Marshall Woods Restoration Project

Transcription

1 Marshall Woods Restoration Project Aquatics Report Prepared by: Aubree Benson Fisheries Biologist for: Missoula Ranger District Lolo National Forest November

2 Table of Contents INTRODUCTION... 3 Aquatic Issues Addressed... 3 AFFECTED ENVIRONMENT... 3 Forest Plan Direction & Regulatory Framework... 3 Species Habitat Requirements... 7 Analysis Area Boundary and Data Sources... 9 Existing Conditions Aquatic Habitat Aquatic Species Status of INFISH Riparian Management Objectives Desired Conditions ENVIRONMENTAL CONSEQUENCES Analysis Methods Alternative A Direct and Indirect Effects Comparison of the Action Alternatives B, C, and D - Direct and Indirect Effects Cumulative Effects for All Alternatives Effects to Bull Trout Critical Habitat Consistency with Regulatory Framework Preliminary Effects Determinations for Threatened and Sensitive Aquatic Species Summary of Effects REFERENCES Tables Table 1. Status of Baseline Conditions with Site-Specific Information for the Upper Rattlesnake Creek, Lower Rattlesnake Creek and Clark Fork River Marshall Creek 6th Field HUCs Table 2. Resource Protection Measures for Aquatic Resources Table 3. Summary of Project Scale Effects on Species and Habitat Indicators Figures Figure 1. Map displaying the aquatic analysis areas, bull trout baseline determinations, and bull trout critical habitat Figure 2. Forest Road #99/Trail # Figure 3. Recreation-based bank stabilization projects completed in 2014 to protect stream habitat within the project area

3 INTRODUCTION The Marshall Woods Restoration Project encompasses a 13,000-acre analysis area which includes Marshall Creek, Woods Gulch, and portions of the Lower Rattlesnake Creek drainage on the Missoula Ranger District of the Lolo National Forest (Lolo NF). National Forest System (NFS) lands consist of about 56% of the analysis area, and include a portion of the Rattlesnake National Recreation Area (RNRA). Proposed activities are designed to restore functioning ecosystems, emulate fire s natural role on the landscape, provide educational and diverse trail-based recreation opportunities, and reduce road density in Section 31. Aquatic Issues Addressed This report, appendices, and Project File describe the existing conditions and the potential effects of the activities proposed within each of the Marshall Woods alternatives on aquatic species and aquatic habitat. Aquatic concerns derived from previous assessments, public scoping and interdisciplinary meetings will be addressed. The primary concerns are any potential effects on aquatic species and habitat through excessive sedimentation or alteration of streams or riparian vegetation. Therefore, the proposed project has been designed to eliminate or minimize sedimentation and impacts to streams and riparian areas. The project area contains bull trout (Salvelinus confluentus), which are listed as a threatened under the Endangered Species Act, as well as designated critical habitat for bull trout. In addition, westslope cutthroat trout (Oncorhynchus clarki lewisi) and western pearlshell mussel (Margaritifera falcata) are currently designated as sensitive species on the Lolo NF. Westslope cutthroat trout inhabit the project area, and western pearlshell mussel may inhabit the project area. Therefore, this report addresses the potential biological effects of the proposed Marshall Woods Restoration Project on bull trout and bull trout critical habitat, westslope cutthroat trout, and western pearlshell mussels and their habitat. AFFECTED ENVIRONMENT Forest Plan Direction & Regulatory Framework The Lolo NF Plan direction and all Federal and State laws, regulations, and agreements applicable to aquatic resources would be applied to the Marshall Woods project. Lolo National Forest Plan (USDA-FS 1986): Forest standards and guidelines for fisheries and water quality are found in the Forest Plan (section II), including site-specific protection for various designated Management Areas (MA) (section III). The Forest-Wide Management Direction (section II) provides 3 pertinent goals, with the objective of emphasizing the protection of water quality and fish habitat: 1) Provide habitat for viable populations of all indigenous wildlife species (II.A.2); 2) For threatened and endangered species occurring on the Forest, manage to contribute to the recovery of each species to non-threatened status (II.A.7); and, 3) Meet or exceed State water quality standards (II.A.8). The Forest Plan also depicts a desired future condition of the Forest. Specific to bull trout management, the plan states that by 1995, habitat to support threatened and endangered species will have been protected consistent with recovery goals (II.D.1). It also states that by

