20030181 Ver 7_Other Agency Comments_20100528 (3)

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United States Department of the Interior
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FISH AND WILDLIFE SERVICE
Asheville Field Office
M4gCH s ?e° 160 Zillicoa Street
Asheville, North Carolina 28801
May 28, 2010
Mr. John Dorney
North Carolina Division of Water Quality
2321 Crabtree Boulevard, Suite 250
Raleigh, NC 27604
t/
Subject: Public Notice of Application for a Section 401 Water Quality Certificate, and
Addendum No. 1, Addendum No.3, Mission Hydroelectric Project, FERC No. 2619,
DWQ #03-0180, Clay County, North Carolina
Dear Mr. Dorney:
This letter is in response to the May 4, 2010 Public Notice, DWQ #03-0180. On June 16, 2009,
Duke Energy Carolinas, LLC (Duke) filed an Application for 401 Water Quality Certificate to
the North Carolina Division of Water Quality (NCDWQ) for the Mission Project.
The United States Fish and Wildlife Service (USFWS), has been engaged in ongoing discussions
with Duke, NCDWQ, North Carolina Division of Water Resources (NCDWR) and the North
Carolina Wildlife Resources Commission (NCWRC) to prepare a Lake Level and Flow
Management Plan, a Maintenance and Emergency Protocol and a Sediment Study Plan to help
further define how the hydro project could operate under a Subsequent License from the FERC.
These discussions culminated in agreement about how the Project should be operated to protect
water quality, fish and wildlife resources, and endangered species habitats.
On May 26, 2010, Duke filed additional information to its 401 Application as Addendum #I
regarding the Mission Project Lake Level and Flow Management Plan along with the Nantahala
Area Run-of-River Projects Maintenance and Emergency Protocol (as an Appendix to the
Mission Project Lake Level and Flow Management Plan). On May 27, 2010, Duke also filed
additional information to its 401 Application as Addendum #3 regarding its Sediment Study
Plan.
RECOMMENDATIONS
We recommend these measures to compensate for the ongoing impacts of this project and its
operation on the natural resources of the area. These measures should include mitigation for
ongoing project impacts and project-induced effects on fish and wildlife populations and their
habitats.
USFWS comments
Mission Hydroelectric Project
Run-of-river Operation. The Project should be operated in a run-of-river mode, with outflow
(discharge) equivelant to inflow. The Lake Level and Flow Management Plan (May 2010), the
Maintenance and Emergency Protocol (May 2010), the Trash Removal Program (July 2003)
should be incorporated incorporated in their entirety in the 401 certification for each of the 3
ROR projects.
Shoreline Management. Consistent with the Tuckasegee Settlement Agreement and Nantahala
Stakeholders Settlement Agreements, we agree that the Bryson project is too small to have
private boat ramps, docks, or piers. And, according to Duke Power's Nantahala Area Shoreline
Management Guidelines, filed with FERC, private boat ramps are not allowed. Therefore, we
recommend that to protect and improve the water quality of the Project, private shoreline
developments should be excluded from the Project waters. A vegetated riparian area should be
maintained (and restored wherever currently degraded) at the Project. Appropriate public access
areas should be developed and maintained consistent with the Tuckasegee Settlement Agreement
and Nantahala Stakeholders Settlement Agreements.
Sediment Management. Downstream habitats are being negatively impacted by sediment
releases (pulses) from the Project and Duke should develop a long-term Sediment Management
Plan to describe its strategy and implementation of a reservoir-wide sediment monitoring and
management. Duke should develop a Long-Term Sediment Management Plan, based upon
results of the Sediment Removal Pilot Study, to guide future sediment removal operations at the
Nantahala Area ROR Projects. The Long-Term Sediment Management Plan should include a
maintenance drawdown and refill protocol that minimizes flow fluctuations and reservoir
sediment mobilization by addressing rates of draw down and refill (to coincide with precipitation
events and rising hydrograph) and scheduling drawdowns to coincide with season of least
potential for harm to downstream aquatic communities, whenever possible.
