist the Tribes with addressing the three major areas of critical deficiency, Reclamation
and the IDT prepared the Yankee Fork Tributary Assessment to evaluate tributary-scale physical
and ecological processes, identify geomorphic reaches with potential for habitat improvement
2
activities, and provide rationale for use by local stakeholders and others in prioritizing those
reaches for further action.
In addition, an analysis of over 20-years of available fisheries data is currently underway by
Gregory Aquatics and should be complete in May 2012. This analysis will address the following:
(a) condition of existing fish populations; (b) fish population trends; (c) juvenile outmigration
and retention; (d) effects of fish supplementation; (e) comparison of fish populations with
similar watersheds (reference watersheds); and (f) determination of in-basin and out-of-basin
effects.
Concurrent with addressing the deficiencies identified during the Step 1 review process, the
Tribes and the IDT have been developing two habitat improvement activities that were
originally identified in the 2008 Implementation Plan. The two activities include adaptive
management actions for Pond Series 2 and Pond Series 3 originally constructed in the 1980s
under agreement with BPA.
A description of the proposed activities and the Tribes’ response to the Step 1 review areas of
critical deficiency follow.
Proposed Activities
Two habitat improvement activities in Pond Series 2 and Pond Series 3 are proposed for
implementation during the summer of 2012. The primary goal of the proposed activities is to
provide high-flow refuge and year-round rearing habitat for juvenile Chinook salmon. The
activities are also expected to improve holding and spawning habitat for returning adult
Chinook salmon, as well as habitat for steelhead and other native salmonids, including bull
trout. Draft conceptual plans dated November 9, 2011 for the Pond Series 3 (Exhibit 1) and for
Pond Series 2 (Exhibit 2) illustrate the proposed work activities. Design development for the
two activities continues with involvement by the IDT, Simplot, and the permitting agencies. The
final scope of work for the activities may be different than shown on the conceptual plans.
The common vision shared by the partners for the two activities is to create each pond series as
a self-sustaining, connected series of small ponds and side channels that are low-velocity, deep,
small with irregular edges, and conveying clear, cold, clean water flowing over clean, coarse
substrate, with abundant hiding cover and well-vegetated riparian zones. The primary goal of
each activity is to create and maintain high-flow refuge and year-round rearing habitat for
juvenile Chinook salmon. The side-channel habitat will be passively accessible to juvenile
salmonids during the rising limb of the spring runoff hydrograph. A description of each activity,
the design criteria, design elements, and anticipated changes in habitat suitability is provided in
the Preliminary Basis of Design Reports for Pond Series 2 (Attachment D) and Pond Series 3
(Attachment E). This submittal does not contain all of the appendices referenced in the Basis of
Design Reports. Only those appendices referenced in this narrative are included. Other
appendices can be made available to the Council by contacting Evelyn Galloway at
egalloway@sbtribes.com.
3
Major design elements for the two proposed activities include: 1) improved hydraulic
conditions at the pond inlets; 2) removal of artificial barriers and constrictions; 3) filling of the
pond areas to create side channel habitat; 4) excavation terracing of adjacent dredge piles to
create low- and high-flow floodplain benches; 5) placement of wood habitat structures and
root-wad bundles; and 6) re-vegetation with appropriate riparian species.
The proposed activities are based on sound scientific principals, will benefit fish and wildlife,
have clearly defined objectives and outcomes, include a monitoring and evaluation plan, and
are consistent with the Council’s fish and wildlife program. The three major areas of critical
deficiency identified in the 2008 ISRP Step 1 review are addressed specific to the proposed
activities in the following sections.
Deficiency Area 1 – Missing proposal components
Fish Populations and Fish Habitats
Fish Species of Interest:
 Snake River spring/summer Chinook salmon (Oncorhynchus tshawytscha)
 Snake River summer steelhead (Oncorhynchus mykiss)
 Bull trout (Salvelinus confluentus)
 Westslope cutthroat trout (Oncorhynchus clarki lewisi)
 Pacific lamprey (Entosphenus tridentatus)
Existing Yankee Fork Chinook Salmon Population
Information compiled in the Yankee Fork Tributary Assessment and provided by other sources,
including the Tribes and Idaho Department of Fish and Game (IDFG), provides data on the
existing spring Chinook salmon population in the Yankee Fork. The Yankee Fork Chinook
population is part of the Snake River spring/summer Chinook Evolutionary Significant Unit (ESU)
which has five major population groups (MPG), including: Lower Snake River, Grande
Ronde/Imnaha, South Fork Salmon River, Middle Fork Salmon River, and the Upper Salmon
River MPG. The ESU contains both spring and summer run Chinook. The Yankee Fork
population is a spring run and resides in the Upper Salmon River MPG.
