Copper Salmon Wilderness Legacy Roads Project

Aquatic Biota Biological Evaluation/Assessment & Specialist Report

COPPER SALMON WILDERNESS LEGACY ROADS PROJECT

Prepared for the Environmental Assessment

Rogue River-Siskiyou National Forest Powers Ranger District 42861 Hwy 242 Powers, Oregon 97366

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 1 of 29 I. TITLE PAGE

Project Name: Copper Salmon Legacy Roads

Project Location:

4th Field HUC Sixes 17100306

Coquille 17100305

5th Field HUC Sixes River 1710030602 Elk River 1710030603 South Fork Coquille 1710030502

6th Field HUC Upper Sixes River 171003060201 Upper Elk River 171003060301 Salmon Creek 171003050202

Watershed Analyses (WA): Sixes River (USFS 1997) and Elk River (USFS 1998)

Land Allocation of Project Area: Wilderness

Administrative Unit: Rogue River-Siskiyou National Forest (RRSNF): Powers Ranger District

Prepared By: Karla Cottom, Fisheries Biologist, Powers Ranger District, RRSNF

Reviewed By: Steve Brazier, Assistant Forest Fisheries Biologist, RRSNF Susan Maiyo, Forest Fisheries Biologist, RRSNF

Document Date: August 29, 2012 Revised January 2, 2013

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 2 of 29 II. EXECUTIVE SUMMARY

Biological Evaluation Background Information This report discusses the fisheries and aquatic dependent species of concern resources of the Copper Salmon Legacy Roads Project. The Biological Evaluation process (FSM 2672.43) is intended to conduct and document activities necessary to ensure Proposed Actions will not likely jeopardize the continued existence or cause adverse modification of habitat for:

A. Fish species listed or proposed to be listed as Endangered (E) or Threatened (T) or Proposed for Federal listing (P) by the National Marine Fisheries Service. B. Aquatic species listed as Sensitive (S) by USDA, Forest Service.

Threatened, Endangered, and Sensitive Fish Species (TES) In compliance with Section 7 of the Endangered Species Act (ESA) and the Forest Service Biological Evaluation process for TES aquatic species, the list of species potentially occurring within the project area was reviewed. Lists for the Rogue River-Siskiyou National Forest (RRSNF) and the Pacific Northwest Region (R-6) were reviewed in regard to potential effects on any of these species, critical and essential fish habitat by actions associated with the Copper Salmon Legacy Road Project. Pre- field and reconnaissance results are summarized in the table below and displayed on Map 1.

Table 1. Potentially Affected Aquatic Species, Status, and Habitats Assessed (Pacific Northwest Regional Forester’s Sensitive Species List updated August, 2011) Species/Habitat Pre-field Review Field Surveys Existing Sighting or Habitat or Species Common name Scientific Name Potential Habitat Confirmed (Yes*/No**) (Yes*/No**) Threatened Species Oncorhynchus SONCC Coho salmon Yes Yes kisutch OC Coho Salmon O. kisutch No No S. DPS North American Acipenser medirostris No No green sturgeon Thaleichthys S. DPS Pacific eulachon No No pacificus Critical Habitat SONCC Coho salmon O. kisutch Yes Yes OC coho salmon O. kisutch No No Essential Fish Habitat Coho salmon O. kisutch Yes Yes Chinook Salmon O. tshawytscha Yes Yes Sensitive Species SONCC Chinook salmon O. tshawytscha No No PC chum salmon O. keta No No OC steelhead O. mykiss No No *Yes – The proposed project’s potential effects on these species will be further analyzed in this document. **No – No further analysis is necessary, and a determination of “No Impact” is rendered.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 3 of 29 Other Sensitive Species shown on the Regional Forester’s list as potentially found on the Rogue River- Siskiyou National Forest were addressed in the Wildlife Biological Evaluation including the Aquatic Mollusks.

This project fits under the aquatic restoration program activity categories described in the Endangered Species Act Section 7 Formal Programmatic Consultation and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for Fish Habitat Restoration Activities in Oregon and Washington, CY2007-CY2012 Biological Opinion (2007 ARBO) for categories #5. Fish Passage Culvert and Bridge Projects; #17. Road Treatments; and #18.Removal of Legacy Structures. The following Project Design Criteria (PDC) as listed in the 2007 ARBO and stated later in the document after the alternative descriptions will meet the intent of the 2007 ARBO and the more stringent bridge project design criteria (PDCs) in the upcoming 2013 ARBO II, which will replace the 2008 version and our required consultation with NMFS for this project.

III. DESCRIPTION OF THE PROPOSED ACTION(S) AND ACTION AREA WITH PROJECT DESIGN CRITERIA (PDC)

A. Proposed Actions and Discussion of Alternatives

The Powers Ranger District of the Rogue-River Siskiyou National Forest proposes decommissioning and recontouring up to 16 miles of previously closed roads, removal of legacy structures below the Blackberry Creek fish barrier culvert and replacement of the Blackberry Creek culvert with a bridge, 12 miles east of Port Orford, Curry County, Oregon. The project would also move up to 5,000 cubic yards of gravel about 800 feet to a location outside of the Wilderness. Funding for the decommissioning and recontouring is primarily through the Legacy Roads and Trails Remediation Initiative. Funding for the Blackberry culvert removal is unknown at this time. Implementation is proposed to begin in 2013.

The proposed activities under the Legacy Roads Project are separated into two Project Elements:

1. Road Decommissioning/Treatments 2. Culvert Replacement with a Bridge and Legacy Structure Removal

Proposed activities include: 1. Road Decommissioning/Treatments - clearing vegetation to allow road access, excavation, recontouring of slopes, revegetating disturbed areas, culvert removal, channel stabilization, erosion control measures, legacy structure removal; and 2) Culvert Replacement with a Bridge and Legacy Structure Removal

There are four alternatives in the Copper Salmon Legacy Roads EA. Table 2 is a comparison of Alternatives by units of measured project activities.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 4 of 29 Table 2. Comparison of Alternatives by Activity ALTERNATIVES

1 2 3 4

Unit of (No (Proposed (Reduced (Reduced Activity Measure Action) Action) Road Work) Road Work) Project Element 1. Road Decommissioning/Treatments Roads decommissioned miles 0 15.3 9.8 3.9 Stream crossings each removed 0 6 6 2 Cross drains removed each 0 70 51 26 Project Element 2. Culvert Replacement with a Bridge/Legacy Structure Removal Removal of Culvert/Bridge Construction each 0 1 1 1 Removal of Legacy Wood Structure each 0 1 1 1

No Action Alternative 1 (No Action)

Under the No Action alternative, no roads would be decommissioned, Blackberry Creek culvert would not be replaced with a bridge and the structures below the culvert would not be removed. Because these activities would not occur, this alternative would not fulfill the purpose and need for action.

Alternative 2 (Proposed Action)

The Rogue River-Siskiyou National Forest and Powers Ranger District propose decommissioning and recontouring up to 16 miles of roads originally closed between 1996 and 1999, replacing the Blackberry Creek culvert with a bridge and removal of legacy structures within the Copper Salmon Wilderness, 12 miles east of Port Orford, Curry County, Oregon. The project would also move up to 5,000 cubic yards of gravel about 800 feet to a location outside of the Wilderness.

Alternative 2 would focus on removing roads, restoring wilderness characteristics, and removing non- conforming structures.

1. Road Decommissioning/Treatments Decommission all roads identified within the wilderness (14 roads, 15.3 miles). Full recontouring of the first 300 feet of all roads (when needed to deter OHV use). Up to 90 percent slope recontouring of all roads beyond the first 300 feet. Remove all culverts, cross drains, and non-conforming structures (70 cross drains). All stream crossings would be fully restored to establish the original stream channel (with banks restored to the above and below natural banks angle) (6 crossings).

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 5 of 29 inappropriate for the given stream type. Removal of legacy structures would include the use of excavator-type machinery, spyders, backhoes, and dump trucks.

Alternative 3

Alternative 3 would focus on removing roads at high risk of delivering sediment to streams, and minimizing vegetation removal.

