United States 

Department of

Agriculture

Forest 

Service

July 2017

Aquatics Resources

Report

Craggy Vegetation Management Project

Salmon/Scott Ranger District, Klamath National Forest

Siskiyou County, California

For Information Contact: Brian Thomas

Supervisors Office

Yreka, CA

(530)-841-4547

Non-Discrimination Policy

The U.S. Department of Agriculture (USDA) prohibits discrimination against its customers, employees, 

and applicants for employment on the bases of race, color, national origin, age, disability, sex, gender 

identity, religion, reprisal, and where applicable, political beliefs, marital status, familial or parental status, 

sexual orientation, or all or part of an individual's income is derived from any public assistance program, 

or protected genetic information in employment or in any program or activity conducted or funded by the 

Department. (Not all prohibited bases will apply to all programs and/or employment activities.)

To File an Employment Complaint

If you wish to file an employment complaint, you must contact your agency's EEO Counselor (PDF) within 

45 days of the date of the alleged discriminatory act, event, or in the case of a personnel action. 

Additional information can be found online at www.ascr.usda.gov/complaint_filing_file.html.

To File a Program Complaint

If you wish to file a Civil Rights program complaint of discrimination, complete the USDA Program 

Discrimination Complaint Form (PDF), found online at www.ascr.usda.gov/ complaint_filing_cust.html, or 

at any USDA office, or call (866) 632-9992 to request the form. You may also write a letter containing all 

of the information requested in the form. Send your completed complaint form or letter to us by mail at 

U.S. Department of Agriculture, Director, Office of Adjudication, 1400 Independence Avenue, S.W., 

Washington, D.C. 20250-9410, by fax (202) 690-7442 or email at program.intake@usda.gov.

Persons with Disabilities

Individuals who are deaf, hard of hearing or have speech disabilities and you wish to file either an EEO or 

program complaint please contact USDA through the Federal Relay Service at (800) 877-8339 or (800) 

845-6136 (in Spanish).

Persons with disabilities who wish to file a program complaint, please see information above on how to 

contact us by mail directly or by email. If you require alternative means of communication for program 

information (e.g., Braille, large print, audiotape, etc.) please contact USDA's TARGET Center at (202) 

720-2600 (voice and TDD).

Aquatics Resource Report Craggy Vegetation Management Project

i

Table of Contents

Aquatics Resource Report .............................................................................................. 1

Introduction............................................................................................................................. 1

Methodology........................................................................................................................... 1

Analysis Indicators.............................................................................................................. 2

Analysis Indicators Excluded From Further Analysis........................................................ 3

Locations Excluded From Further Analysis....................................................................... 4

Summary of Analysis Indicators and Locations Retained for Analysis............................. 4

Measures (for Analysis Indicators)..................................................................................... 5

Spatial and Temporal Bounding of Analysis Area ............................................................. 9

Background............................................................................................................................. 9

Affected Environment....................................................................................................... 11

Environmental Consequences............................................................................................... 16

Alternative 1...................................................................................................................... 16

Direct and Indirect Effects............................................................................................ 16

Cumulative Effects ....................................................................................................... 16

Alternative 2...................................................................................................................... 17

Direct Effects................................................................................................................ 17

Indirect Effects.............................................................................................................. 18

Cumulative Effects ....................................................................................................... 33

Alternative 3...................................................................................................................... 34

Direct Effects................................................................................................................ 34

Indirect Effects.............................................................................................................. 35

Cumulative Effects ....................................................................................................... 36

Comparison of Alternatives.................................................................................................. 36

Compliance with law, regulation, policy, and the Forest Plan ............................................. 38

Literature Cited ..................................................................................................................... 39

Appendix A: Riparian Reserve Treatments............................................................................................ 42

Literature Cited ..................................................................................................................... 44

Appendix B: Life history and biological requirements of Pacific salmonids and lamprey .................... 45

References............................................................................................................................. 56

Appendix C: Table of Pathway and Indicators....................................................................................... 59