The Idaho Salmon Recovery Plan (NMFS 2011) identifies the Yankee Fork spring/summer
Chinook population as currently Not Viable, with a high abundance/productivity and spatial
structure/diversity risk status. The population targeted desired status is Maintained. The
habitat recovery actions identified in the recovery plan expected to occur over the next 10
years have a reasonable chance of bringing the population to its desired status under moderate
to good ocean conditions (NMFS 2011). The habitat recovery actions identified in Table 4.4-31
of the recovery plan include the activities identified in the 2008 Implementation Plan.
4
Current Abundance and Productivity
IDFG has conducted redd counts in the Yankee Fork mainstem since 1957. The Tribes have also
conducted annual redd counts in the Yankee Fork mainstem since 1987. Spawning survey data
for Chinook salmon indicate that the Yankee Fork redd counts have ranged between 615 redds
(1968) and zero redds (1995). The IDFG data, as well as the Tribes’ data, show a declining trend
from 1969 through 2007 that has also occurred throughout the Salmon River drainage. Redd
counts have increased in recent years as a result of IDFG’s captive rearing program and the
Tribes’ Chinook Salmon Supplementation Program. Tardy (2009) indicated that juvenile
Chinook salmon densities remained low in 2008, but increased dramatically in 2009 with adult
outplanting activities in 2008. Overall, the Tribes estimated 685 natural and hatchery adults
returned to the Yankee Fork in 2008-2010 and an additional 2,955 Sawtooth hatchery adults
were outplanted. Of the returning adults, 473 were hatchery (69.1%) and 212 were natural
(30.9%). Yankee Fork natural-returned fish included 131 (61.8%) males and 81 (38.2%) females.
Yankee Fork hatchery fish were comprised of 209 (44.2%) males and 264 (55.8%) females. The
total spawning aggregate comprised 3,640 adults with 3,428 hatchery returns and hatchery
outplants (94.2%) and 212 natural (5.8%) spawners.
The Tribes annually install two rotary screw traps in the Yankee Fork for the purposes of
counting, tagging, and genetic tissue sampling of migrating juvenile salmonids for research,
monitoring, and evaluation. Based on capture rates since screw trap operations were initiated
in 2009, approximately 534,024 brood-year (BY) 2008 and 129,661 BY 2009 juvenile Chinook
salmon were estimated to have passed the lower screw trap in the Yankee Fork. The Tribes’
survival estimate for BY 08 natural Chinook salmon parr and pre-smolt migrating from the
Yankee Fork equaled 0.121 percent to Lower Granite Dam. Assuming this survival rate as the
minimum, 64,617 out of 534,024 natural parr and pre-smolt juveniles survived to Lower Granite
Dam.
The first adult returns from juvenile Chinook salmon that were PIT tagged during 2009 screw
trap operations are expected to return to the Yankee Fork in 2012.
The Tribes conducted snorkel surveys in Pond Series 1 through 4 (parallel to the dredge reach)
from 1997-2009 and in the Yankee Fork mainstem from Polecamp Creek at RM 3 to the mouth
of the West Fork at RM 7 from 1984-2009. The purpose of the surveys was to evaluate changes
in fish populations along the lower Yankee Fork. Based on Chinook salmon redd counts and
snorkel survey information, juvenile Chinook salmon population for each pond series was
estimated. Data analyses indicate the number of juvenile Chinook salmon present in each pond
series for the study period was a function of the available habitat or habitat suitability in
addition to how many fish spawned in the Yankee Fork drainage the previous year. Based on
the information presented by Gregory and Wood (2012), juvenile Chinook salmon prefer slower
moving habitat in the pond series connecting channels over the higher velocity habitat in the
Yankee Fork mainstem.
5
Existing Fish Habitat Condition
Based on findings in the Yankee Fork Tributary Assessment, historical mining impacts have
reduced channel migration and floodplain interaction through the dredged reaches of the
Yankee Fork, resulting in a less complex channel. The more homogenous channel conditions
limit the quantity, quality, and availability of habitat for juvenile salmonids. Information on
historic and present fish usage was completed at the watershed-scale in Section 6 (Watershed
Fish Usage and Supplementation) of the Yankee Fork Tributary Assessment. Reach
descriptions, anthropogenic disturbances, fish usage, channel condition, and habitat elements,
and potential habitat actions are discussed at the geomorphic reach-scale in Section 8 (Valley
Segments and Geomorphic Reaches) of the Yankee Fork Tributary Assessment.