4 sufficient habitat will exist for threatened and endangered species to meet the objectives of the recovery plans. Factors limiting recovery will have been eliminated where possible (II.D.2). Lolo Forest Plan Standards (section II.E) are designed to supplement national and regional policies, standards, and guidelines. Forest-wide standards applicable to this project proposal and bull trout management include: the application of Best Management Practices (BMPs) to assure that water quality is maintained and to meet or exceed Federal and State standards (II.E.15); limiting humancaused increases in water yield so that channel damage will not occur as a result of land management activities (II.E.19); protecting species and managing habitat to be consistent with Endangered Species Act recovery goals to non-threatened status and to maintain population viability (II.E.27); and designing land management practices to have a minimum impact on the aquatic ecosystem (II.E.28). In addition to these Forest-wide standards, the Forest Plan emphasizes site-specific protection of fisheries and water quality through management area standards and guidelines (section III). There are 28 MAs on the Forest, each with different management goals, resource potentials and limitations. MAs in the Marshall Woods project area are outlined in Chapter 1 of the Environmental Assessment (EA). Several specific MAs and standards which pertain to aquatic resources are summarized below. For a more detailed explanation, see the Forest Plan (section III). MA 13: This MA consists of lakes, lakeside lands, major 2 nd order and larger streams and the adjoining lands that are dominated by riparian vegetation and lie outside of existing grazing allotments. Briefly, MA 13 lands are managed to maintain and enhance the value of riparian areas for fishery and aquatic habitat and water quality (III-56.B.1). Pertinent standards for MA 13 lands are to maintain natural habitat for indigenous aquatic organisms, protect riparian vegetation, and minimize impacts on water quality through project prescriptions developed in coordination with the Forest Fisheries Biologist, Hydrologist, and/or Soil Scientist (III-56.C.5,9,10). The standards also state that streams containing pure westslope cutthroat will be managed specifically for that subspecies (III-56.C.20). No standards apply directly to bull trout. MA 28: This MA consists of the non-wilderness portion of the RNRA and Wilderness. The area is important for its value as a portion of Missoula s municipal watershed, a dispersed recreation area, an environmental education area, and habitat for a variety of wildlife (III- 144). Pertinent standards for this proposed project in MA 28 are to improve trails to enhance accessibility, disperse concentrated recreation use, and protect other resource values (III-144.C.2), design management activities to minimize impacts on water quality and other riparian values (III-145.C.4) and manage streamside vegetation or shade and filtering of overland flows (III-145.C.9). LAC amendment to the Forest Plan: The Lolo NF Plan was amended in February 1993 to include specific management direction for the RNRA and Wilderness based on Limits of Acceptable Change, which can be found in Appendix O-4 of the Forest Plan (USDA-FS 1986). The management direction recognizes riparian and wildlife habitat and water quality as key components of the resource setting, and directs management of the area to maintain and enhance important riparian and wildlife habitat, and protect and limit the effects of visitor use on water quality. INFISH Amendment to the Forest Plan: The Lolo NF Plan was amended on August 30, 1995, by the Inland Native Fish Strategy (INFISH) (USDA-FS 1995). This interim strategy was designed to provide additional protection for existing populations of native trout, outside the range of anadromous fish, on 22 national forests in the Pacific Northwest, Northern and Intermountain Regions. Implementing this strategy was necessary because these species were at risk due to habitat degradation, introduction of exotic species, loss of migratory forms, and over-fishing. As part of this strategy, the Regional Foresters designated a network of priority watersheds. Priority 4

5 watersheds are drainages which still contain excellent habitat or assemblages of native fish, provide for metapopulation objectives, or are watersheds which have excellent potential for restoration. Rattlesnake Creek is a designated priority watershed. INFISH also established Riparian Management Objectives (RMOs) and Riparian Habitat Conservation Areas (RHCAs). RMOs are habitat parameters that describe good fish habitat. These RMOs for stream channel conditions provide the criteria against which attainment or progress toward attainment of riparian goals is measured. Where site-specific data is available, these RMOs can be adjusted to better describe local stream conditions. The Lolo NF has developed site-specific RMOs for most of the habitat variables based on information collected in roadless watersheds (Riggers et al. 1998). Where habitat data exists, these site-specific RMOs can help reveal what the stream condition should be for undisturbed streams with similar characteristics. INFISH RHCAs are portions of watersheds where riparian dependent resources receive primary emphasis. RHCAs are variable width zones designated by INFISH around bodies of water, and are commonly referred to as riparian buffers. RHCAs help maintain the integrity of the aquatic ecosystem by: a) influencing the delivery of coarse sediment, organic matter, and woody debris to streams; b) providing root strength for channel stability; c) shading streams; and d) protecting water quality. INFISH default RHCAs include those areas: within 300 feet of perennial, fish bearing streams; within 150 feet of perennial, non-fish bearing streams; within 100 feet of intermittent streams and wetlands within priority watersheds; and within 50 feet of intermittent streams and wetlands within non-priority watersheds. INFISH buffer widths exceed state Best Management Practice (BMP) standards. INFISH also contains standards and guidelines applicable to the Marshall Woods project, including those for timber management, road management, recreation management, fire/fuels management, general riparian area management, and fisheries and wildlife restoration. Activities that retard the attainment of the RMOs are not allowed within these default RHCAs. Young stand thinning and prescribed fire are allowed to occur to a certain extent within RHCAs, as described in the Resource Protection Measures within the Environmental Consequences section below. Endangered Species Act and NEPA Requirements for Sensitive Species: On June 10, 1998, the United States Fish and Wildlife Service (USFWS) listed bull trout as a threatened species within the Columbia River Basin under the Endangered Species Act (USDI-FWS 1998a), and on November 17, 2010, the USFWS issued a final rule with a revised designation of critical habitat for bull trout (USDI-FWS 2010). Section 7(a)(2) of the Endangered Species Act of 1973 as amended, requires all Federal agencies to consult with the USFWS to ensure that activities they authorize, fund, or carry out are not likely to jeopardize the continued existence of listed species or to destroy or adversely modify their critical habitat (USDI-FWS 1973). In addition, westslope cutthroat trout and western pearlshell mussel are currently designated as sensitive species on the Lolo NF. As part of the National Environmental Policy Act of 1969, the U.S. Forest Service (USFS) is required, through a biological evaluation (BE), to review activities to determine their potential effect on sensitive species and avoid or minimize impacts and/or analyze the significance of potential adverse effects on these species and their habitat within the area of concern (FSM ). To meet these requirements, a combined Biological Assessment (BA) and Biological Evaluation (BE) that addresses the potential biological effects of the proposed project on bull trout and bull trout critical habitat, westslope cutthroat trout, and western pearlshell mussel would be prepared following selection of the desired alternative. Federal Clean Water Act: Forest management practices with the potential to affect water quality are governed by the Federal Water Pollution Control Act Amendments of 1972 referred to as "The Clean Water Act of 1972" (CWA). This Act (Public Law ), as amended in 1977 (Public Law 5