1. Road Decommissioning/Treatments Decommission roads and cross-drains with a high risk of sediment delivery to streams (5 roads, 9.8 miles). High risk includes most stream crossings and mid-slope cross drains. Full slope recontouring of the first 300 feet of 11 roads (when needed to deter OHV use). No recontouring of roads beyond the first 300 feet. Remove culverts, cross drains, and non-conforming structures (51 cross drains) at high risk of sediment delivery. All stream crossings would be fully restored to establish the original stream channel (with banks restored to the above and below natural banks angle) (6 crossings).

2. Culvert Replacement with a Bridge and Legacy Structure Removal Blackberry Creek - remove the culvert and replace it with a bridge along with removing large wood, boulders, rock gabions, and other in-channel structures that were constructed to improve fish habitat but were installed in a manner that was, and continues to be, inappropriate for the given stream type. Removal of legacy structures would include the use of excavator-type machinery, spyders, backhoes, and dump trucks.

Alternative 4

Alternative 4 would focus on preventing the spread of Phytophthora lateralis (PL) by only decommissioning roads outside of areas with measurably contributing Port-Orford-cedar (POC) and outside of P. lateralis infested areas.

1. Road Decommissioning/Treatments Ground disturbance would not occur in areas with POC/PL, as described above. Roads outside of POC/PL areas would be decommissioned (4 roads, 3.9 miles). Full slope recontouring of the first 300 feet of 8 roads where the first 300 feet of the road is outside of POC/PL areas (when needed to deter OHV use). No recontouring of roads beyond the first 300 feet. Remove culverts, cross drains, and non-conforming structures (26 structures) outside of POC/PL areas. Stream crossings would be fully restored to establish the original stream channel (with banks restored to the above and below natural banks angle) (2 crossings) outside of POC/PL areas.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 6 of 29 inappropriate for the given stream type. Removal of legacy structures would include the use of excavator-type machinery, spyders, backhoes, and dump trucks.

Project Design Criteria (PDC)

Taken from Endangered Species Act Section 7 Formal Programmatic Consultation and Magnuson- Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for Fish Habitat Restoration Activities in Oregon and Washington, CY2007-CY2012 Biological Opinion (2007 ARBO). These Design Criteria are only needed when working directly in areas that are designated Coho Critical Habitat (CCH) or effecting CCH (which in this case would be any activity 1000 feet upstream of the designated habitat or within riparian areas adjacent CCH See Map 1, page 29).

General Practices and Requirements for Each Activity under ARBO

Technical Skill and Planning Requirements

Ensure that an experienced professional fisheries biologist, hydrologist or technician is involved in the design of all projects covered by ARBO. The experience should be commensurate with technical requirements of a project. If ESA-listed wildlife or plant species occur in the planning area, as determined by a unit wildlife biologist or botanist, the appropriate specialist will assist with project design.

1. Planning and design include field evaluations and site-specific surveys, which may include a reference reach evaluation that describes the appropriate geomorphic context in which to implement the project. Planning and design involve appropriate expertise from professional staff or experienced technicians (e.g. engineer, silviculturist, and fire and fuels specialists.) 2. The project biologist shall ensure that design criteria and conservation measures are incorporated into any implementation contract agreements. If a biologist is not the contracting officer representative (COR), then the biologist must regularly coordinate with the project COR to ensure the design criteria and conservation measures are being followed.

State and Federal Requirements

1. Follow the appropriate state (ODFW) guidelines for timing of in-water work. Exceptions to ODFW in-water work windows must be requested and granted from the appropriate state agency. Exceptions can be approved through documented phone conversations or email messages with the state agencies. Such guidelines have been developed to prevent project implementation in fish spawning habitat when spawning is taking place or while eggs and alevins are in gravel. ODFW timing for Elk River is July 15-Sept 30th. 2. Project actions will follow all provisions and requirements (including permits) of the Clean Water Act for maintenance of water quality standards as described by Oregon Department of Environmental Quality (Oregon FS and BLM), Washington Department of Ecology (Washington FS and BLM) and the memorandum of understanding between WDFW and the USFS regarding Hydraulic Projects Conducted by USDA Forest Service, Pacific Northwest Region, January 2005. 3. All regulatory permits and official project authorizations will be secured prior to project implementation.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 7 of 29 Pollution and Erosion Control Plans (PECP)

Develop and implement a PECP for each authorized project. The PECP will include methods and measures to minimize erosion and sedimentation associated with the project. The following measures will assist in the creation of a PECP:

1. Spill Prevention Control and Containment Plan (SPCCP) – The contractor will be required to have a written SPCCP, which describes measures to prevent or reduce impacts from potential spills (fuel, hydraulic fluid, etc.). The SPCCP shall contain a description of the hazardous materials that will be used, including inventory, storage, handling procedures; a description of quick response containment supplies that will be available on the site (e.g., a silt fence, straw bales, and an oil-absorbing, floating boom whenever surface water is present). 2. The PECP shall be included in construction contracts or force account work plans. 3. The PECP must be commensurate with the scale of the project and include the pertinent elements listed below.

a. Minimize Site Preparation Impacts i. Establish staging areas (used for construction equipment storage, vehicle storage, fueling, servicing, hazardous material storage, etc.) beyond the 100-year floodplain in a location and manner that will preclude erosion into or contamination of the stream or floodplain. ii. Minimize clearing and grubbing activities when preparing staging, project, and or stockpile areas. Stockpile large wood, trees, vegetation, sand, topsoil and other excavated material, that is removed when establishing area(s) for site restoration. iii. Materials used for implementation of aquatic restoration categories (e.g. large wood, boulders, fencing material etc.) may be staged within the 100-year floodplain. iv. Prior to construction, flag critical riparian vegetation areas, wetlands, and other sensitive sites to prevent ground disturbance in these areas. v. Place sediment barriers prior to construction around sites where significant levels of erosion may enter the stream directly or through road ditches. Maintain barriers throughout construction. vi. Where appropriate, include hazard tree removal (amount and type) in project design. Fell hazard trees within riparian areas when they pose a safety risk. If possible, fell trees towards the stream. Keep felled trees on site when needed to meet coarse woody debris objectives.

b. Minimize Heavy Equipment Impacts i. The size and capability of heavy equipment will be commensurate with the project. ii. All equipment used for instream work shall be cleaned and leaks repaired prior to entering the project area. Remove external oil and grease, along with dirt and mud prior to construction. Thereafter, inspect equipment daily for leaks or accumulations of grease, and fix any identified problems before entering streams or areas that drain directly to streams or wetlands. iii. All equipment shall be cleaned of all dirt and weeds before entering the project area to prevent the spread of noxious weeds. iv. Equipment used for instream or riparian work shall be fueled and serviced in an established staging area outside of riparian zone. When not in use, vehicles shall be stored in the staging area.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 8 of 29 v. Minimize the number and length of stream crossings and access routes through riparian areas. Crossings and access routes should be at right angles. Stream crossings shall not increase risks of channel re-routing at low and high water conditions and shall avoid potential listed fish spawning areas when possible. vi. Existing roadways or travel paths will be used whenever reasonable. Minimize the number of new access paths to minimize impacts to riparian vegetation and functions. vii. Project operations must cease under high flow conditions that inundate the project area, except for efforts to avoid or minimize resource damage. viii. Minimize time in which heavy equipment is in stream channels, riparian areas, and wetlands. Operate heavy equipment in streams only when project specialists believe that such actions are the only reasonable alternative for implementation, or would result in less sediment in the stream channel or damage (short- or long-term) to the overall aquatic and riparian ecosystem relative to other alternatives.

c. Site Restoration i. Upon project completion, remove project related waste. ii. Initiate rehabilitation of all disturbed areas in a manner that results in similar or better than pre-work conditions through spreading of stockpiled materials, seeding, and/or planting with local native seed mixes or plants. Planting shall be completed no later than spring planting season of the year following construction. iii. Short-term stabilization measures may include the use of non-native sterile seed mix (when native seeds are not available); weed-free certified straw, jute matting, and other similar techniques. Short-term stabilization measures will be maintained until permanent erosion control measures are effective. Stabilization measures will be instigated within three days of construction completion. iv. All riparian plantings shall follow Forest Service direction described in the Regional letter to Units, Use of Native and Nonnative Plants on National Forests and Grasslands May 2006 (Final Draft). v. When necessary, loosen compacted areas, such as access roads, stream crossings, staging, and stockpile areas.