In 2001, the USFS conducted a R1/R4 Fish Habitat Inventory (USFS Unpublished) on the
mainstem of the Yankee Fork. Results of the survey indicated a lack of pools and high
width/depth ratios. This survey was completed from the mouth of the Yankee Fork upstream
to the confluence with Jordan Creek at RM 9. Spawning and rearing habitat were identified as
in poor condition in the dredged area and in fair to good condition upstream of the dredge
tailings and in the West Fork. The 2001 survey also found that pool frequency, pool quality,
large woody debris, and in-stream cover were limiting for juvenile Chinook salmon rearing
habitat.
In 2010, a Level II Stream Inventory Survey was conducted by the USFS (Attachment F) covering
the Yankee Fork mainstem between RM 17 and RM 3 and Jordan Creek from between RM 3.6
to its confluence with the Yankee Fork. Results of this survey indicated that overall, stream
habitat conditions have not changed substantially between the 2001 R1/R4 Fish Habitat
Inventory and the 2010 Level II Stream Habitat Survey and likely have changed only within
Reach 3 since a 1934 survey (Rodeheffer 1935).
Because the Yankee Fork mainstem is relatively steep and confined by narrow valley walls and
dredge piles, high velocities exist throughout the mainstem during spring runoff. The Yankee
Fork and the West Fork through the dredged segment is confined with a straight channel
pattern and channel/floodplain interactions are disconnected. Off-channel areas with low
velocity rearing habitat and high flow refuge preferable to juvenile Chinook salmon are limited.
Limiting Factors
Factors limiting the recovery and sustainability of salmon populations identified through
extensive stakeholder input are listed in the Idaho Salmon Recovery Plan (NMFS 2011). The
current primary limiting factors within the Yankee Fork watershed affecting the abundance,
productivity, spatial structure, and genetic diversity of the fish species of concern are reduced
floodplain connectivity and riparian function, and excess sediment (Table 1).
Potential concerns not yet limiting factors or threats were also identified and includes: 1)
habitat degradation from dispersed recreation; 2) habitat degradation from off-highway use; 3)
reduced water quality due to new mineral exploration and development; 4) reduced water
quality due to heavy metals; and 5) habitat degradation from noxious weeds (NMFS 2011).
6
Table 1. Yankee Fork Habitat Limiting Factors (NMFS 2011) and Casual Factors.
Limiting Factors Causal Factors
Reduced floodplain
connectivity and
riparian function
Excess Sediment
Dredge tailings piles disconnected the Yankee Fork from much of its floodplain by constricting the
stream channel. The tailings piles blocked access for fish to off-channel habitat and covered riparian
vegetation. Tailings piles do not contain sufficient soil for riparian vegetation growth and the current
riparian zone does not provide either large wood recruitment or shade to the Yankee Fork stream
channel. Tributaries are either disconnected or have eroded downward to adjust to the lowered
elevation of the mainstem causing excess fine sediment in the channel.
Land uses including mining and road building have delivered elevated levels of fine sediment to
streams in the Yankee Fork watershed, reaching levels detrimental to egg incubation and rearing
habitat. The upper Yankee Fork from Jordan Creek to Eightmile Creek is currently listed for siltation on
the 2008 Clean Water Act 303(d) list. High turbidity levels are often seen in the watershed during
spring snowmelt. The watershed is also subject to periodic heavy summer thunderstorms causing
landslides and high sediments loads, possibly exacerbated by ground disturbances from human land
uses.
Quantitative Biological Objectives
Biological objectives describe the physical and biological changes needed to achieve the vision.
There are two components to biological objectives: 1) biological performance, describing
population responses to habitat conditions in terms of capacity, abundance, productivity and
life history diversity; and 2) environmental characteristics, describing the environmental
conditions necessary to achieve the desired population characteristics. The following biological
objectives have been established for the proposed Pond Series 2 and Pond Series 3 activities.
Biological Performance
1. Increase juvenile Chinook abundance in the activity area relative to control areas after
completion.
2. Increase survival to Lower Granite Dam for juvenile Chinook that use the activity area
compared to juveniles that remain in the Yankee Fork mainstem.
Environmental Characteristics
3. Increase availability of habitat suitable for juvenile rearing and high-flow refuge for
Chinook salmon.
a. Route water from the mainstem into each activity area (e.g., pond series) during
the time when recently emerged salmonids are seeking high-flow refuge
(primarily the overlap of spring runoff with juvenile Chinook salmon emergence).
b. Maintain a surface water connection at each outlet.