6 95-217) and 1987 (Public Law 100-4), was intended by Congress to provide a means to protect and improve the quality of the water resources and maintain their beneficial uses. The CWA (sections 208 and 319) recognized the need for control strategies for nonpoint source pollution. To provide environmental protection and improvement emphasis for water and soil resources and waterrelated beneficial uses, the National Nonpoint Source Policy (December 12, 1984), the Forest Service Nonpoint Strategy (January 29, 1985), and the U. S. Department of Agriculture Nonpoint Source Water Quality Policy (December 5, 1986) were developed. Soil and water conservation practices were recognized as the primary control mechanisms for nonpoint sources of pollution on NFS lands. This perspective is supported by the Environmental Protection Agency (EPA) in their guidance, "Nonpoint Source Controls and Water Quality Standards" (August 19, 1987). Section 404 of the CWA outlines the permitting process for discharging dredged or fill material into waters of the United States, including wetlands. The U.S. Army Corps of Engineers administers the 404 program. Under Section 401 of the Act, states and tribes may review and approve, set conditions on, or deny Federal permits (such as 404 permits) that may result in a discharge to State or Tribal waters, including wetlands. Applications for Section 404 permits are often joint 404/401 permits to ensure compliance at both the State and Federal levels. Federal agency compliance with water pollution control mandates are addressed through section 313 of the CWA and in Executive Order of January 23, Agency compliance is to be consistent with requirements that apply to "any nongovernmental entity" or private person. Compliance is to be in line with "all Federal, State, interstate, and local requirements, administrative authority, and process and sanctions respecting the control and abatement of water pollution". The National Core BMP Program was developed to improve agency performance and accountability in managing water quality consistent with the Federal CWA and State water quality programs (USDA-FS 2012). Current Forest Service policy directs compliance with required CWA permits and State regulations and requires the use of BMPs to control nonpoint source pollution to meet applicable water quality standards and other CWA requirements. The Lolo NF upholds the Federal CWA through the application and enactment of appropriate federal and state water quality protection permits, the application of BMPs and monitoring for effectiveness, and by participating with the State of Montana in BMP forestry audits, water quality data collection, and implementation of Total Maximum Daily Loads (TMDLs) and Water Quality Restoration Plans (WQRPs). BMPs were designed with the purpose to avoid, minimize, or mitigate adverse effects to soil, water quality, and riparian resources that may result from management activities. National Core BMPs (USDA-FS 2012), State of Montana BMPs (Logan 2001) and Lolo NF BMPs would be applied to the proposed project. Montana Water Quality Act: describes water quality management requirements, water classifications, and water quality standards for the State of Montana. The Lolo NF participates with the Montana Department of Environmental Quality (DEQ) towards the protection of water quality through the application of BMPs, water quality data collection, and implementation of TMDLs and WQRPs. Montana Stream Protection Act: The Lolo NF participates in the 124 permitting process with the Montana Department of Fish, Wildlife & Parks when Forest projects affect any stream bed and/or bank areas (e.g., culvert and stream rehabilitation projects). If during construction stream turbidity and sediment loads are anticipated to exceed state water quality standards, a 3A authorization is acquired from the Montana DEQ. 6

7 Memorandum of Understanding and Conservation Agreement for Westslope Cutthroat Trout and Yellowstone Cutthroat Trout in Montana (2007) This agreement is a collaborative and cooperative effort among resource agencies, conservation and industry organizations, tribes, resource users, and private landowners to reduce threats that currently warrant the designation of these two subspecies as Sensitive Species by the Forest Service (MCTSC 2007). The agreement outlines management goals and associated objectives for conservation of cutthroat trout in Montana. The management goals for cutthroat trout in Montana are to: 1) ensure the long-term, self-sustaining persistence of each subspecies distributed across their historical ranges as identified in recent status reviews; 2) maintain the genetic integrity and diversity of non-introgressed populations, as well as the diversity of life histories, represented by remaining cutthroat trout populations; and 3) protect the ecological, recreational, and economic values associated with each subspecies. One objective particularly important to the Marshall Creek westslope cutthroat trout population is Objective 1: maintain, secure, and/or enhance all cutthroat trout populations designated as conservation populations, especially the genetically pure components. Species Habitat Requirements Bull Trout (Salvelinus confluentus) USFWS Status: Listed as a threatened species within Columbia River Basin on July 10, 1998 USFS Region 1 Status: Sensitive The following discussion of bull trout habitat requirements in Montana is taken directly from the Montana Bull Trout Scientific Group publication (MBTSG 1998, pg i-ii, citations within), with some additional information: The majority of migratory bull trout spawning in Montana occurs in a small percentage of the total stream habitat available. Spawning takes place between late August and early November, principally in 3 rd and 4 th order streams. Spawning adults use low gradient areas (less than 2 percent) of gravel/cobble substrate with water depths between 0.1 and 0.6 meters and velocities from 0.1 to 0.6 meters per second to construct a redd (nest). Proximity of cover for the adult fish before and during spawning is an important habitat component. Spawning tends to be concentrated in reaches influenced by groundwater where temperature and flow conditions may be more stable. The relationship between groundwater exchange and migratory bull trout spawning requires more investigation. Successful incubation of bull trout embryos requires water temperatures below 8 C (46.4 F), less than 35 to 40 percent of sediments smaller than 6.35 millimeters in diameter, and high gravel permeability. Eggs are deposited as deep as 25.0 centimeters below the streambed surface and the incubation period varies depending on water temperature. Spawning adults alter streambed characteristics during redd construction to improve survival of embryos, but conditions in redds often degrade during the incubation period. Mortality of eggs or fry can be caused by scouring during high flows, freezing during low flows, superimposition of redds, or deposition of fine sediments or organic materials. A significant inverse relationship exists between the percentage of fine sediment in the incubation environment and bull trout survival to emergence (Bowerman et al. 2014). Entombment appeared to be the largest mortality factor in incubation studies in the Flathead drainage. Groundwater influence plays a large role in embryo development and survival by mitigating mortality factors. Rearing habitat requirements for juvenile bull trout include cold summer water temperatures (less than 15 C, (59 F)) provided by sufficient surface and groundwater flows. Warmer temperatures are associated with lower bull trout densities and can increase the risk of 7