Replace Culvert with Bridge Description The project proposes to remove a culvert and replace the existing road-stream crossing structure with a bridge. The current culvert restricts fish passage and natural flows. The new structure would be designed as a stream simulation structure that would restore up- and downstream fish passage for all life stages of native fish. Construction could involve use of heavy equipment, such as excavators, cranes, backhoes, front-end loaders, dump trucks, and bull dozers.

Design Criteria 2007 ARBO I 1. Fish passage projects will be designed by an experienced engineer with design input from an experienced fish biologist and hydrologist. Such personnel shall oversee or review the project during construction to ensure that project designs and conservation measures are being properly implemented. 2. Forest Service Design Assistance Teams or the BLM and Coquille Tribe equivalent will provide design review for project if it exceeds $100,000 or will result in structures that are greater than 20 feet wide.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 9 of 29 3. The site must be reviewed for the potential to head-cut below the natural stream gradient. If the project leads to head-cutting below the natural stream gradient it is to be excluded from this project and consultation with NOAA will be required. 4. Design Standards a. Structure Type – Structure types include closed-bottomed culverts, open-bottomed arch culverts, and bridges. Structure material must be concrete or metal. b. Structure Width – The structure width shall never be less than the bankfull channel width. (The stream width inside the culvert or between bridge footings shall be equal to or greater than the bankfull width.) The minimum structure width and height for a closed bottom culvert shall be 6 feet to allow manual placement of stream simulation material. Structures must accommodate a 100-year flood flow while maintaining sediment continuity (similar particle size distribution) within the culvert as compared to the upstream and downstream reaches. To meet this requirement, unconfined channel types (Rosgen C, E, and B channel types (Rosgen 1996)) may require structures wider than bankfull and/or the addition of flood relief culverts or other comparable flood relief methods. c. When possible, flood relief culverts will be designed to restore and maintain access to off- channel rearing and high flow areas for juvenile and adult fish. Therefore, existing floodplain channels should be the first priority for location of flood relief culverts which should be installed in a manner that matches floodplain gradient and does not lead to scour at the outlet. d. Channel Slope – The structure slope shall approximate the average channel gradient of the natural stream up- and downstream of the structure. The maximum slope for closed- bottomed culverts shall not exceed 6% because of difficulties in retaining substrate in the culvert at higher gradients. Open-bottom arches can be placed in channel gradients that exceed 6%. e. Embedded Culvert – If a closed culvert is used, the bottom of the culvert shall be buried into the streambed not less than 20% and not more than 50% of the culvert height. For open-bottomed arches and bridges, the footings or foundation shall be designed to be stable at the largest anticipated scour depth. Substrate and habitat patterns within the culvert should mimic stream patterns that naturally occur above and below the culvert. Coarser material may be incorporated to create velocity breaks during high flows, thereby improving fish passage, and to provide substrate stability. f. Riprap – The use of riprap is permissible above bankfull height to protect the inlet or outlet of new culverts or open-bottomed arches. If the use of riprap is required for culvert stability, then an additional analysis may be required to ensure that the structure is not undersized. Riprap may only be placed below bankfull height when necessary for protection of abutments and pilings for bridges. However, the amount and placement of riprap around the abutments and/or pilings should not constrict the bankfull flow. g. Grade Control Structures – Grade control structures are permitted to prevent head-cutting above or below the culvert or bridge. Grade control typically consists of boulder structures that are keyed into the banks, span the channel, and are buried in the substrate. h. Where applicable, incorporate road dips into crossing designs, to ensure catastrophic flood events will transport overflow back into the downstream channel instead of the road bed. i. Structures containing concrete must be sufficiently cured or dried before they come into contact with stream flow. j. In cases of structure removal or when removing an existing structure and replacing it with a bridge, consideration should be given to restoring the stream channel and reconnecting the floodplain at the site.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 10 of 29 k. When removing woody debris from the road-crossing inlet, place the debris downstream of the road crossing. l. Monitor structures after high flow events, which occur during the first fall/winter/spring after project completion. Assess the following parameters: head-cutting below natural stream gradient, substrate embeddedness in the culvert, scour at the culvert outlet, and erosion from sites associated with project construction. Apply remedial actions (using project design criteria and conservation measures) if projects do not meet the intended goals. m. If other aquatic restoration activities are used as complementary actions, follow the associated design criteria and conservation measures.

Conservation Measures Along with the general conservation measures summarized at the end of this section, the following conservation measures will be used to minimize sediment and turbidity and the effects of fish handling/transport:

Isolate construction area and remove fish from project area. Fish shall be removed from project area (see fish capture guidelines below). 1. Dewater Construction Site – Upstream of the isolated construction area, coffer dams (diversions) constructed with non-erosive materials are typically used to divert stream flow with pumps or a by-pass culvert. Diversions constructed with material mined from the streambed or floodplain is not permitted. Pumps must have fish screens and be operated in accordance with NMFS fish screen criteria. Dissipate flow energy at the bypass outflow to prevent damage to riparian vegetation or stream channel. If diversion allows for downstream fish passage, (i.e., is not screened), place diversion outlet in a location to promote safe reentry of fish into the stream channel, preferably into pool habitat with cover. When necessary, pump seepage water from the dewatered work area to a temporary storage and treatment site or into upland areas and allow water to filter through vegetation prior to reentering the stream channel. 2. Stream Re-Watering – Upon project completion, slowly re-water the construction site to prevent loss of surface water downstream as the construction site streambed absorbs water and to prevent a sudden increase in stream turbidity. Monitor downstream during re-watering to prevent stranding of aquatic organisms below the construction site 3. Fish Handling – If capture, removal, and relocation of fish are required, follow these steps:

a. All fish capture, removal, and handling activities shall be conducted by an experienced fisheries biologist or technician. b. Isolate capture area – Install block nets at upstream and downstream locations and leave in a secured position to preclude fish from entering the project area. Leave nets secured to the stream channel bed and banks until fish capture and transport activities are complete. If block nets or traps remain in place more than one day, monitor the nets and or traps at least on a daily basis to ensure they are secured to the banks and free of organic accumulation and to minimize fish predation in the trap. c. Fish Capture Options 1) Collect fish by hand or dip nets, as the area is slowly dewatered. 2) Seining – Use seine with mesh of such a size to ensure capture of the residing ESA- listed fish. 3) Minnow traps – Traps will be left in place overnight and in conjunction with seining 4) Electro fishing – Prior to dewatering, use electro fishing only where other means of fish capture may not be feasible or effective. The protocol for electro fishing includes the following: Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 11 of 29 i. If fish are observed spawning during the in-water work period, electro fishing shall not be conducted in the vicinity of spawning adult fish or active redds. ii. Only Direct Current (DC) or Pulsed Direct Current (PDC) shall be used. iii. Conductivity <100 use voltage ranges from 900 to 1100. Conductivity from 100 to 300 then use voltage ranges from 500 to 800. Conductivity greater than 300 then uses voltage to 400. iv. Begin electro fishing with minimum pulse width and recommended voltage and then gradually increase to the point where fish are immobilized and captured. Turn off current once fish are immobilized. Do not allow fish to come into contact with anode. Do not electro fish an area for an extended period of time. Remove fish immediately from water and handle as described below. Dark bands on the fish indicate injury, suggesting a reduction in voltage and pulse width and longer recovery time. 5. Handling and Release –Fish must be handled with extreme care and kept in water for the maximum extent possible during transfer procedures. A healthy environment for the stressed fish shall be provided—large buckets (five- gallon minimum to prevent overcrowding) and minimal handling of fish. Place larger fish in buckets separate from smaller prey-sized fish. Monitor water temperature in buckets and well-being of captured fish. As rapidly as possible (especially for temperature-sensitive bull trout), but after fish have recovered, release fish upstream of the isolated reach in a pool or other area that provides cover and flow refuge. Document all fish injuries or mortalities and include in annual report.

ARBOII 2013: The ARBOII will not be finalized until 2013, and therefore design criteria could differ from ARBO I criteria. The ARBO I calls for “structure width between bridge footings shall be equal to or greater than the bankfull width”, while the ARBO II could be more conservative and state that the “structure width shall be 1.5 times the bankfull width between the abutments.”

Excluded Activities The project does not include the use of treated wood in replacement bridges. When installing bridges, piers and abutments will not occur within the bankfull width.