4. Increase the quality (complexity, cover, and hydraulic conditions) and quantity of
aquatic (juvenile Chinook salmon) and benthic (macroinvertebrate) habitat in the
activity area.
a. Maintain or increase the aerial extent of habitat-appropriate depths greater than
two (2) feet (Maret et al. 2006).
b. Develop conditions within off-channel activity areas that provide winter habitat
and increase over-winter survival (do not freeze).
7
5. Maintain water temperatures from greater than 0 degrees Celsius (°C) in winter to
approximately 15° C during summer base flows.
6. Maintain water quality without detectible increases in mercury and selenium
concentrations in the aquatic environment.
a. Reduce conditions conducive to methylization of mercury (such as low dissolved
oxygen, high sulfur concentrations, high organic carbon, and fine sediments),
thereby reducing bioaccumulation and biomagnifications.
b. Maintain mercury and selenium concentrations at levels below those which
cause adverse effects to aquatic resources and upper trophic-level consumers.
7. Increase the quality (diversity) and quantity of riparian and wetland habitat within the
activity area.
Monitoring and Evaluation
A two-tiered approach to effectiveness monitoring and evaluation is proposed by the Tribes.
The proposal includes monitoring fish habitat and population changes resulting from habitat
improvement activities throughout the Yankee Fork watershed. To assess the effectiveness of
habitat changes, biophysical baseline information will be collected and used to assess whether
juvenile Chinook abundance increases relative to control areas after activity completion.
Baseline information will be collected at the site scale for individual activities. Snorkeling will
be conducted above, within, and below activity areas, as well as at control locations within the
same strata.
To assess the effects on fish population, passive integrated transponder (PIT) tag interrogation
systems will be installed to track movement in and out of project areas. Fish residence time can
be determined from this monitoring, which will allow for determining whether survival is
increased due to habitat rehabilitation actions. All life stages of juvenile Chinook salmon down
to about 50 mm in length will be captured and tagged at rotary screw trap installations in midsummer as they enter activity areas. Tagging will take place prior to mass migration and
movement downstream, which typically begins in early September each year. Tagging will also
provide a means to tie fish movement into a larger PIT tag interrogation network that is being
established at the subbasin scale on the mainstem Salmon River to help determine survival for
fish on their route to Lower Granite Dam. At locations downstream of activity areas, several
dual PIT tag arrays will be installed and operated year-round; including locations at the mouth
of the Yankee Fork and at several locations on the mainstem Salmon River near Challis, and
Salmon, Idaho.
Information on the supplementation and habitat enhancement programs, and monitoring
efforts was compiled at the watershed-scale in Section 6 (Watershed Fish Usage and
Supplementation) of the Yankee Fork Tributary Assessment.
Mercury and Selenium Contamination
The Yankee Fork Tributary Assessment Section 7 (Watershed Condition) and Appendix B (Water
Quality) summarize mercury and selenium issues as follows:
8
Low to moderate concentrations of mercury were most likely deposited by hydrothermal
processes during the Challis Volcanics episode, but there are no indications that high
concentrations naturally occur (i.e., cinnabar deposits) (Fisher and Johnson 1995). However,
elemental mercury was used in some areas where the extraction and processing of ore and
placer deposits occurred. Varying concentrations of elemental mercury could be anticipated
wherever placer mining, hard-rock mining, and ore processing have occurred throughout the
watershed (Frost and Box 2009).
Mercury levels found in fish and fish tissues within the Yankee Fork do not indicate any
considerable contamination. Studies in the Yankee Fork (Rhea et al. 2008; Frost and Box 2009)
suggest there is little bioconcentration of mercury from the sediments to the fish tissues. According
to the EPA and State of Idaho human health concern criteria, there is little or no risk to human
health and the aquatic environment from mercury in the fish tissues of the second trophic level fish
that were analyzed.
Selenium naturally occurs as varying compounds in many volcanic rocks and soils, and can be
concentrated by hydrothermal processes associated with volcanism. Weathering and erosion
processes can liberate the soluble forms of selenium which can be readily transported by
runoff. Mining of the epithermal veins to recover precious metals may have produced higher
concentrations of selenium by increasing the surface area of the source rock that is exposed to
weathering (Frost and Box 2009).
Background selenium concentrations appear to have low to no risk to aquatic life (Frost and
Box 2009). Bioaccumulation of selenium appears to be occurring through the food chain,
suggesting a slight elevated risk of toxicity to aquatic life based on Environmental Protection
Agency (EPA) guidelines (EPA 2004, Rhea et al. 2008).