8 invasion by other species that could displace, compete with, or prey on juvenile bull trout. Juvenile bull trout are generally benthic foragers, rarely stray from cover, and prefer complex forms of cover. High sediment levels and embeddedness can result in decreased rearing densities. Unembedded cobble/rubble substrate is preferred for cover and feeding and also provides invertebrate production. Highly variable streamflow, reduction in large woody debris, bedload movement, and other forms of channel instability can limit the distribution and abundance of juvenile bull trout. Habitat characteristics important for juvenile bull trout of migratory populations are also important for stream resident subadults and adults. However, stream resident adults are more strongly associated with deep pool habitats than are migratory juveniles. Both migratory (fluvial/river-dwelling or adfluvial/lake-dwelling) and stream-resident bull trout move in response to developmental and seasonal habitat requirements. Migratory individuals can move great distances (up to 250 kilometers (155 miles)) among lakes, rivers, and tributary streams in response to spawning, rearing, and foraging habitat needs. Streamresident bull trout migrate within tributary stream networks for spawning purposes, as well as in response to changes in seasonal habitat requirements and conditions. Open migratory corridors, both within and among tributary streams, larger rivers, and lake systems are critical for maintaining bull trout populations. Westslope Cutthroat Trout (Oncorhynchus clarki lewisi) USFWS Status: Not warranted under the Endangered Species Act USFS Region 1 Status: Sensitive Westslope cutthroat trout have two distinctive life forms: migratory and resident. Migratory life forms are either fish that spend most of their adult lives in lakes (adfluvial) or rivers (fluvial) and migrate into tributaries to spawn. Resident cutthroat trout generally spend their entire lives in the tributaries where they were reared and are usually much smaller than their migratory counterparts. Spawning takes place from March to early July with water temperature near 10 C (50 F) (McIntyre and Rieman 1995). Westslope cutthroat trout begin to sexually mature at age three and usually are spawning by ages four and five (McIntyre and Rieman 1995). Spawning adults can be as small as 15 centimeters with females containing as few as 100 eggs (Meehan and Bjornn 1991). Fry emerge from spawning gravels from June to mid-july and usually stay within their natal streams from one to four years (if they are the migratory form). Western Pearlshell Mussel (Margaritifera falcata) USFWS Status: No status USFS Region 1 Status: Sensitive The western pearlshell mussel has similar habitat requirements of westslope cutthroat, thus both have similar home ranges across western and south-central Montana (Stagliano and Maxell 2010). The western pearlshell prefers stable gravels and pebbles in small to medium cold water rivers typical of Rosgen classification C channel morphology (relatively sinuous, with well-developed floodplain, channel slope of 2% or less and a riffle/pool configuration (Rosgen 1996)) (Stagliano 2010) and relatively stable substrates (Nedeau et al. 2009). Substrate composition is usually composed of sand, gravel, and cobbles that are open graded enough to allow for physical movement and water percolation. In steeper streams, larger boulders may provide small suitable sites immediately downstream. In larger streams, the streambank provides for flow disruption and energy dissipation which can result in the formation and maintenance of desired substrates. The species seems to be intolerant of excess sedimentation. Burial by suction dredge tailings in a Washington stream demonstrated a high mortality rate because the mussels were not able to 8