Klamath National Forest Matrix: Table of Population and Habitat Indicators for Use on the 

Klamath National Forest in the Northwest Forest Plan Area ............................................... 59

Aquatic Habitat Conditions Analysis Guidelines................................................................. 59

Literature Cited ..................................................................................................................... 67

Appendix D: Environmental Baseline and Proposed Effects Checklist................................................. 69

References:............................................................................................................................ 75

Appendix E: Distance between Fish Habitat and Treatments ................................................................ 76

List of Tables

Table 1: Summary of Analysis Species, Including Status of Each...............................................................2

Table 2: Actual and Potential Occupancy by Aquatic Species by 7th and 5th Field Watersheds.................11

Table 3: Baseline for Analysis Indicators for Anadromous Streams in the Project Area...........................15
Aquatics Resource Report Craggy Vegetation Management Project

ii

Table 4: Summary of the Effects on Salmonid Fish for Action Alternatives in the Craggy Project by 

Indicator and Project Element.............................................................................................................31

Table 5: Summary of the Effects on Salmonid Fish for Action Alternatives in the Craggy Project by 

Indicator and Project Element.............................................................................................................33

Table 6: Indicator Summary for Craggy Project Alternatives....................................................................36

Table 7: Summary of Determinations for Action Alternatives for the Craggy Project ..............................37

Table C-1: Klamath National Forest Tributaries Table of Pathways and Indicators..................................60

Table D-1: Pathway and Indicators for 7th Field Watershed: Lower Humbug Creek (for Humbug Creek)70

Table D-2: Pathway and Indicators for 7th Field Watershed: Upper Humbug Creek (for Humbug Creek 

above the Confluence with Middle Fork Humbug Creek)..................................................................71

Table D-3: Pathway and Indicators for 7th Field Watershed: Middle Fork Humbug Creek (for Middle 

Fork Humbug Creek and South Fork Humbug Creek).......................................................................72

Table D-4: Pathway and Indicators for 5th Field Watershed: Humbug Creek-Klamath River (for mainstem 

Middle Klamath River).......................................................................................................................73

Table E-1: Summary of Closest Distance between Project Activities and Anadromous Fish and Their 

Habitat (Including Critical Habitat) in 7th and 5th Field Watersheds ................................................76

List of Figures

Figure B-1: Craggy Project Fish Distribution Map ....................................................................................53
Aquatics Resource Report Craggy Vegetation Management Project

1

AQUATICS RESOURCE REPORT

Introduction

The purpose of this report is to discuss the effects of the Craggy Vegetation Management Project

(Craggy Project) on aquatic threatened, endangered and candidate species listed for protection 

under the Endangered Species Act. Threatened, endangered, and candidate species proposed for 

listing are designated by the U.S. Fish and Wildlife Service and National Marine Fisheries 

Service (also known as NOAA-Fish) under authority of the Endangered Species Act of 1973, as 

amended. The Endangered Species Act requires federal agencies ensure that any action 

authorized, funded, or carried out by such agency is not likely to jeopardize the continued 

existence of any endangered or threatened species or result in the destruction or adverse 

modification of those species’ habitat. Additionally, essential fish habitat consultation occurs 

under the Magnuson-Stevens Fishery Conservation and Management Act.

This report will also discuss the effect of the project on aquatic Forest Service sensitive and 

management indicator species. Federal law and direction applicable to sensitive aquatic species 

include the National Forest Management Act and Forest Service Manual (FSM 2670). Sensitive 

species are classified at the Regional level, and management indicator species by the Forest. 

Direction applicable to management indicator species is provided by the Klamath Land and 

Resource Management Plan (Forest Plan) which directs the Forest to manage streams and lakes 

“to maintain or improve habitat for aquatic species, especially TE&S [threatened, endangered 

and sensitive]” (forest-wide standard 9-1, page 4-34). The Forest Plan also provides direction to 

“prohibit and regulate activities in RRs [riparian reserves] that retard or prevent attainment of the 

Aquatic Conservation Strategy objectives” (Management Area 10 description, page 4-106). One 

of these objectives is to “maintain and restore habitat to support well-distributed populations of 

native plant, invertebrate and vertebrate riparian-dependent species (Forest Plan, page 4-6). 