Anadromous and fluvial fish populations may be at lower risk of selenium bioaccumulation,
while resident fish populations may be at a higher risk for selenium bioaccumulation. This
difference in risk is due to the length of time (period) and life stage(s) they utilize the watershed
which directly influences the fish’s rate of selenium bioaccumulation.
There remains a potential risk of chemical contamination from past and present mining
activities (i.e., selenium, mercury, cyanide, etc.). Past mining activities are known to have had
negative water quality impacts. For example, Rodeheffer (1935) reported “that creek (Jordan
Creek) is so badly polluted by several small mines along its course that no fish or fish foods are
found.” Pollution control efforts have been implemented at the Grouse Creek Mine which is
being reclaimed to control discharge of cyanide from leaking tailings ponds into Jordan Creek,
and Preachers Cove ore processing site on the Yankee Fork near RM 7.3 has been reclaimed
(IDEQ 2003).
Reclamation commissioned CH2M Hill in 2011 to conduct a geochemical characterization study
of Pond Series 2 and 3 to evaluate the potential risk to aquatic and benthic resources and their
potential consumers under reasonably anticipated habitat rehabilitation activities. The
9
constituents of potential concern (COPCs) in the Yankee Fork are considered to be selenium
(Se), mercury (Hg), and methyl mercury (meHg).
In October 2011, CH2M HILL (Attachment G) collected surface water grab samples at 15
locations and sediment grab samples at 15 locations to use for evaluating current exposure and
environmental risks potentially associated with the proposed habitat improvement activities.
These data were sampled to provide the most accurate representation of current conditions at
Pond Series 2 and Pond Series 3 and to serve as the primary abiotic data set for evaluating the
activity risks to aquatic organisms and their potential consumers.
When considering the collective weight of evidence using multiple lines of analysis (benchmark
comparisons, background comparisons, findings from historical investigations, available
analytical data, and modeling), the following conclusions can be drawn regarding the exposure
pathways of concern under the current conditions at Pond Series 2 and Pond Series
(Attachment H):




Potential risk from dermal and incidental ingestion of surface water and sediment by human
receptors is negligible.
Potential risk from consumption of fish containing bioaccumulated selenium and mercury by
humans and wildlife is likely minimal. Modeling and historical fish tissue data indicate that
tissue levels under the most conservative assumptions (e.g., permanent residence of upper
trophic‐level predatory fish with ponds and/or pools) could be at or slightly above the screening
levels. These conditions are even less likely for anadromous fish. COPC concentrations in
sediment are below screening levels that are assumed to be protective of benthic
macroinvertebrates.
COPC concentrations in surface water are below screening levels that are assumed to be
protective of aquatic resources.
Selenium and mercury concentrations measured in Pond Series 2 and Pond Series 3 appears to
be generally consistent with background levels (i.e., those measured from areas of the Yankee
Fork basin not impacted by historical mining activities).
The CH2M Hill geochemical characterization (Attachment H) provides a conservative
(“worst‐case”) evaluation of the potential risks under the current conditions and land use at
Pond Series 2 and Pond Series 3. The greatest risk appears to be from the potential
bioaccumulation and biomagnification of selenium and mercury. Conditions that enhance the
transformation and accumulation of these constituents include low dissolved oxygen, high
organic carbon, and high sulfur concentrations. The proposed habitat improvement activities
are intended to increase connectivity between both pond series and the Yankee Fork
mainstem, thereby creating an increase of flow rates through the pond series, increase of
dissolved oxygen, and decrease fine sediment deposition. These expected future conditions are
anticipated to reduce the bioaccumulation potential for selenium and mercury, and
subsequently reduce the overall exposure and risk to human health and the environment (i.e.,
aquatic resources and wildlife).
10
Consideration of the proposed activities in the larger watershed
An analysis of watershed conditions was completed using NOAA Fisheries matrix of pathways
and indicators to identify potential systemic problems within the watershed and is summarized
in Section 7 (Watershed Condition) of the Yankee Fork Tributary Assessment. Further analysis
was completed to delineate and prioritize geomorphic reaches based on the potential to
improve reach-scale processes that address key limiting factors to protect and improve survival
of salmon and steelhead in Section 8 (Valley Segments and Geomorphic Reaches) of the Yankee
Fork Tributary Assessment and is summarized as follows. Geomorphic reaches in the Yankee
Fork are illustrated in Figure 1.
Valley segments and geomorphic reaches were delineated along the Yankee Fork mainstem in
the middle and lower Yankee Fork subwatersheds; and along lower Jordan Creek in the Jordan
Creek subwatershed:

In the middle Yankee Fork subwatershed, three geomorphic reaches were identified
(upstream to downstream): (1) Reach YF-6 from RM 16.5 to 13.3; (2) Reach YF-5 from
RM 13.3 to 11.7; and (3) Reach YF-4 from RM 11.7 to 9.1.