9 excavate themselves out. Krueger et al. (2007) and Nedeau et al. (2009) cite studies where an increase in sand and gravel in the Snake River resulted in high mortality. Individual western pearlshell mussels can be long lived (100 years), but likely average 50 to 70 years. The life history of freshwater mussels consists of four basic life stages: reproductive, larval or parasitic, juvenile, and adult (Stagliano 2010). The larval stage (glochidium) must briefly parasitize a vertebrate host (typically a fish) in order to complete its development. The western pearlshell mussel is perhaps the most specialized, evolving with westslope cutthroat trout and has a host preference to salmonids of the genus Oncorhynchus (Stagliano 2010). Breeding is thought to occur during the early spring and the release of glochidia occurs during late spring and early summer. Glochidia attach to the gills of host fish where they transform to a cyst and reside (and are transported) for several weeks to months. The cysts eventually release from the gill structure and fall to substrate where they burrow in and eventually mature to an adult. This dependency to fish has resulted in the same connected perils of habitat modifications, water temperature changes, and instream barriers that impair many of our inland native fish species. Analysis Area Boundary and Data Sources The analysis area for direct and indirect effects on aquatic resources is defined as the Lower Rattlesnake 6 th code HUC (which encompasses both the middle & lower Rattlesnake 7 th code HUCs as described in the Hydrology Specialist s Report), and the Marshall Creek portion (7 th code HUC) of the larger Clark Fork River-Marshall Creek 6 th code HUC (see map in Figure 1). This area corresponds with project level effects, which will be described in further detail in the Environmental Consequences section. However, for fish species population effects and cumulative effects, the analysis area is expanded to include the entire Rattlesnake Creek watershed boundary (encompassing the Upper Rattlesnake 6 th code HUC as well). This area corresponds with the baseline assessment described below, and effects at the 6 th code HUC scale. This area was selected because activities that have occurred or are occurring upstream of proposed activities may influence habitat or populations downstream, and both watersheds contain migratory fish that may forage, migrate, and overwinter throughout the watersheds. The area was not expanded to include the Clark Fork River because effects of the project would be diluted at that scale. Multiple site visits to various portions of the project area by hydrology and fisheries personnel were conducted during the summers of 2009, 2010, and Field visits were to collect qualitative information on road and trail systems, stream crossings, stream and riparian area conditions, and fish species presence/absence. GIS data displaying Forest Plan MAs, streams, existing roads and trails, fire and timber harvest histories, land ownership, topography, and soils were considered to describe and evaluate the existing condition and effects. As part of the listing of bull trout under the Endangered Species Act, the USFWS developed a systematic process defined as A Framework to Assist in Making Endangered Species Act Determinations of Effect for Individual or Grouped Actions at the Bull Trout Subpopulation Watershed Scale (USDI-FWS 1998b). The framework was developed to include the biological and habitat elements needed to evaluate baseline conditions and effects of proposed and ongoing land management activities on the persistence and potential recovery of bull trout. It was also designed to facilitate and standardize determinations of potential effects resulting from management activities. The framework involves a systematic assessment through a matrix of seven diagnostics/pathways and a series of four species indicators and 19 habitat indicators. This assessment through the matrix leads to a condition rating of functioning appropriately (FA), functioning at risk (FAR), or functioning at unacceptable risk (FUR) for each of the indicators. These ratings are then integrated into one determination for each 6 th field HUC. 9

10 Analysis of the habitat indicators also provides a thorough evaluation of the baseline condition and potential effects of management activities on the primary constituent elements (PCEs) of designated bull trout critical habitat. A crosswalk between the bull trout matrix of pathways and indicators and PCEs of designated critical habitat is displayed in the Environmental Consequences section as associated with individual indicators. Following the listing of bull trout and the consultation process defined within USDI-FWS 1998b, the Lolo NF conducted an analysis using many GIS parameters as well as local survey data and knowledge, and navigated through the systematic assessment process to document the baseline condition of bull trout populations and habitat by 6 th field HUC (USDA-FS 2000). The Lolo NF periodically updates the bull trout baseline assessment as more data is gathered to help document identifiable status changes to habitat or the subpopulation (USDA-FS 2007, 2010a). Due to the comprehensive nature of the framework and the baseline assessment, and the similarity of habitat requirements, the systematic process is also used to assess the status and potential impacts of management activities on westslope cutthroat trout and western pearlshell mussels. For the Marshall Woods project, the bull trout baseline assessment information was combined with existing site-specific Forest Service and Montana Fish, Wildlife and Parks (MFWP) survey data to assess the distribution, relative abundance, and trends of aquatic species and habitat within the Rattlesnake Creek and Marshall Creek watersheds. Local biologists familiar with the project area also provided knowledge of habitat and fish population conditions and past activities conducted on non-nfs lands (Shane Hendrickson, USFS Fisheries Biologist and Ladd Knotek, MFWP Fisheries Biologist). The interaction of roads and streams, particularly with regard to road density, road encroachment (proximity) and sediment delivery, is an important factor in the evaluation of the existing condition and potential effects of management activities within a watershed. Sediment contributed from roads and delivered to streams can affect water quality, channel morphology, quality of instream habitat, and the behavior, growth, and survival of aquatic species. A description of how these issues were analyzed can be found within the Analysis Data Sources and Methods section in the Hydrology Specialist s Report. Similarly, road density and encroachment analyses, sediment delivery modeling, and water yield modeling were conducted by the project hydrologist and are discussed in detail in the Existing Conditions and Environmental Consequences sections within the Hydrology Specialist s Report. Culverts and stream crossings increase the connectivity of the road system to the stream system, and thus increase the potential for sediment to be delivered to streams. Improperly sized culverts can lead to changes in channel morphology via erosion and deposition, and can create velocity barriers or jump heights that aquatic species cannot navigate through, thus fragmenting habitat and increasing the risks of genetic isolation. There are two sites within the Rattlesnake watershed that are monitored through PIBO (Pacfish- Infish Biological Opinion) Effectiveness Monitoring efforts (USDA-FS 2013). One site is located on Rattlesnake Creek in the headwaters, well above the proposed project site, and the other is located within the project area on Spring Gulch, a tributary to Rattlesnake Creek. There are no other recent rigorous habitat surveys of Rattlesnake Creek near the project area, so baseline assessment information and field survey observations will be used to address the status of INFISH RMOs. 10

11 Figure 1. Map displaying the aquatic analysis areas, bull trout baseline determinations, and bull trout critical habitat. 11