Road Decommissioning – ARBO I 2007

1. For road removal projects within riparian areas, recontour the affected area to mimic natural floodplain contours and gradient to the greatest degree possible. 2. For those road segments immediately adjacent to the stream or where the road fill is near the wetted stream, consider using sediment control barriers between the project and the stream. 3. Drainage features should be spaced to hydrologically disconnect road surface runoff from stream channels. 4. Dispose of slide and waste material in stable sites out of the flood prone area. Waste material other than hardened surface material (asphalt, concrete, etc.) may be used to restore natural or near-natural contours. 5. Minimize disturbance of existing vegetation in ditches and at stream crossings to the greatest extent possible. 6. Conduct activities during dry-field conditions – low to moderate soil moisture levels. 7. When removing a culvert from a first or second order, non-fishing bearing stream, project specialists shall determine if culvert removal should follow the isolation criteria as describe in Activity #5 above. Culvert removal on fish bearing streams shall adhere to the measures described in #5 above. Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 12 of 29 8. For culvert removal projects, restore natural drainage patterns and when possible promote passage of all fish species and life stages present in the area. Evaluate channel incision risk and construct in-channel grade control structures when necessary. 9. If other aquatic restoration activities are used as complementary actions, follow the associated design criteria and conservation measures.

Removal of Legacy Structures – ARBO I 2007

1. Reuse the nature material to implement habitat improvements. 2. The portion of the log structure keyed into the bank, fill in “key” holes with native materials to restore contours of streambank and floodplain. Compact the fill material adequately to prevent washing out of the soil during over bank flooding. Do not mine material from the stream channel to fill in “key” holes. Bring in clean top soil, if necessary, to improve vegetation reestablishment. 3. If the removal of buried (keyed) structures may result in significant disruption to riparian vegetation and/or the floodplain, consider using a chainsaw to extract the portion of log within the channel, leaving the buried sections within the streambank. 4. The legacy structures (log, rock, or gabion weirs) provides grade control, therefore the site will need evaluated for potential head-cutting and incision due to structure removal. If head- cutting and channel incision are likely to occur due to structure removal, additional measures must be taken to reduce these impacts consult Hydrologist. 5. Protect riparian vegetation that has grown around legacy structures to the greatest degree possible.

Note: decommissioning and removal of legacy structures: The ARBOII will not be finalized until 2013, and therefore design criteria could differ from ARBO I criteria. If ARBO II has more conservative criteria than ARBO I, then ARBOII criteria will be utilized for project implementation. Little if any changes to the criteria for these to category are not anticipated.

B. ESA Action Area

The Action Area, as defined by the Endangered Species Act (ESA), is all areas to be affected directly or indirectly by the federal action and not merely the immediate area involved in the action [50 CFR § 402.02]. The Action Area not only includes the immediate footprint of the road related activities, but also the downstream reaches which may be affected indirectly.

The Action Area for this project is the Upper Elk River 6th field watershed. A list of Region Six Forest Service sensitive aquatic species that may occur in the Action Area are listed in Table 1. No other fishes found in this watershed have special federal status, however, there are other native fishes, including Pacific lamprey.

Less than 1% of the project area is located within the Salmon Creek 6th field, and there will be discussion of affects for this portion of the South Fork Coquille 5th field. The Salmon Creek 6th field comprises 13% of the South Fork Coquille 5th field. With the location of the project in the Copper Salmon Wilderness in Salmon Creek, the project will have no effect on the aquatic resource and will not be detailed in this report.

Less than 1% of the project area is located in in the Middle Fork Sixes River 6th field watershed, part of the Sixes River 5th field. The Middle Fork 6th field comprises less than 10% of the Sixes River 5th Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 13 of 29 field. With the location of the project in the Copper Salmon Wilderness in Middle Fork Sixes, the project will have no effect on the aquatic resource and will not be detailed in this report.

Consistency with Watershed Analysis

Watershed Analyses for the affected watersheds were used to help develop the proposed activities. None of the proposed activities are inconsistent with the findings and recommendations of the Watershed Analyses. The Elk River Watershed Analyses 1998 and the Sixes River Watershed Analyses 1997 are pertinent to this project.

IV. DESCRIPTION OF AFFECTED SPECIES AND HABITAT

SONCC Coho Salmon and Critical Habitat (threatened)

Coho salmon in the Elk River basin are part of the Southern Oregon Northern California Coasts (SONCC) Evolutionarily Significant Unit (ESU), and were listed as Threatened under the Endangered Species Act on 6 May 1997(62 FR 24588). This status was reaffirmed on 15 Aug 2011 (76 FR 50447). SONCC coho critical habitat (CCH) was delineated by NOAA Fisheries on 5 May 1999 (64 FR 24049) and includes all streams within the project area that are accessible to the species. CCH is defined in Section 3(5)(A) of the ESA as “the specific areas within the geographical area occupied by the species on which are found those physical or biological features (I) essential to the conservation of the species and (II) which may require special management considerations or protection.” The CCH designation includes all river reaches accessible to SONCC coho salmon between Cape Blanco, Oregon, and Punta Gorda, California. Critical habitat consists of the water, substrate, and adjacent riparian zones of estuarine and riverine reaches (including off-channel habitats). Accessible reaches are those within the historical range of the ESU that can still be occupied by any life stage of coho salmon. Inaccessible reaches are those above specific dams or above long-standing, naturally impassable barriers (i.e., natural waterfalls in existence for at least several hundred years).

The Elk River contains 59,322 acres within the watershed and 53.2 miles of CCH and EFH with 40.2 miles of that as occupied Coho habitat see Map 1, page 29.

SONCC CCH Primary Constituent Elements (PCE’s)

The list of Primary Constituent Elements (PCEs) essential for the conservation of the SONCC coho ESU include, spawning sites, food resources, water quality and quantity, and riparian vegetation (64 FR 24050, May 5, 1999). Specifically, the adjacent riparian area is defined as the area adjacent to a stream that provides the following functions: shade, sediment, nutrient or chemical regulation, streambank stability, and input of large woody debris or organic matter. NOAA Fisheries defines 10 essential habitat features to include substrates, water quality, water quantity, water temperature, water velocity, cover/shelter, food, riparian vegetation, space, and safe passage conditions (64 FR 24059, May 5, 1999). For the purposes of this BE, the 10 essential habitat features are cross referenced with the respective Habitat Indicators in Table 3 below.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 14 of 29 Table 3. Essential Habitat Features and Respective Habitat Indicators of SONCC CCH Essential Feature Habitat Indicator of CCH Substrate Sediment, Pool Quality, Landslide Rates, Large Woody Debris Water Quality Temperature, Sediment, Road Density & Location Water Quantity Peak/base flows, Drainage Network Increase, Road Density and Location Water Temperature Temperature, Riparian Reserves, Refugia, Width/Depth Ratio, Streambank Condition, Peak/base flows, and Floodplain Connectivity. Water Velocity Peak/base flows, Drainage Network Increase, Floodplain Connectivity, Off- channel Habitat, Width/Depth Ratio, Road Density and Location, Streambank Condition, Large Woody Debris Cover/shelter Sediment, Pool Quality, Streambank Condition, Riparian Reserves, Refugia, Large Woody Debris, Off-channel Habitat, Width/Depth Ratio, Floodplain Connectivity Food Sediment, Riparian Reserves, Floodplain Connectivity, Large Woody Debris, Temperature Riparian Vegetation Riparian Reserves, Large Woody Debris, Disturbance History, Floodplain Connectivity Space Pool Quality, Off-channel Habitat, Floodplain Connectivity Safe Passage Refugia, Physical Barriers, Change in Peak/Base Flows Conditions

Essential Fish Habitat

Interim final rules for Essential Fish Habitat (EFH) under the Magnuson-Stevens Act (16 U.S.C. 1855(b)) were published in the Federal Register/ Vol. 62, No. 244, December 19, 1997 and final rules published in the Federal Register/ Vol. 67, No. 12, January 17, 2002. These rules are pertinent to Chinook salmon and coho salmon habitat within the Southern Oregon Coastal Basin. Essential Fish Habitat (EFH) has been defined by NMFS as “those waters and substrate necessary to fish for spawning, breeding, feeding, or growth to maturity.” This definition includes all waters historically used by anadromous salmonids of commercial value. EFH within the Action Area is the same as CCH as shown on Map 1 (page 29).