In the lower Yankee Fork subwatershed, three geomorphic reaches were identified: (1)
Reach YF-3 from RM 9.1 to 6.8; (2) Reach YF-2 from RM 6.8 to 3; and (3) Reach YF-1
from RM 3 to the Yankee Fork/Salmon River confluence.

Two geomorphic reaches were identified in the Jordan Creek subwatershed: (1) Reach
JC-2 from RM 4 to 1.4 and (2) Reach JC-1 from RM 1.4 to the Yankee Fork/Jordan Creek
confluence.
11
Figure 1. Yankee Fork Geomorphic Reaches Identified in the Yankee Fork Tributary Assessment
12
The Yankee Fork Tributary Assessment categorized the geomorphic reaches in order of their
potential to improve physical processes and habitat quantity and quality, along with identified
needs for further assessment. The categorization of reaches based on the potential to provide
the most significant opportunities for habitat improvement is described below:
1. Yankee Fork Reach YF-3: The physical and ecological processes have been significantly
impacted by dredging operations in this reach. Dredge piles artificially constrain the
Yankee Fork and West Fork channels, disconnect relatively large floodplain areas from
the Yankee Fork, and have changed the convergence between the Yankee Fork and
West Fork from a dynamic interaction that created a mosaic of habitat patches to a
static condition that no longer provides the complex habitat types. A more detailed
reach assessment is needed to evaluate current physical and ecologic processes, and to
evaluate the overall potential to improve these processes and their benefit and risks to
the resource.
2. Yankee Fork Reach YF-2: The Tribes have worked with the IDT to implement habitat
improvement activities in this reach. Alternatives should continue to be pursued to
reconnect isolated tributaries and improve channel/floodplain interactions. In addition,
the four dredge pond series have the potential to provide replacement of juvenile
rearing habitat that was lost when dredging obliterated the lower sections of some
tributaries. If flows were increased into these pond series, it would also reduce peak
flows in the Yankee Fork mainstem resulting in a reduction in sediment transport
capacity and lower flow velocities which would improve spawning gravel retention and
juvenile fish movement.
3. Jordan Creek Reach JC-1: A reach assessment is not necessary to address the localized
anthropogenic impacts in this reach. Modifications to localized channel constrictions
(i.e., mine tailing and road embankments) could be pursued on a case-by-case basis
dependent on landowner cooperation. Replanting riparian vegetation (i.e., 30 foot
buffer zone) to improve channel boundary roughness and ecologic connectivity could
also be considered. It is unlikely these actions would result in a reach-scale changes that
would significantly increase juvenile rearing habitat. Essentially, the in-stream bedforms
and structure and resulting habitat are within the range of variability that should be
expected for the channel type and physical characteristics, but the riparian vegetation
and hydraulic conditions at specific locations along the channel could be improved.
4. Yankee Fork Reach YF-4: Physical and ecological processes are negatively impacted
primarily from past timber harvests along the valley bottoms and margins. The riverine
system appears to be on a recovering trend as vegetation progresses through varying
successional stages, albeit at a slower rate due to continued recreational and private
landowner usage. Maintaining and actively managing a riparian corridor (i.e., about 100
foot buffer zone) along both sides of the channel to insure proper species assemblage
and improve growth rates would be an appropriate approach for long-term
rehabilitation. Addressing localized constrictions along the channel (i.e., levee,
13
deflection berm and bridge crossings) and identifying potential locations for large wood
placements could be pursued on a case-by-case basis dependent on landowner
cooperation.
5. Yankee Fork Reach YF-6: Physical and ecological processes have been negatively
impacted primarily from past timber harvest along the valley bottoms and margins. The
riverine system appears to be on a recovering trend, as the vegetation progresses
through varying successional stages. Active management of these stands to insure
proper species assemblage and improve growth rates would be an appropriate
approach for long-term rehabilitation. Potential short-term rehabilitation approaches
to increase availability of wood to the system could be pursued on a case-by-case basis
which includes: (1) ensuring that wood and sediment inputs from tributaries are not
impeded by obstructions (i.e., undersized culverts), and (2) wood placement along the
channel and floodplain if the anticipated ecologic benefits outweigh the disturbances to
the channel or floodplain.
6. Jordan Creek Reach JC-2: A reach assessment is not necessary to address the localized
anthropogenic impacts in this confined reach. Specific alternatives could be pursued on
a case-by-case basis to address the localized anthropogenic disturbances that constrict
the channel and/or affect channel boundary roughness and ecological connectivity.