12 Existing Conditions The two major watersheds within the immediate project area are Marshall Creek and Rattlesnake Creek (including Woods Gulch and the lower portion of Spring Gulch). All other mapped tributaries are largely ephemeral. Complete descriptions of the basic characteristics and features influencing the existing condition of these watersheds including land ownership, climate and hydrology, stream channel characteristics, water quality, road densities and road encroachment, and watershed improvement activities can be found in the Existing Conditions section within the Hydrology Specialist s Report, and therefore are not repeated within this report. Factors influencing aquatic populations will be emphasized below, but primary concerns are focused on proposed management activities that occur near, or have the potential to affect stream channels that are known to contain aquatic species. Aquatic Habitat The Lolo NF baseline assessment rated each of the 19 habitat indicators and the 4 species indicators for each of the three 6 th code HUCs within the Rattlesnake and Marshall Creek watersheds, which can be found in Table 1 below (USDA-FS 2007, 2010a). The Lower and Upper Rattlesnake Creek 6 th code HUCs are listed as Functioning at Risk for most habitat and species indicators, whereas the Clark Fork River Marshall Creek 6 th code HUC is listed as Functioning at Unacceptable Risk for most habitat and species indicators. The baseline information is combined with site-specific data and local knowledge of the project area to assess aquatic habitat and species condition. Due to limitations with the large-scale, primarily GIS-based baseline assessment, sitespecific information led to some minor changes in the 2010 baseline calls for specific indicators: the indicator for Physical Barriers in Marshall Creek was changed from FA to FAR; and the indicator for Floodplain Connectivity in the Lower and Upper Rattlesnake was changed from FUR to FAR. 12

13 Table 1. Status of Baseline Conditions with Site-Specific Information for the Upper Rattlesnake Creek, Lower Rattlesnake Creek and Clark Fork River Marshall Creek 6th Field HUCs. (FUR = Functioning at unacceptable risk, FAR = Functioning at risk, FA = Functioning appropriately). Diagnostic Pathways: Indicators Upper Rattlesnake Creek Lower Rattlesnake Creek Clark Fork River Marshall Creek HABITAT Pathways: Indicators Water Quality: Temperature FAR FAR FUR Sediment FAR FAR FUR Chemical Contaminants / Nutrients FAR FAR FUR Habitat Access: Physical Barriers FA FA FAR Habitat Elements: Substrate Embeddedness FAR FAR FUR Large Woody Debris FAR FAR FUR Pool Frequency & Quality FAR FAR FUR Large Pools FAR FAR FUR Off-Channel Habitat FAR FAR FUR Refugia FA FA FUR Channel Condition & Dynamics: Wetted Width/Max Depth Ratio FA FA FUR Streambank Condition FA FA FUR Floodplain Connectivity FAR FAR FUR Flow & Hydrology: Change in Peak/Base Flows FA FA FUR Drainage network Increase FA FA FUR Watershed Conditions: Road Density & Location FUR FUR FUR Disturbance History FA FA FA Riparian Conservation Area FAR FAR FAR Disturbance Regime FAR FAR FAR Integration of Habitat Determination FAR FAR FUR SPECIES Pathways: Indicators Subpopulation Characteristics: Subpopulation Size FAR FAR FUR Growth & Survival FAR FAR FUR Life History Diversity & Isolation FAR FAR FUR Persistence and Genetic Integrity FAR FAR FUR Integration of Species Determination FAR FAR FUR Integration of Species & Habitat Condition FAR FAR FUR 13

14 Rattlesnake Creek Rattlesnake Creek drains high elevation watersheds and maintains relatively stable base flows throughout the winter and summer. Due to the undeveloped nature of the upper watershed, water quality and instream habitat is generally regarded as high quality. Prior to the wilderness designation, differing land uses including logging, road development, and dam construction all occurred in the watershed and had varying levels of undesirable effects on aquatic habitat and aquatic species. The effect of the dams in the headwaters on stream temperature is unknown. Stream gradients are relatively steep, so bull trout habitat is naturally limited. Wildfires were historically a major disturbance factor. A large portion of the Rattlesnake watershed burned in the wildfire of Only small wildfires have occurred since then, most recently in the headwaters of Pilcher Creek upstream of the project area. Fires are actively suppressed within the project area and have been since the advent of the Fire Control Policy of The main access road leading up to the dams (Forest Road #99/Trail #515) is along the valley bottom, and likely influenced the baseline indicator call of functioning at unacceptable risk for road density and location for both 6 th code HUCs. However, the road is restricted for administrative use only, and has a low impact on sediment or large woody debris and temperature/shading because it has a low gradient and is located up on the high terrace with adequate buffering distance from the Rattlesnake floodplain for most of its length (Figure 2A). Still, there are areas in need of BMPs/drainage improvements, particularly in areas where the road curves near the stream (Figure 2B). Since 1999, the Forest Service has replaced four culverts with bridges on upper Rattlesnake tributaries. The stream corridor has a long history of impacts, including riparian logging and log drives down the stream channel. These activities likely had a devastating effect on aquatic habitat and fish populations through the removal of riparian vegetation and shading, loss of large woody debris jams and the associated pools and spawning and overwintering habitat. Field surveys indicated sections of creek have a fairly healthy riparian corridor with abundant acting and potential large woody debris, but there were also areas where large woody debris was lacking and the surrounding riparian had young trees, indicative of historic harvesting. Currently there are no stream crossings that limit the movement of large woody debris in the system (all are bridges). There is no hazard tree or firewood cutting in the upper watershed, but hazard tree removal in the lower watershed, primarily associated with private lands and recreation sites likely contributes to a loss of large woody debris within RHCAs. Development is apparent in the Lower Rattlesnake HUC as ownership shifts to approximately 60% NFS lands and 40% private. This HUC also supports important rearing habitat for the local bull trout population in Rattlesnake Creek (USDA-FS and USDI-FWS 2013). Roads in the upper portion of the Lower Rattlesnake Creek HUC are in low density and most are under Forest Service jurisdiction, whereas high densities of private and county roads dominate the lower portion. The Mountain Water Company dam was constructed in 1903, and the lower reaches of Rattlesnake Creek below the dam are extensively developed, with small ranchettes and subdivisions along both banks for most of the 5 mile reach. This infrastructure and development has altered stream form and function and has resulted in channel straightening, loss of side channels, loss of riparian vegetation, loss of woody debris, and reduced complexity and quality of fish habitat. In 2002, the City of Missoula and the Greenough Park Advisory Committee sponsored a project on Lower Rattlesnake Creek that reconstructed a side channel of the creek and improved floodplain access. In 2010, the City of Missoula completed mainline construction on the Rattlesnake Valley Sewer Project, a special improvement district to connect the remaining homes in the Rattlesnake to sewer (replacing densely packed septic tanks). There are six relatively large diversions which take 14