Maintaining suitable fish habitat that will support well distributed, viable populations of native 

and desirable non-native fish is a part of providing biological diversity (Forest Plan, standard and 

guideline 6-7, page 4-22). To this end, the Forest has adopted an aquatic conservation strategy, 

including the designation of riparian reserves and standards and guidelines to maintain habitat 

for aquatic species (USDA 1995).

Methodology

A list of threatened, endangered, and candidate species was obtained online from the U. S. Fish 

and Wildlife Service on June 20, 2017 (USDI 2017). Species considered as Forest Service 

sensitive were compiled by the Forest Service Pacific Southwest Regional Office (the most 

recent update was in 2013). These lists were used as a basis for determining which aquatic

species were to be considered in this specialist report. See Table 1 for a summary. Terrestrial 

and semi-aquatic species, including amphibians, are analyzed in the Terrestrial Wildlife resource

report.

The only threatened or endangered fish in the analysis area is the Southern Oregon/Northern 

California Coasts Coho Salmon (Oncorhynchus kisutch), protections for which include their 

critical habitat. Sensitive fish species for the Klamath National Forest (Forest) in the project area 

are the Upper Klamath-Trinity Rivers Chinook (Oncorhynchus tshawytscha), Klamath 

Mountains Province steelhead (Oncorhynchus mykiss), Klamath River lamprey (Entosphenus 
Aquatics Resource Report Craggy Vegetation Management Project

2

similis), and Pacific lamprey (Entosphenus tridentatus). Both steelhead and resident rainbow 

trout (Oncorhynchus mykiss) are management indicator species in the Forest Plan. Additionally, 

essential fish habitat designation is associated with Coho and Chinook Salmon. See Table 1 for a 

summary of aquatic species in the Craggy Project. Since analyzed species have overlapping 

needs and habitat, the same analysis indicators are used to measure effects to all analysis species. 

These indicators are outlined in the following section.

Table 1: Summary of Analysis Species, Including Status of Each

Species

Endangered

Threatened

Forest Service Sensitive

Management Indicator 

Species

Critical Habitat

Essential Fish Habitat

Salmonids

Coho Salmon

(Southern Oregon/Northern California Coasts) Oncorhynchus kisutch X X X

Chinook Salmon (Spring/Fall runs) Oncorhynchus tshawytscha X X

(Upper Klamath-Trinity Rivers)

Steelhead Trout Oncorhynchus mykiss X X

(Klamath Mountains Province)

Rainbow Trout Oncorhynchus mykiss X

Lamprey

Pacific Lamprey Entosphenus tridentatus X

Klamath River Lamprey Entosphenus similis X

Data sources used to determine historic and current anadromous and resident salmonid 

distribution and habitat condition include:

• Forest geographic information system layers

• CalFish on-line database

• Habitat and fish presence surveys performed by Forest Service personnel or contractors

This information, as well as scientific literature, field review, project watershed and geology 

reports, and best professional judgment, was the basis for evaluating impacts to aquatic resources 

in the project area.

Information specific to the biological requirements of the species under consideration in this 

document is found in Appendix B.

Analysis Indicators

The analysis of the potential effects to fish and their habitat is organized by direct and indirect 

effects, and by effects to seventeen analysis indicators of anadromous fish habitat conditions.

The indicators originate from the “Analytical Process for Developing Biological Assessments for 
Aquatics Resource Report Craggy Vegetation Management Project

3

Federal Actions Affecting Fish within the Northwest Forest Plan Area” (Analytical Process)

(USDI, USDA, and NOAA 2004). Further discussion of the indicators is found in Appendix C. 