Essentially, the in-stream bedforms and structure and resulting habitat are within the
range of variability that should be expected for the channel type and physical
characteristics.
7. Yankee Fork Reaches YF-5 and YF-1: These geomorphic reaches are primarily Chinook
salmon and steelhead migratory corridors. In these reaches the river flows through Vshaped canyons that have bedrock-type channels with predominantly step-pool
bedforms. There are no anthropogenic features that significantly impact reach-scale
channel processes. Therefore, no further assessments are recommended for these
reaches.
Deficiency Area 2 – Land access and conservation easement
Within the lower Yankee Fork subwatershed, there are numerous stakeholders, two of which
are primary landowners: USFS and Simplot. There are several other smaller landowners also
within the area with relevant interest in work proposed and conducted in the area: mine claim
owners and private residences near the West Fork confluence, and the Dredge Camp
community. The two proposed activities currently in the design and permit phases are being
coordinated with the landowners (Simplot and USFS). The Sponsor, TU, is developing
conservation easement agreements with the landowners.
TU is working with Simplot as one of the two landowners within proposed activity areas to
secure agreements for a five-year access agreement and a twenty-year restoration easement.
14
The access agreement is anticipated to grant access to TU for all construction phases of the
proposed activities. Additionally, five years of access will be negotiated to allow TU to monitor
the implemented actions. The scope and extent of the access granted in this agreement,
including any limitations, will explicitly be stated in the access agreement.
The restoration agreement will define the responsibilities of TU and Simplot. The restoration
agreement will incorporate the design and objectives and spell out the implementation and
long-term monitoring and maintenance of the activity. Items that will be specifically addressed
include road and development setbacks, future mining operations, invasive species and noxious
weed management, recreation, and long-term restoration maintenance. The restoration
agreement also describes the legal remedies for violations of the agreement. The restoration
agreement includes the property’s legal description and property maps and can be recorded
with the county to be permanently associated with the deed.
Neither of these forms of agreement are permanent conservation easements and do not
function to limit development on the property in perpetuity. However, TU has previously used
restoration agreements of this sort, with a limited lifespan of twenty years, as this is generally
considered to be the standard life of restoration projects. Agreement templates are currently
being reviewed by Simplot’s attorneys and TU is working to draft specific language for the
agreements. The parties will meet in spring 2012 to finalize the agreements for the Pond Series
2 and Pond Series 3 activities proposed for implementation in the summer of 2012.
Deficiency Area 3 – Benefits analysis demonstrating the proposed
activities are favorable to fish and wildlife resources
Anticipated benefits to fish and wildlife resources from the proposed activities include the
following:





Filling the ponds to create more side-channel habitat has been shown to be desirable
for juvenile Chinook salmon. Water velocities will increase in the side channels
compared to pond areas resulting in increased dissolved oxygen and the transport of
fine sediment.
Improving the hydraulic conditions at the pond inlets will direct additional flow into the
side channels during the rising limb of the spring runoff hydrograph. Juvenile Chinook
salmon that are searching for high flow refuge should be attracted to the side channel
habitat.
Side channel habitat should have increased water flow with passable water velocities
during most of the year and flows through the side channels should be large and
frequent enough to flush fine sediment.
A downstream connection from the side channels to the Yankee Fork mainstem would
be maintained so that fish would not be stranded.
Creating high- and low-flow floodplain benches adjacent to the side channels and revegetating with appropriate riparian plants should develop into species and age-class
15


diversified communities. The resulting riparian and floodplain areas should increase
nutrient and large wood material recruitment and provide beneficial edge habitat and
refuge for juvenile Chinook salmon.
Habitat complexity components such as plantings, boulders, and large woody material
incorporated into the design along the side channel edges should increase cover and
provide shelter for rearing juveniles and holding adults.
The resulting side channel habitat would be allowed to evolve in response to physical
processes that create and maintain aquatic and riparian habitat that support improved
Chinook salmon productivity.
Changes in aquatic habitat suitability for velocity, depth, substrate, and cover are being
estimated by CH2M Hill (Attachment I) using quantitative geospatial analyses using the results
of two dimensional hydraulic modeling. The analyses combine juvenile Chinook salmon habitat
suitability criteria with site specific information obtained from model results and field data
collection. Fish and wildlife population response to the anticipated habitat changes have not
been estimated at this time. The Tribes continue to look for opportunities to verify activity
objectives and the respective monitoring and evaluation strategies by predicting the population
response.