15 a significant flow volume (up to 32 cfs) out of the stream throughout the summer. While four of these diversions now have fish screens, the operation and maintenance of the screens is problematic and not always effective in eliminating entrainment of native fish. Stream temperatures in the lower reaches of Rattlesnake Creek regularly approach 18 C (64.4 F), which is of concern for supporting cold water species like bull trout and cutthroat. Temperatures are likely affected by the presence and operation of the Mountain Water Company Dam as well as other developments and associated vegetation removal. Figure 2. Forest Road #99/Trail #515. A. Photo taken from Forest Road #99/Trail #515 running along the high terrace above Rattlesnake Creek with adequate buffer distance to minimize or eliminate effects on shading/temperature, sediment and large woody debris. B. Forest Road #99/Trail #515 running along the high terrace above Rattlesnake Creek in an area near Unit 2 that curves near the stream and is need of BMP improvements to route water onto vegetated areas away from the stream. Recreational use is high due to the proximity of the area to Missoula and the opportunities available via the existing road and trail network near and within the RNRA. Missoula s growing population and the desires of multiple recreation users results in a number of user-created trails across the landscape. Due to concern about the natural resource damage some of them were causing, in 2002 the Missoula Ranger District initiated an analysis of the system and non-system trails in the RNRA. The Forest issued a Decision Notice in 2005 which designated areas for use and monitoring, improved trails, and closed some trails to reduce resource damage in steep or erosive areas (USDA- FS 2005). Overall, bank trampling and erosion associated with trail use is localized to small areas and does not continue for long channel distances. Concern is raised for these areas when they expand in size, or occur in important spawning areas. The Forest continues to monitor, improve, and eliminate portions of the trail system as necessary to help decrease resource damage (see Recreation Specialist s Report). The Forest implemented a project in Spring 2014 to stabilize a 15

16 user-created access point on Rattlesnake Creek to decrease bank trampling and eliminate a chronic sediment source (Figure 3A). Figure 3. Recreation-based bank stabilization projects completed in 2014 to protect stream habitat within the project area. A. Rattlesnake Creek user-created access point before and after bank stabilization and revegetation treatments to limit expansion of the area and reduce bank erosion. B. Spring Gulch trail before and after bank stabilization treatments using native materials to reduce bank erosion. Spring Gulch Spring Gulch is the only perennial tributary (third-order) to Rattlesnake Creek within the project area. There is a PIBO (Pacfish-Infish Biological Opinion) monitoring site near the mouth that is treated as a reference site, representing a minimally managed condition. In the spring of 2014, the Forest repaired a small area where the recreational trail was actively eroding into the creek. Through the use of brush, woody debris, and hand labor, the Forest was able to re-route the flow and reduce erosion near the trail (Figure 3B). Woods Gulch Woods Gulch is a second-order intermittent tributary, but lacks a surface connection to Rattlesnake Creek. Surface flow is captured in the Quast irrigation ditch which may overtop to spill into Rattlesnake Creek for only a few weeks a year during high flows. Fish may have inhabited Woods Gulch in the past, as there are anecdotal accounts of cutthroat, but it was sampled in 2009 by Forest Service crews and no fish were found. 16