V. DESCRIPTION OF ENVIRONMENTAL BASELINE AND POTENTIAL EFFECTS OF THE ALTERNATIVE ACTIONS

This analysis evaluates the potential direct and indirect effects of the alternative actions on SONCC coho salmon individuals and its Critical Habitat (CCH), and to EFH for SONCC coho salmon and OC Chinook. Through this project, there is potential to affect CCH and EFH. CCH and EFH overlap each other in the Action Area, so any potential effect to one (i.e. CCH) would subsequently result in an effect to the other (EFH). This analysis will discuss affects to CCH for feasibility and readability, recognizing that the same effect would apply to EFH. Different PEs and Habitat Indicators will be lumped together when appropriate. This analysis also evaluates the direct and indirect potential effects to other fish species above CCH.

Four alternatives were developed to compare potential effects. Action alternatives were compared to Alternative 1 (no action) to determine the effects to resources from implementation of each alternative.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 15 of 29 The two common actions related to all action alternatives are: road decommissioning/treatment, and replacement of the Blackberry Creek culvert with a bridge and removal of the legacy structures immediately downstream of the culvert.

Alternative 1 is the no action alternative. It represents the current condition and is the basis for comparison of effects from implementation of the three action alternatives. Alternative 2 focuses on restoring wilderness characteristics, hydrological function by decommissioning ~16 miles of road to include: recontouring some road sections, removing fish passage barrier, removing 6 stream crossings, removing 70 road cross-drain culverts, and removing 95 culverts. Alternative 3 focuses on minimizing disturbance while removing structures at high risk of delivering sediment to streams by reestablishing 6 stream crossings and removing 51 cross-drain culverts along ~10 miles of lower and mid-slope road and removing a fish passage barrier. To prevent vehicle use, road recontouring would only occur on the first 300 feet of road on the five roads affected. Alternative 4 focuses on preventing the spread of Port-Orford-cedar root disease by limiting decommissioning to areas with low probability of disease spread. As a result, decommissioning and recontouring would occur on ~4 miles of road, 2 stream crossings, 26 cross-drain culverts and a fish passage barrier would be removed.

The proposed activities in the Action Area are defined as two Project Elements:

1. Road Decommissioning/Treatments 2. Culvert Replacement with Bridge and Legacy Structure Removal

Table 4 (below) describes the months when implementation would occur. Table 5 (below) describes the proximity of CCH to the respective project element.

Table 4. Timing Project Element Month Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec Road Decommissioning X X X /Treatment Culvert Replacement with Bridge / Legacy X X X Structure Removal

Table 5. Proximity of Project Elements to CCH within Upper Elk River 6th Field Watershed Project Elements (PE) Distance to CCH Road Varies from a minimum of 1 Decommissioning/Treatment mile upstream Culvert to Bridge/Legacy At CCH Structure Removal

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 16 of 29 Overall Environmental Baseline Conditions

The Elk River is located primarily in Curry County, and drains approximately 92 square miles or 58,678 acres (Maguire 2001b). It is located in the Northern part of the Klamath Mountains/Siskiyou Province and consists of Cretaceous Rocky Point sandstones and siltstones, Humbug Mountain conglomerates, Galice metasediments, and peridotite. The Elk River native fisheries are supplemented by a hatchery at river mile 13. Major tributaries of the Elk River include the North Fork, South Fork, Blackberry Creek, Panther Creek, Butler Creek, and Bald Mountain Creek. The upper portion of the Elk River watershed is characterized by steeply sloped forested areas with narrow valleys and tributary streams that have steep to very steep gradients. Grazing, rural residential development and other agricultural uses are the dominant land uses on private land in the lower portion of the basin (Maguire 2001b). The Elk River watershed has two wilderness areas, Grassy Knob and Cooper Salmon. Historic logging, mining, and road building have degraded stream and riparian habitats in the Elk River basin. Limiting factors identified for salmonid production in the basin include weak riparian cover (especially in the lower sections), fine sediment sources (present and potential), high water temperatures, and noxious weed invasions (Maguire 2001b).

The project area is in the following river segments and tributaries within the Copper Salmon Wilderness Area or just upstream of the wilderness boundary: North Fork Elk River, South Fork Elk River, Upper Mainstem Elk River, Blackberry Creek, and Butler Creek.

North Fork Elk River The North Fork begins at approximately river mile 30 and has a drainage area of about six thousand acres all on National Forest Systems lands within the wilderness area. The riparian area consists of red alder, big leaf maple, tanoak, Douglas fir and western hemlock in the small tree size in the inner riparian zone. Large woody material is more prevalent in the upper reaches and declines subsequently downstream. The aquatic habitats consist of mid channel scour pools, moderate gradient rapids and low gradient riffles.

The unconfined stream reach in the lower two miles is accessible to anadromous fish and exhibits all of the benefits to aquatic diversity associated with productive flats. This reach contains high quality cold water fish habitat, and all salmonid species (except chum salmon) indigenous to the watershed are present in high numbers. This reach is particularly important for Chinook and coho salmon production and winter steelhead rearing. This lower reach is characterized as being a two percent gradient reach containing a pool to dominated channel (Siskiyou Research 2007).

The upper reach of the North Fork is blocked to anadromous fish but contains resident trout. It contains an area of V-shaped canyons of bedrock and cobble with a steep slope and then opens up to a low gradient gravel dominated channel (Siskiyou Research 2007)..

South Fork Elk River The South Fork Elk River begins at approximately river mile 30 and has a drainage area of about five thousand acres all on National Forest Land. The riparian area consists of red alder, big leaf maple, tanoak, Douglas fir, western hemlock and Port Orford cedar in the small tree size in the inner riparian zone. Large woody material is more prevalent in the upper reaches and declines as you move downstream. The aquatic habitats consist of moderate gradient rapids, low gradient riffles, mid channel scour pools, plunge pools and side channels. In the South Fork, a large earth flow constricts the channel, providing a barrier to fish migration approximately one mile upstream from the mouth of the creek. The South Fork is noted for running cold during the summer peak temperatures; a random Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 17 of 29 temp sample was to be observed to be at 11 degrees Celsius which is 2 degrees cooler than they observed on the North Fork (Siskiyou Research 2007). The stream runs subsurface during the summer, through the aggraded reach, so it is not exposed to solar heating. This may account for the unusually cold temperature.

The South Fork Elk River contains moderate numbers of steelhead and resident trout, with the occasional presence of Chinook and coho salmon. Sedimentation from natural and anthropogenic sources within the South Fork drainage has resulted in habitat conditions that tend to not be conducive to coho salmon production. The Anadromous habitat is limited to the lower mile of the stream and nearly all steelhead rear in the lowest quarter mile of this stream. The anadromous fish use is extremely limited due to steep gradients and numerous barriers.

Upper Elk River Mainstem The Upper Mainstem Elk River located downstream of the confluence of the South Fork and North Fork Elk River, and extends downstream to the Oregon State Fish Hatchery. The north side of the entire Upper Mainstem is bordered by the Grassy Knob and Copper Salmon Wilderness. The riparian area consists of red alder, big leaf maple, tanoak Douglas fir and western hemlock in the small tree size in the inner riparian zone. The habitat generally consists of riffles, rapids, steep cascades, scour pools and plunge pools. Cobble and boulder substrate is dominant throughout with gravel and bedrock sub dominant. Sand/silt was found in moderately low amounts. This channel has a high degree of resistance to change and is considered highly stable. Large woody material is not abundant throughout the entire Upper Mainstem watershed and consists of widely scattered individual pieces. The Upper Mainstem contains all salmonid species (except chum salmon) indigenous to the watershed.

Butler Creek Butler Creek is a northern tributary located at approximately river mile 25 and has a drainage area of about four thousand acres all on NFS land. The Butler Creek drainage is characterized by deep stable V-Shape canyons, dissected mountainous terrain, sharp drainage divides, bedrock outcrops, and colluvial constrained stream channels with a mild gradient. The riparian area consists of a mixed conifer overstory of Douglas fir, western red cedar, Port Orford cedar and western hemlock in large tree size as a dominate vegetation class. Large woody material is more prevalent in the upper reaches and declines as you move downstream. The aquatic habitats consist of gravel rich scour pools and riffles, cobble dominated rapids and non-turbulent and deep bedrock trench pools. All salmonid species (except chum salmon and coho) indigenous to the watershed were present during the 2006 Level II Stream Survey in the lower two and half miles (Siskiyou Research 2007).