The Long-term Sediment Management Plan should include the following elements at a
minimum:
1. Sediment Assessment
2. Evaluation of Sediment Management Options for a) Project Operations and b) for
protection of downstream habitats
3. Monitoring/Notification/Reporting
4. Schedule for implementation
We recommend permit conditions that are consistent with the proposed pilot Sediment Study
Plan and Short-term Sediment Monitoring Study proposed in Addendum #3 by Duke, as well as
that described in the License Application for this Project.
Fish Passage. The USFWS has reserved authority under §18 of the Federal Power Act to
prescribe fishways at the Project. We recommend the water quality certificate include similar
provisions to incorporate any future Fishway prescriptions, in order to maintain or restore the
biological integrity of the Project waters. In particular, we are concerned about the needs of
potamodromous fishes, including the "sicklefin" redhorse (Moxostoma sp.) Hydropower
projects such as the subject run-of-river projects can fragment a river system, impede or block
USFWS comments
Mission Hydroelectric Project
fish movement, and kill or injure fish. The viability and mobility of fish species that would
otherwise move to and from different habitats within the river system may diminish
substantially, if not completely, due to a hydropower project. These species can be important
components of aquatic food webs and can support populations of commercially and
recreationally important fish that are of economic significance to the nation.
Fishways help mitigate the impacts of hydropower projects by providing safe, timely, and
effective fish passage around a project for spawning, rearing, feeding, growth to maturity,
dispersion, migration, and seasonal use of habitat. Fishway prescriptions also help to achieve
resource goals and objectives. These goals and objectives may be identified in national,
regional, or watershed-level planning documents or may be established by the Services on a site-
specific basis. Examples of resource goals and objectives include: (1) the enhancement,
protection, or restoration of existing fish populations within a river system; (2) the reunification
of fragmented fish populations; and (3) the reintroduction or reestablishment of fish runs. In
addition, fishways may be necessary to protect tribal resources for the exercise of American
Indian rights.
Sicklefin Redhorse. The Sicklefin redhorse is currently confined to the Hiwassee and Little
Tennessee rivers of the upper Tennessee River basin. Both populations are confined within
reaches enclosed by water impoundments. The population in the Little Tennessee system is
enclosed downstream by Fontana Dam and upstream by Franklin, Bryson, and Cullowhee dams.
Due to the limited geographic distribution and threats associated with physical alteration of the
habitat, restoration and reintroduction efforts for this undescribed species are critical to its long-
term existence.
The species is currently known to occupy cool to warm, moderate gradient creeks and rivers,
and, during at least parts of its early life, large reservoirs (Jenkins 1999). In streams, it is
generally associated with moderate to fast currents, in riffles, runs, and well-flowing pools and
feeds and spawns over gravel, cobble, boulder, and bedrock substrates with no, or very little, silt
overlay (Jenkins 1999, Favrot 2008).
Like many other redhorse species, the Sicklefin Redhorse is known mainly from flowing
streams. Current observations indicate that adults are year-round residents of rivers and large
creeks (Jenkins personal communication 2007; Favrot 2008) and that young, juveniles, and sub-
adults occupy primarily the lower reaches of creeks and rivers and near-shore portions of certain
reservoirs (Jenkins 1999). It is likely that after emerging from the stream substrata, many of the
larvae and post-larvae are carried downstream to the mouths of streams or into reservoirs
(Jenkins 1999). Newly mature fish (?5 years of age) appear to migrate from the reservoirs to
spawn; after which, most remain in the streams with the other adults (Jenkins 1999). Although, a
few adult Sicklefin Redhorse have been observed in the Hiwassee and Fontana Reservoirs,
Favrot (2008) reported in his study of Sicklefin Redhorse movement and habitat utilization
within the Hiwassee River system that he was unable to detect radio-tagged adult Sicklefin
Redhorse utilizing Hiwassee Reservoir for other than brief periods between occupying a
spawning tributary and the Hiwassee River or Valley River, suggesting these fish were only
migrating between streams. This suggests that, while reservoirs may serve as maturation sites
USFWS comments
Mission Hydroelectric Project
for sub-adult Sicklefin Redhorse, they do not provide suitable spawning, foraging, or winter
habitat for adults of the species but rather are a factor limiting habitat for adult Sicklefin
Redhorse.