Effects of project elements to an indicator may be (1) neutral (no effect), (2) discountable 

(extremely unlikely to occur) or have insignificant (effects are not able to be meaningfully 

measured, detected, or evaluated), or (3) significant (effects able to be measured). Furthermore, 

effects may be either positive or negative. After the appropriate analysis indicators have been 

evaluated, the resulting information is used to determine overall effects on aquatic species, 

including Coho critical habitat and essential fish habitat.

Although the methodology for effects analysis only technically applies to anadromous fish 

within the project area (e.g., Coho, Chinook, and steelhead), it may also be used for resident 

rainbow trout to ensure a consistent assessment of fish species; and indirect effects to 

anadromous fish will serve as a proxy for lamprey. Additionally, indicators are used to assess the 

existing environment of anadromous systems, with each indicator labeled as to if it is “Properly 

Functioning,” “Functioning-At-Risk,” or “Not Properly Functioning” for a given stream 

(Appendix C, D).

Analysis Indicators Excluded From Further Analysis

The following indicators are to be excluded from analysis because project components will not 

affect anadromous fish, resident fish, lamprey or their habitat:

Chemical Contamination and Nutrients – Nutrient enrichment is not expected to change in 

area streams as a result of the actions proposed in this project, and no point sources are known. 

No fertilizers will be used.

Pool Frequency and Quality – Potential project related changes to the sediment regime are 

described by the substrate indicator under indirect effects. There will be no meaningful change to

sediment input and stream flows in fish-bearing reaches and, therefore, there will be no effect to 

pool frequency or quality.

Physical Barriers – There are human-made barriers on private land on lower Humbug Creek

which is within the project area footprint. Lower Humbug Creek supports Coho Salmon, 

steelhead trout and resident rainbow trout. Removal or modification of these barriers for fish 

passage is outside the scope of this project. No new barriers will be built as a consequence of this 

Project.

Off-Channel Habitat – Nearly all project area streams are on steep slopes with no off-channel 

habitat. Project activities are not adjacent to where off-channel or side channel habitat is present 

(Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek). There will be no 

effect to off-channel habitat.

Refugia – There will be no change in the ability of riparian or instream habitat elements to 

maintain present fish populations, and nor will connectivity between local and distal populations 

be altered.

Width to Depth Ratio – Potential project related changes to sediment composition are described 

by the substrate indicator under indirect effects. There will be no measurable change in sediment 

input in fish-bearing reaches and, thus, no change in channel morphology.

Streambank Condition – While some project units include activities which will occur within a 

riparian reserve, they are not inclusive of the streambanks of fish-occupied systems. Drafting 
Aquatics Resource Report Craggy Vegetation Management Project

4

will use existing access and no bank modification will occur because of the project design 

features included in all of the action alternatives.

Floodplain Connectivity – As peak or base flows are expected to maintain their proper 

functioning status, flow access from upper banks will continue to occur at expected rates.

Floodplains are generally not a significant component in mountainous channel types such as 

those present in most of the (non-anadromous) fish-bearing reaches of the project footprint. 

Additionally, the primary floodplain habitat within the project area is immediately adjacent to 

upper Humbug Creek, lower Humbug Creek, Middle Fork Humbug Creek, and South Fork 

Humbug Creek. Ground-disturbing project activities are not planned within the floodplains of 

these areas.

Road Density and Location – No new system roads will be constructed or decommissioned so 

there will be no change to road density or location.

Locations Excluded From Further Analysis

The following 7th field watersheds which have no fish resources, and thus no chance for effects 

to fish resources, are not carried further in the analysis:

• Clear Creek – Clear Creek is the principal stream of this 7th field watershed. Clear Creek 

is an intermittent stream and is fishless.

• Long Gulch – Long Gulch is the principal stream of this 7th field watershed. Long Gulch 

is an intermittent stream and is fishless.

• Rocky Gulch-Yreka Creek – Rocky Gulch is the principal stream of this 7th field 

watershed. Rocky Gulch is an intermittent stream and is fishless.

• Greenhorn Creek – Greenhorn Creek is the principal stream of this 7th field watershed 

within the project area. This portion of the creek is above Greenhorn Reservoir (the dam 

blocks all anadromous fish migration). In addition, Greenhorn Creek upstream of the 

reservoir is intermittent and no resident rainbow trout are present.