Blackberry Creek Blackberry Creek is a southern tributary located at approximately river mile 28 and has a drainage area of about three thousand acres all on NFSland. Blackberry Creek has two branches, known as the east and west forks. Large wood is abundant, stable, and of natural origin. Stream banks along these reaches are also stable, much of it being composed of bedrock walls. Riparian areas are intact, with large alders, big leaf maple, and Douglas fir providing 85-95 percent shading. Anadromous fish access is impaired by the culvert under Forest Service Road 5325 (Siskiyou Research 2011).

Summary In general the aquatic habitats in the Action Area have been modified and simplified during the past 100 years. Elk River is one of the last areas impacted by European settlement and development. Timber harvest and road construction have had the most impact on the aquatic and riparian zones in the Action Area. Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 18 of 29

For more specific descriptions of aquatic habitat quality and quantity of streams in the Action Area refer to the hydrology report (USDA FS 2011), the Blackberry Fish BE (USDA FS 2004), Elk River Watershed Analyses (USDA FS 1998), or stream inventories of pertinent streams, such as 2006 survey of Butler Creek (Siskiyou Research 2006).

EFFECTS OF EACH PROJECT ELEMENT

Alternative 1 – Effects on Fish

With the no action alternative, adverse effects to fish would continue to occur due to: sediment delivery to streams from culvert failures and road run-off, the diminished growth of shade-producing trees due to compacted soils in the road bed, and blocked anadromous fish passage on about 1.5 miles of Blackberry Creek.

If no action is taken, potential sediment from future crossing failures is estimated to be 8,193 cubic yards which is the current estimate at the culvert location and it would typically occur during periods of high rainfall when turbidity is already high. While it is unknown the extent or exact timing to which this sediment would reach streams, the likelihood is high due to the steep geology and high rainfall of the area. Road sediment has been described as the primary aquatic habitat degradation factor within the Upper Elk River watershed. This sediment could affect several miles of aquatic habitat depending on how much of the sediment gets delivered and transported downstream.

Increased sediment production in stream systems has been shown to adversely affect Pacific Northwest salmonid species through reduction in gravel permeability and reduced egg to fry survival (Cederholm et al. 1980; Furniss et al. 1991). Further, sediment can reduce macro invertebrate production and fill pools, reducing habitat quantity and salmonid food availability (Suttle et al. 2004; Harvey et al. 2009). A direct linkage also exists between sediment supply and stream habitat indicators such as gravel permeability and pool depth (Cover et al. 2008). Likewise, inverse relationships exist between sediment-related stream habitat indicators and fish survival (Suttle et al. 2004; Harvey et al. 2009).

Tree growth would remain diminished due to soil compaction and loss of soil productivity on about 27 acres (The effects on soil productivity from each alternative are summarized in Table 3-3 of the soils report) of existing road bed. This diminished growth would slow or prevent trees from reaching a height where they could provide shade to streams or contribute coarse wood to the stream.

All Action Alternatives – Common Effects on Fish and CCH Habitat

Effects from all action alternatives would be beneficial to fish and aquatic organisms in the long-term. There would be some short-term (less than one year) detrimental effects caused by an increase in turbidity as a result of removing culverts and legacy structures, and recontouring slopes where culverts are removed.

Detailed effects can be reviewed in the Endangered Species Act Section 7 Formal Programmatic Consultation and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat Consultation for Fish Habitat Restoration Activities in Oregon and Washington, CY2007- CY2012 Biological Opinion (2007 ARBO) for categories #17. Road Treatments; and #18.Removal of Legacy Structures. Direct effects can occur directly by harming (killing or injuring) or harassing an animal. Harassing is defined as an intentional or negligent act that creates the likelihood of injuring Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 19 of 29 wildlife by annoying it to such an extent as to significantly disrupt normal behavior patterns such as breeding, feeding, or sheltering (50 CFR §17.3).

Harm may also include habitat modification or degradation that actually kills or injures a listed species by significantly impairing essential behavior patterns such as breeding, spawning, rearing, migrating, feeding, or sheltering (50 CFR 217.12). Therefore, indirect adverse effects are those that reduce fish growth and ultimately survival through changing the quality or quantity of physical (e.g. temperature, cover, pool depth, spawning gravels), chemical (e.g. pH), or biological (e.g. decreased prey availability) parameters. Indirect effects that improve habitat parameters could also be beneficial to the species. For example, indirect effects caused by treating (storm proofing, closing, or decommissioning) forest roads are those that could also modify critical or essential fish habitats depending on proximity, magnitude, duration, and timing of the road treatments.

A. Direct Effects

Alternative 1 No Action

CCH Habitat Indicators (includes all indicators): Water Quality (Temperature, Chemical Contaminants/Nutrients, Sediment & Pool Character & Quality, Large Wood, Off-channel Habitat, Width: Depth Ratio by Channel Type, Stream bank Condition, Floodplain Connectivity, and Changes in Peak and Base Flows.

CCH Watershed Condition Indicators (includes all indicators): Road Density/Location, Human Disturbance History, Riparian Reserves, and Landslide and Erosion Rates

There are no causal mechanisms from the No Action Alternative to affect CCH Habitat Indicators or CCH Watershed Condition Indicators. Therefore, no direct effects would occur to sensitive, threatened fish or aquatic species and other fish or aquatic species because no work would occur in streams where these species or their habitat are present.

Element & Indicator Summary: There is no direct causal mechanism for the No Action Alternative proposes no work in the streams or adjacent to the stream channel where ESA species are found. The no action alternative would result in a neutral (0) effect to all habitat or watershed condition indicators.

Alternative 2, 3 and 4 (Action Alternatives)

Alternatives 2, 3 and 4 Actions have no mechanism to alter the following CCH Habitat Indicators : Water Quality (Temperature, Large Wood, Off-channel Habitat, Width: Depth Ratio by Channel Type, Stream bank Condition, Floodplain Connectivity, and Changes in Peak and Base Flows) and they will not be analyzed any further.

Alternatives 2, 3 and 4 Actions have a mechanism to alter the following CCH Habitat Indicators: Chemical Contaminants/Nutrients, Sediment & Pool Character & Quality Stream bank Condition along with a mechanism that would alter the following CCH Watershed Condition Indicators (includes all indicators): Road Density/Location, Human Disturbance History, Riparian Reserves, and Landslide and Erosion Rates.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 20 of 29 1. Proximity All three action alternatives include the same two project elements: Road Decommissioning/Treatments and Culvert Replacement with a Bridge/Legacy Structure Removal that would have work occurring near and or directly in streams that contain CCH.

Road Decommissioning/Treatments, Legacy Structure Removal

The removal of the legacy on Blackberry Creek would require the operation of heavy equipment in the riparian areas and active stream channel. The unavoidable short-term adverse effects resulting from these activities include disturbance of riparian vegetation, exposure of bare soil, increased stream turbidity, increased fine sediments in stream substrates, and increased risk of chemical contamination from fuel and lubricants. The stream construction activities for this project are likely to last two weeks at a maximum. During that time, juvenile salmonids may experience decreased feeding, stress, or be unable to use the action area, depending on the severity of the turbidity. Although this represents a major behavioral change, the temporal and spatial scale of the impact is too small to cause measurable effects at the population level. Soil productivity would be restored on as little as 7 acres (Alternative 4) and as much as 27 acres (Alternative 2). This enhanced soil productivity would allow trees to grow more quickly; and, potentially, contribute to streamside shade, riparian vegetation, and in-stream wood. These mechanisms would ultimately benefit fish and riparian species.

There would be a net decrease in future sediment delivery to streams with all action alternatives, although Alternative 4 would only be marginally beneficial. As shown in Table 6, alternatives 2 and 3 would decrease the potential for sediment delivery from future culvert failure during winter storm events to 194 cubic yards (a 98% decrease) and 377 cubic yards (95%), respectively. Alternative 4 would decrease sediment to 7,241 cubic yards (a 12% decrease). Because the timing of winter events and location of this sediment delivery cannot be predicted exactly, the extent of the benefit to fish is uncertain, but aquatic organisms would benefit overall due to decreases in turbidity and substrate embeddedness.