17 Marshall Creek Marshall Creek is a third-order perennial tributary to the Clark Fork River with a narrow, high gradient valley. As summarized in the Hydrology Specialist s Report, the creek has been subject to a number of disturbances: extensive timber harvest and ski area development in the headwaters; a dense network of roads including the main County Road #357 which is within the RHCA of Marshall Creek for most of its length and has multiple undersized crossings, impoundments that truncate fish habitat and genetically isolate the fish population; and private land developments. Roads have a large influence on the Marshall Creek watershed, with approximately 11 miles within 300 feet of streams, 4.5 miles within 100 feet of streams, and a crossing frequency of 4 times for every one square mile of road. Although the immediate streamside riparian area is vegetated along Marshall Creek, the full RHCA buffer of 300 on a fish-bearing stream is nonexistent due to the presence of roads. This likely influences temperature (due to reduced density of large trees for overhead canopy cover), large woody debris recruitment, sediment delivery, and floodplain connectivity. The effect of the recent fill slope failure on Highway 200 near the mouth at the Clark Fork River is unknown, and did not impact the fish ladder, but may have influenced the lower end of the channel. MFWP, in conjunction with private landowners, has completed a number of major habitat and fisheries improvement projects within the lower 2 miles of Marshall Creek (below the first impoundment). These efforts include: a fish ladder at the mouth on the Clark Fork River, two culvert replacements on private property, a fish screen, large woody debris additions in four reaches, and riparian fencing on private property. The partial barrier at the undersized culvert on FS road #2122 (proposed for replacement within the Marshall Woods action alternatives), two culvert barriers on County Road #357, and the private land impoundments at and above stream mile 2.0 continue to fragment fish habitat and genetically isolate fish. Aquatic Species Bull Trout Rattlesnake Creek is the only creek that is known to support a bull trout population within the project area. Both Spring Gulch and Marshall Creek have been sampled via electrofishing, but bull trout have not been detected. The Bull Trout Draft Recovery Plan (USDI-FWS 2002) as updated by the USFWS status review in (USDI-FWS 2008) delineates Rattlesnake Creek as one of the seven local populations within the Clark Fork River Section 2 (Milltown Dam to Flathead River) Core Area of the Clark Fork River Recovery Unit. Rattlesnake Creek is also designated critical habitat for bull trout under the USFWS (2010) final rule (Figure 1). Within the Clark Fork River Section 2 Core Area (hereafter referred to as the MCFR Middle Clark Fork River Core Area), distributions of bull trout are largely restricted from historical patterns, bull trout densities have declined, and the proportion of fluvial to resident forms is likely much different than historically (USDA-FS and USDI-FWS 2013). Historic management activities that resulted in the modification of habitat conditions in Rattlesnake Creek (decreasing large debris jams or increasing fine sediment) likely have a large influence on the population today. Redd numbers for the seven local populations in the MCFR Core Area are very low. Although bull trout spawning occurs in other tributaries, the vast majority of fluvial spawning occurs in four areas - Rattlesnake Creek, Fish Creek, Little Joe Creek (St. Regis River), and Cedar Creek. Redd counts in index reaches tend to be highest in Fish Creek and Rattlesnake Creek. Although annual variability is high, redd counts in all index reaches combined average approximately These numbers suggest that over the entire MCFR Core Area, the fluvial adult bull trout population currently ranges from about 120 to 300 fish annually. The declines are largely attributed to habitat alteration, fragmentation and loss, and introduction of nonnative species (USDA-FS and USDI-FWS 2013). Rattlesnake Creek is the uppermost large tributary in the MCFR Core Area, lying just downstream of the confluence of the Blackfoot and Upper Clark Fork Rivers. The Rattlesnake Creek local 17

18 population has high significance to the MCFR Core Area. In 1903, Mountain Water Company Dam was constructed approximately 5 miles up from the mouth of Rattlesnake Creek, effectively eliminating all upstream migration of fluvial bull trout. The dam negatively impacted the population for nearly a century. In 2001, a cooperative interagency project was initiated with the intent to improve passage at the dam. From , MFWP and Lolo NF personnel manually moved large, migratory fish past the dam until a fish ladder was installed to allow passage in April The current distribution of bull trout is probably similar to historic, with some restrictions due to the smaller overall population size. MFWP conducts annual redd counts in select index reaches where spawning tends to be concentrated. These spawning reaches are located upstream of the project area, with incidental spawning occurring in other locations throughout the mainstem. Rattlesnake Creek within the project area is largely considered a migratory corridor and rearing habitat (MFWP, unpublished data). Although fluvial redd counts have been variable from 4 to 36 in the past 15 years, Rattlesnake Creek generally supports the second highest number of redds amongst the local populations in the MCFR Core Area. Redd counts prior to 2000 averaged about 12 per year and then increased substantially as a result of manual transport and installation of the fish ladder at Mountain Water Company Dam in Redd counts appeared to remain relatively stable until Milltown Dam was removed in 2008, and from 2009-present, redd numbers in index reaches have remained relatively low, (ranging from 4 to 15). It is unclear what proportion of the decrease in redds within Rattlesnake Creek is attributable to the removal of Milltown Dam (and the ability of some fish to return to their natal streams in the Blackfoot or Upper Clark Fork Rivers), the possibility that some fluvial spawners died or moved out of the area as a result of metals and sediment suspension, or simply natural variability in the spawning population. Monitoring via redd counts will continue into the future to determine the general population trend. Rattlesnake Creek is the only south facing drainage in the MCFR Core Area with a measurable fluvial bull trout population. It is unclear what effect the aspect, historic management activities, or dams in the headwater lakes have on current temperature patterns, but the fact that temperatures in the lower reaches regularly approach 18 C is of concern (MFWP, unpublished data), particularly when future climate projections and interactions with non-native species are taken into account (Rieman et al. 2007, Rieman and Isaak 2010, Wenger et al. 2011, Isaak et al. 2012). Effects of nonnative species are discussed below. Westslope Cutthroat Trout Westslope cutthroat trout are well distributed throughout the project area, and are found within Rattlesnake Creek, Spring Gulch, and Marshall Creek. Rattlesnake Creek supports both fluvial and resident westslope cutthroat trout that are connected to the Clark Fork since the ladder installation on the Mountain Water Company dam in Prior to passage, the dam had a pronounced effect on fluvial cutthroat. Estimates of individuals congregated at the dam during spawning migrations in late May-early June, so successful passage there has an obvious benefit for cutthroat as well (Knotek 2004). Additional tagging information collected at the time of ladder evaluation and construction ( ) indicated that cutthroat from Rattlesnake Creek span the Clark Fork River from 5 miles upstream to 25 miles downstream of Rattlesnake Creek. This indicated that Rattlesnake Creek is an important source population of cutthroat to a large portion of the Clark Fork River near Missoula (Knotek 2004). Westslope cutthroat are well distributed throughout the mainstem of Rattlesnake Creek in moderately high densities, averaging around 24 fish/100m, and the area throughout the project area is used as spawning and rearing habitat (MFWP, unpublished data). Although some tributaries are fishless, others hold similar densities of cutthroat as well. The replacement of culverts with bridges likely had a marked benefit for cutthroat in the Rattlesnake watershed. Spring Gulch supports a similar density of cutthroat per 100M, although non-native brook trout are also present. In the lower reaches of Rattlesnake Creek (near the project area), 18