Stomach analysis indicates that the Sicklefin Redhorse feeds on benthic macro invertebrates
(insect larvae, crustaceans, snails, etc.) (Jenkins, personal communication 2004). The species
has rarely been observed foraging on substrates with even a thin covering of silt (Jenkins 1999).
When feeding, the species exhibits a well-defined preference for the coarse substrates with
abundant riverweed (Podostemum ceratophyllum). Studies indicate that riverweed significantly
enhances the abundance of benthic macroinvertebrates and that after spawning, the species
typically relocates to stream reaches supporting high densities of river weed, where individuals
appear to feed almost exclusively over riverweed beds (Favrot 2008).
Sicklefin redhorse spawning typically occurs over cobble, with usually only a small portion of
sand and gravel, in moderate to fast flowing water in open areas and pockets formed by boulders
and outcrops (Jenkins 1999, Favrot 2008). Unlike the Sicklefin Redhorses' foraging habitat, the
species' appears to spawn exclusively over coarse substrates lacking riverweed (Favrot 2008).
Favrot's study (2008) indicates the species begins upstream migration to spawning sites in late
winter/early spring when water temperatures reach 10.0-12.0 degrees Celsius and peak at water
temperatures of 15.0-16.0 °C. The species appears to exhibit strong spawning site fidelity,
returning to the same stream and stream reach each year to spawn (Favrot 2008), possibly
returning to their natal streams and spawning reaches similar to many salmonids (Favrot 2008).
Following spawning, the species appears to generally move downstream to deeper waters and
more suitable foraging areas (Favrot 2008); and, to migrate further downstream to even deeper
waters for the winter (Favrot 2008). Except during its migrations to and from spawning and
wintering sites, the Sicklefin Redhorse appears relatively sedentary at its spawning, post-
spawning, and wintering sites, travelling only short distances up and down stream within the
occupied river reach; and, in addition to exhibiting strong spawning site fidelity, the Sicklefin
Redhorse also appears to show a high degree of site fidelity to its post-spawning and wintering
sites, returning to the same stream, and generally the stream reaches each year (Favrot 2008).
Assuring the long-term survival of the Sicklefin Redhorse will require, at a minimum: (1)
protecting the existing water and habitat quality of the reaches of the river systems were the
species is still surviving; and (2) improving degraded portions of the species' habitat to allow for
the expansion of existing populations and reestablishment of the extirpated populations.
The Sicklefin Redhorse has been observed feeding and spawning only in substrates with no or
very little silt accumulation. Excessive siltation and suspended sediment affects the habitat of
the Sicklefin Redhorse by making it unsuitable for feeding and reproduction. It eliminates
breeding sites and results in increased mortality of eggs and juveniles; it eliminates feeding
areas, reduces the species' ability to detect prey, and eliminates aquatic insect larvae and other
food items of the Sicklefin. Suspended sediment also irritates and clogs fishes' gills affecting
their respiration (Waters 1995, Sutherland and Meyer 2007). Favrot (2008) reported that fine
sediments are abundant in the section of the Hiwassee River between Mission Dam and
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USFWS comments
Mission Hydroelectric Project
Hiwassee Reservoir and that Brasstown Creek appears to be a significant contributor to this
sediment loading.
CONCLUSION
We appreciate the opportunity to provide these comments and information about water quality at
the Mission Hydroelectric Project. If you have questions, please contact me at 828/258-3939,
Ext. 227.
Sincerely,
- original signed -
Mark A. Cantrell
Fish & Wildlife Biologist
cc via email: Duke Energy Carolinas, LLC, Lineberger, Johnson
NCWRC, Goudreau
NCDWR, Mead
NCDWQ, Barnett