Culvert Replacement with a Bridge

Fish Passage Culvert and Bridge Projects. The current culvert will be will be replaced with a bridge using a stream simulation method. The long-term beneficial effects of this project include restoration of fish passage and restoration of natural stream channel processes through removal of a channel constricting structures. Removing fish-passage blockages would restore spatial and temporal connectivity of streams within and between drainages where fish movement is currently obstructed. This, in turn, would permit fish access to areas critical for fulfilling their life history requirements, especially foraging, spawning, and rearing. However, the removal of fish passage barriers could have short-term (typically lasting less than one week, depending on the duration of in-stream work) temporary negative effects to fish. Heavy equipment could be used in the stream for unblocking, removing and replacing the existing culvert with a bridge.

Fish Removal. Direct effects on juvenile salmonids from work area isolation and fish relocation include mechanical mortality and injury during capture, holding, or release, and potential horizontal transmission of disease and pathogens and stress-related phenomena.

Element and Indicator Summary: There is a causal mechanism for Road Decommissioning/Treatments and Culvert Replacement with a Bridge/Legacy Structure Removal impacts to the Habitat Indicators: Chemical Contaminants/Nutrients, Sediment & Pool Character & Quality Stream bank Condition, and Watershed Condition Indicators: Road Density/Location, Human Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 21 of 29 Disturbance History, Riparian Reserves, and Landslide and Erosion Rates because these are in-stream projects directly in CCH.

B. Indirect Effects

Alternative 1 No Action

CCH Habitat Indicators (includes all indicators): Sediment & Pool Character & Quality, Road Decommissioning/Treatments.

Proximity The No Action alternative would have no causal mechanism; and therefore, no effect since no activities are proposed on NFS lands. However, there is a possible causal mechanism from not implementing these projects from sediment delivery to CCH Habitat or CCH Watershed Condition Indicators The indirect effect would occur to sensitive, threatened fish or aquatic species and other fish or aquatic species because no work is occurring to remove the potential for sediment to move into streams where these species or their habitat is present; see Table 6 for the possible amounts of sediment that could be delivered to the stream channels below these locations.

Road Decommissioning/Treatments

Probability The Hydrology report ranked the locations in the current road structures (culverts) in Table 6 as having a high probability of failure.

Magnitude Table 6 displays the amount sediment for potential delivery. In some portions of the watershed, road-related sediment has been implicated as the major limiting factor to fish production. Road sediment has been described as the primary aquatic habitat degradation factor within the Upper Elk River sub watershed. This sediment could affect several miles of aquatic habitat depending on how much of the sediment does get delivered and transported downstream.

Element and Indicator Summary: The causal mechanism is the potential for possible sediment delivery which may affect the Habitat and Watershed Condition Indicators because the amount of sediment projected to be left on site. No Action may result in a negative effect to these indicators.

Table 6. Amounts of Potential Sediment ROAD DITCH ROAD-SURFACE EROSION ROAD STREAM CROSSINGS CROSS-DRAINS Potential Potential Sediment Sediment Risk of Sediment Delivery Delivery Delivery to the From From Potential Sediment Stream Channel # of Crossing Number Cross-Drain Delivery From Drainage Road Length with No Stream Failures of Cross Failures Unmaintained Road Name No. (Miles) Treatment Crossings (cu.yds) Drains (cu.yds) Surfaces (cu.yds/yr) North Fork Elk 3353320 1.28 High 2 1200 20 200 68 River North Fork Elk 3353330 2.18 High 5000 27 River Total N. 3.46 2 6200 20 200 95 Fork Elk

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 22 of 29 ROAD DITCH ROAD-SURFACE EROSION ROAD STREAM CROSSINGS CROSS-DRAINS South 5325- Fork Elk MP18 1.63 High 1 5 222 River Spur Total S. 1.63 Fork Elk 1 5 0 0 222 Elk River 5201350 2.03 High 1 700 26 270 150 Mainstem Total Elk R. Mainstem 2.03 1 700 26 270 150

Alternatives 2, 3 and 4 Actions have a mechanism to alter the following CCH Habitat Indicators: Chemical Contaminants/Nutrients, Sediment & Pool Character & Quality Stream bank Condition along with a mechanism can indirectly alter the following CCH Watershed Condition Indicators (includes all indicators): Road Density/Location, Human Disturbance History, Riparian Reserves, and Landslide and Erosion Rates.

1. Proximity All three action alternatives include the same two project elements: Road Decommissioning/Treatments and Culvert Replacement with a Bridge/Legacy Structure Removal that will have work occurring near and or directly in streams that contain CCH.

Road Decommissioning/Treatments

Probability The Hydrology report ranked the locations in the current road structures (culverts) in Table 6 that have a high probability of failure.

Cumulative Effects

Cumulative effects are those that result from the incremental accumulations of all land management activities across all ownerships. In the Elk River sub-basin, historic land management activities such as mining, riparian timber harvest and road construction have had an enduring and significant impact on salmonid production. These impacts are especially apparent in the lower reaches of the river where private land ownership predominates. Effects on fish would remain insignificant for the proposed

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 23 of 29 project because the Upper Elk River watershed is almost entirely under Forest Service management, negative effects from project activities would be short-term in nature, and no other activities with measurable effects are on-going or planned in the watershed.

There is virtually no private or other Federal ownership upstream of the project area. The Forest Service has is planning future projects for the area as listed in the Watershed Condition Framework document (USFS 2001). There are no campground expansions or road construction projects planned. Maintenance of roads would continue to occur on the primary Forest Service roads which bound the Wilderness to provide public access. This maintenance includes clearing of rocks and trees from the road surface, when needed, and road-side brushing to maintain sight-distances. Vegetation would remain in place and could potentially add to available in-stream wood to the benefit of fish. However, those benefits would be tempered by the negative impacts from the cutting of shade-producing trees and shrubs along streams. Riparian disturbance and disturbed soils resulting from accessing work sites will stabilize and begin to revegetate within one year. When added to other activities, there would continue to be no measurable impact to fish.

Sediment from the use of existing Forest Service roads in the Elk River watershed would continue. This sediment would be minimal during the period of project activities because the roads involved are either rocked or paved aggregate, and they are primarily used during the summer for recreation. Adverse effects resulting from the proposed activities are expected to be minor and of short duration. Minor reductions in invertebrate forage will occur as a result of increased fine sediment generated by construction activities. This would affect to a few hundred feet below construction sites, and these areas will be recolonized by invertebrates within a few months. The short -term cumulative sediment effects would occur but in the long term these cumulative sediment effects would diminish.

Because project design features would avoid periods of adult fish presence and ongoing activities are concentrated during the summer, when adult fish are not present, detrimental cumulative effects to fish would not be measurable.

The restoration actions addressed by the ARBO Programmatic Opinion all have long-term beneficial effects on three salmon and steelhead parameters – abundance, productivity, and spatial structure. As these improvements are realized, the extinction risk for salmonids addressed by this Opinion will decrease. The proposed restoration activities would have measurable short-term sediment effects.

Most adverse effects resulting from the proposed activities are expected to be minor and of short duration (weeks to one year). Degraded water quality and increased turbidity resulting from instream construction will last a maximum of a few weeks. Riparian disturbance and disturbed soils resulting from accessing work sites will stabilize and begin to revegetate in one year.

Fish relocation will result in stress and possible mortality for a small number of fish. The stress of relocation will last only a few hours and will only happen once. A small number of other adverse effects resulting from the proposed restoration actions (such as bank trampling at water crossings and preclusion of riparian vegetation at graveled recreation sites) will persist into the future but occur at such a small scale that they will not have any observable effects on population abundance and productivity.

All the populations of salmon and steelhead addressed by ARBO are at abundance levels far below historic and are listed as threatened or endangered.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 24 of 29

VI. COMPARISON OF EFFECTS BY ALTERNATIVES

Table 7. Comparison of Effects to TES Species for Each Alternative by Activity Type Culvert Replacement Legacy Structure Road Alternative with Bridge Removal Decommissioning

1 Fish Passage obstruction Fish Passage obstruction will Long Term Negative will Remain Remain 2 Short Term Negative/Long Short Term Negative/Long Beneficial Term Beneficial Term Beneficial

3 Short Term Negative/Long Short Term Negative/Long Beneficial Term Beneficial Term Beneficial

4 Short Term Negative/Long Short Term Negative/Long Beneficial Term Beneficial Term Beneficial

The No Action Alternative would not alter the project area on NFS land. Thus, a long term negative effect to TES aquatic species or habitat would occur.