16
Exhibits
Exhibit 1 Pond Series 3 Conceptual Restoration Plans Yankee Fork of Salmon River Draft 11/9/11
Exhibit 2 Pond Series 2 Conceptual Restoration Plans Yankee Fork of Salmon River Draft 11/9/11
Attachments
Attachment A Tribes 2008. Yankee Fork Floodplain Restoration Project Implementation Plan
2008-2024. Shoshone-Bannock Tribes, Fort Hall, Idaho, 24 p.
Attachment B ISRP 2008. Review of the Yankee Fork Floodplain Restoration Project
Implementation Plan 2008-2018. Independent Scientific Review Panel for the
Northwest Power and Conservation Council. Portland, Oregon. 15 pp.
Attachment C Reclamation 2012. Yankee Fork Tributary Assessment for the Upper Salmon
Subbasin, Custer County, Idaho. United States Department of Interior, Bureau of
Reclamation, Pacific Northwest Region, Boise, Idaho. February, 2012.
Attachment D CH2M Hill 2011a. Pond Series 2 Preliminary Basis of Design Draft Report. Boise,
Idaho.
Attachment E CH2M Hill 2011b. Pond Series 3 Preliminary Basis of Design Draft Report. Boise,
Idaho.
Attachment F USFS 2010. Yankee Fork of the Salmon River: 2010 Stream Survey Report. U.S.
Department of Agriculture, Salmon-Challis National Forest, Yankee Fork Ranger
District, Clayton, ID.
Attachment G CH2M Hill 2011c. Appendix F Geochemical Data Summary Draft Technical
Memorandum. Boise, Idaho.
Attachment H CH2M Hill 2011d. Appendix G. Geochemical Characterization Draft Technical
Memorandum. Boise, Idaho.
Attachment I CH2M Hill 2011e. Appendix D. Hydraulic and Habitat Suitability Analysis Draft
Technical Memorandum. Boise, Idaho.
References
EPA 2004. Draft aquatic life criteria for selenium – 2004. Environmental Protection Agency
EPA-822-D-04-001. Office of Water, Office of Science and Technology, Washington D.C.
Fisher, F. and K. Johnson. 1995. Geology and Mineral Resource Assessment of the Challis 1º X
2º Quadrangle. U.S. Geological Survey Professional Paper 1525.
17
Frost, Thomas P., and S.E. Box. 2009. Stream-sediment geochemistry in mining-impacted
drainages of the Yankee Fork of the Salmon River, Custer County Idaho. U.S. Geological Survey
Scientific Investigation Report 2009-5115.
IDEQ 2003. Upper Salmon River Subbasin Assessment and TMDL. Idaho Department of
Environmental Quality, Boise, Idaho, 217 p.
Gregory, J. and C. Wood. 2011. Evaluation of Juvenile Anadromous Fish Populations in Pond
Series 2 and 3 and Adjacent Areas in the Yankee Fork Drainage.
Maret, T.R., J.E. Hortness, and D.S. Ott. 2006. Instream Flow Characterization of Upper Salmon
River Basin Streams, Central Idaho. U.S. Geological Survey Scientific Investigations Report
2006-5230. 110p.
NOAA Fisheries 2010. Supplemental Consultation on Remand for Operation of the Federal
Columbia River Power System, 11 Bureau of Reclamation Projects in the Columbia Basin and
ESA Section 10(a)(1)(A) Permit for Juvenile Fish Transportation Program. NOAA National
Marine Fisheries Service. May 20, 2010, F/NWR/2010/0209.
NMFS 2011. Draft Recovery Plan for Idaho Snake River Spring/Summer Chinook and Steelhead
Populations. National Marine Fisheries Service. Boise, Idaho.
NWPC 2004. Salmon Subbasin Assessment and Management Plan. Northwest Power and
Conservation Council. Portland, Oregon.
Rhea, D.T., A.M. Farag, E. McConnell, and W.G. Brumbaugh. 2008. Mercury and selenium
concentrations in biofilm, macroinvertebrates, and fish collected in the Yankee Fork of the
Salmon River, Idaho. U.S. Geological Survey Final Report Agreement No. 01-IA-11041303-090.
Rodeheffer, I.A. 1935. A Survey of the Waters of the Challis National Forest, Idaho.
Department of Commerce, Bureau of Fisheries. Washington.
Tardy, K. 2009. Steelhead Streamside Incubation (SSI) Program. Annual Report. October 1,
2008 – September 30, 2009. Shoshone Bannock Tribes, Fort Hall, Idaho.
USFS Unpublished. United States Forest Service Fish Habitat Inventory 2001 Data.
18