The effects from the Culvert Replacement with a Bridge and Legacy Structure Removal at Blackberry Creek are identical within all Action Alternatives, 2 through 4. Under any Action Alternative, the effects would be positive since the culvert would be replaced with a bridge and the legacy structure removed, thereby facilitating passage of all life stages of native fish. Direct negative effects on juvenile salmonids from work area isolation and fish relocation could occur from mechanical mortality and injury during capture, holding, or release, and potential horizontal transmission of disease and pathogens and stress-related phenomena.

The effects from the Road Decommissioning/treatments to the TES aquatic species are similar under all of the Action Alternatives, 2 through 4. There would be short term negative sediment effects, with long term benefits to CCH through decreased road generated sediment influx within the watershed. The differences in activities between the Action Alternatives are not large enough to create any measurable difference on TES aquatic species and habitat. Alternative 2 would be most beneficial to CCH due to greater road decommissioning resulting in an increased sediment reduction. Alternatives 3 and 4 would provide similar benefits, but at a reduced spatial scale (when compared to Alternative 2) due to fewer road miles being decommissioned.

Conclusions of Determinations

Alternative 1 – No Action

Alternative 1 will have direct, indirect or cumulative effects to SONCC coho salmon, SONCC coho CH, OC coho salmon, OC coho CH, SONCC Chinook salmon, and OC steelhead by not removing the upstream migration barrier at Blackberry Creek. This Alternative will also result in direct, indirect or cumulative effects to SONCC coho salmon, SONCC coho CH, OC coho salmon, OC coho CH, SONCC Chinook salmon, or OC steelhead if the roads begin to fail. The Alternative 1 will have no

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 25 of 29 direct, indirect or cumulative effects on Southern DPS North American green sturgeon, Southern DPS Pacific eulachon or PC chum salmon.

Alternative 2- Proposed Action and Alternatives 3 and 4 (Action Alternatives)

Based on a review of best available science, ARBO and my professional judgment, I find direct, indirect, and cumulative effects from Alternative 2 to the Copper Salmon Legacy Roads project would be “Likely to Adversely Affect” (LAA) SONCC coho salmon, and its Critical Habitat (CCH).

Essential Fish Habitat is the same as CCH in the Action Area. Therefore, the same determination of effects applies to EFH. The project is “Likely to Adversely Affect” Essential Fish Habitat for coho salmon or Chinook salmon. However, the beneficial effects to fish would be greater under Alternative 2 if the sediment predictions are accurate. The less sediment that is stored in the upper watershed to move into the stream during winter storms will be better for the habitat.

The Action Alternatives will have No Impact to PC chum salmon, OC steelhead and SONNCC Chinook salmon since they are not in the project area.

Table 8. Summary of Conclusion of Effects for Forest Service Sensitive Fish Species Species Alt. 1 Alt. 2 Alt. 3 Alt. 4 SONCC coho NE LAA LAA LAA SONCC coho CH NE LAA LAA LAA OC coho NE NE NE NE OC coho CH NE NE NE NE S. DPS North NE NE NE NE American green sturgeon S. DPS Pacific NE NE NE NE eulachon EFH – OC NE LAA LAA LAA Chinook SONCC Chinook NI NI NI NI OC steelhead NI NI NI NI PC Chum NI NI NI NI LAA= Likely to Adversely Affect NE = No Effect B-NLAA = Beneficial, Not Likely to Adversely Affect NI = No Impact MIIH = May Impact Individuals or Habitat, But Will Not Likely Contribute to a Trend towards Federal Listing or Cause a Loss of Viability to the Population or Species BI = Beneficial Impact

VII. DICHOTOMOUS KEY FOR MAKING SECTION 7 DETERMINATION OF EFFECTS

Location: Rogue River-Siskiyou National Forest Project Name: Copper Salmon Legacy Roads Species: SONCC Coho Salmon Watersheds within Project Area: Upper Elk River

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 26 of 29

1. Are there any proposed/listed anadromous salmonids and/or proposed/designated critical habitat in the watershed or downstream from the watershed?

NO…………………………………………………………………………… No Effect YES………………………………………………………………… May affect, go to 2

2. Will the proposed action(s) have any effect whatsoever* on the species and/or critical habitat?

NO…………………………………………………………………………… No Effect YES………………………………………………………………………….. Go to 3

3. Does the proposed action(s) have the potential to hinder attainment of relevant properly functioning indicators from checklist?

NO……………………………………………………………………………. Go to 4 YES……………………………………………………………….. Likely to adversely affect

4. Does the proposed action(s) have the potential to result in “take”** of proposed/listed anadromous salmonids or destruction/adverse modification of proposed/designated critical habitat?

NO. There is a negligible (extremely low) probability of take of proposed/listed anadromous salmonids or destruction/adverse modification of proposed/designated critical habitat…………………………………………… Not likely to adversely affect

YES. There is more than a negligible probability of take of proposed/listed anadromous salmonids or destruction/adverse modification of proposed/designated critical habitat……………………………………….…….. Likely to adversely affect***

*”Any effect whatsoever” includes small effects that are unlikely to occur, and beneficial effects, i.e. a “no effect” determination is only appropriate if the proposed action will literally have no effect whatsoever on the species and/or critical habitat, not a small effect, an effect that is unlikely to occur, or a beneficial effect. **”Take” – The ESA (Section 3) defines take as “to harass, harm, pursue, hunt, shoot, wound, trap, capture, collect or attempt to engage in any such conduct”. The USFWS further defines “harm” as “significant habitat modification or degradation that results in death or injury to listed species by significantly impairing behavioral patterns such as breeding, feeding, or sheltering” and “harass” as “actions that create the likelihood of injury to listed species to such an extent as to significantly disrupt normal behavior patterns which include, but are not limited to, breeding, feeding or sheltering”. ***Document expected incidental take on appropriate form.

Name of Biologist: /s/ Karla M. Cottom Date: Aug 29, 2012 Final Jan 2, 2013

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 27 of 29 VIII. References Cited

Brazier J., 2011. Copper Salmon Legacy Roads Project Soils Report, USDA, USFS, Pacific Northwest Region.

Federal Register. 1999. Designated critical habitat; Central California Coast and Southern Oregon Northern California Coasts coho salmon 64(86) 5 May 1999.

National Marine Fisheries Service (NMFS), 2007. Endangered Species Act- Section 7 Programmatic Consultation Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential fish Habitat consultation. Fish Habitat Restoration Activities in Oregon and Washington, CY2007-CY2012. (ARBO)

[ODFW] Oregon Department of Fish and Wildlife. 2004b. Random coho coastal spawning fish summary. Available on the internet at: http://oregonstate.edu/Dept/ODFW/spawn/pdf%20files/coho/PopEst2003.pdf

Park, C.S. 2011. Copper Salmon Legacy Roads Project Hydrology Report, USDA, USFS, Pacific Northwest Region.

Siskiyou Research Group. 2006-2012. Various Level II Stream Survey Reports for Elk River and Tributaries of Elk River. Cave Junction, Oregon.

[USDA FS] United States Department of Agriculture (USDA) Forest Service. 1994a. Northwest Forest Plan Record of Decision, Portland, Oregon.

[USDA FS] USDA Forest Service. 1997 Sixes River Watershed Analyses, Powers Ranger Station. USDA FS] USDA Forest Service. 1998. Elk River Watershed Analyses, Powers Ranger Station. Available from Powers Ranger District, Powers, OR.

[USDA FS] USDA Forest Service. 2004. Powers Ranger Station, Blackberry Creek Fisheries Biological Evaluation. Available from Powers Ranger District, Powers, OR.

Available from Powers Ranger District, Powers, OR.

[USDA FS] USDA Forest Service. 2011. Region Six Sensitive Species List updated December 2011. http://www.fs.usda.gov/r6

[USDA FS] USDA Forest Service. 2012. Rogue River-Siskiyou National Forest fish distribution GIS data. Available from Powers Ranger District, Powers, OR.

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 28 of 29 Map. 1. Fish Distribution

Aquatic Biota Biological Evaluation for the Copper Salmon Wilderness Legacy Roads Project, RRSNF Page 29 of 29