• Yreka City-Yreka Creek – Humbug Gulch is the principal stream of this 7th field 

watershed within the Project area. Humbug Gulch is an intermittent stream and is 

fishless.

The Long Gulch, Rocky Gulch-Yreka Creek, Yreka City-Yreka Creek, and Greenhorn Creek 7th

field watersheds listed above are within the Yreka Creek-Shasta River 5th field watershed. Since 

these 7th field watersheds have no fish resources and are not carried further in the analysis, the 

Yreka Creek-Shasta River 5th field watershed will also not be carried further in the analysis.

Summary of Analysis Indicators and Locations Retained for Analysis

The following analysis indicators are potentially affected by the Project and will undergo further 

discussion:

• Temperature

• Sediment and Substrate

• Turbidity

• Large Woody Debris
Aquatics Resource Report Craggy Vegetation Management Project

5

• Disturbance History and Regime

• Peak and Base Flows

• Drainage Network

• Riparian Reserves

7th Field Watershed Scale

Lower Humbug Creek

Humbug Creek is the principal stream of this 7th field watershed within the Project area. Coho 

Salmon, Steelhead trout, resident rainbow trout, and Pacific lamprey are found in Humbug 

Creek. Chinook Salmon are not present in Humbug Creek due to the fact that the portion of 

Humbug Creek from the Klamath River confluence to approximately one quarter mile upstream 

is dry during the time that adult Chinook Salmon are present in the Klamath River.

Middle Fork Humbug Creek

Middle Fork Humbug Creek and South Fork Humbug Creek are the principal streams of this 7th

field watershed within the project area. Steelhead trout and resident rainbow trout are found in 

Middle Fork Humbug Creek and South Fork Humbug Creek.

Upper Humbug Creek

Humbug Creek is the principal stream of this 7th field watershed within the Project area.

Steelhead trout, resident rainbow trout, and Pacific lamprey are found in Humbug Creek. In 

Sucker Creek, natural gradient barriers near the mouth prevent anadromous fish access upstream. 

Only resident rainbow trout are found in Sucker Creek.

5th Field Watershed Scale

Humbug Creek – Klamath River

All fish species of interest: (i.e., Coho and Chinook Salmon, steelhead trout, resident rainbow 

trout, Pacific lamprey, and Klamath River lamprey) are present in the Klamath River. Coho, 

steelhead, rainbow trout and lamprey are present in Humbug Creek. This scale considers impacts 

on a large landscape scale.

Measures (for Analysis Indicators)

Temperature

Temperature of fish-bearing reaches of stream channels can affect aquatic species, lower 

temperatures are more beneficial to fish. This indicator is measured by the amount of shade 

adjacent to streams because increased shade keeps temperatures low. (Appendices C, D). 

Temperature is also discussed in the hydrology resource report with stream shade changes being 

used as a proxy for analyzing temperature.

Sediment and Substrate

This indicator is rated by the percentage of substrate composition of fine material. Considered 

data includes composition of the surface and subsurface of non-pool units, as well as the volume 

of pools filled with fines. Where no or limited survey data is available, evaluation may use

cumulative watershed effects (the universal soil loss equation, equivalent roaded area or geology
Aquatics Resource Report Craggy Vegetation Management Project

6

models) models and professional judgment (Appendices C, D). Details about the cumulative 

watershed effects models and assumptions can be found in: Cumulative Watershed Effects: The 

Abridged Version (Bell 2012) and the cumulative watershed effects model results for Craggy; 

the latter can be found on the project website at http://www.fs.usda.gov/project/?project=31770. 

The Geology Report is also available at this location and it discusses the geology model. The 

Hydrology resource report, also available at this location, uses the equivalent roaded area model 

to estimate sediment.

Sediment in streams is a part of the natural geological process. Certain erosive geologies, such as 

granitic soils, can impart a high amount of fines to a stream system even from wilderness locales. 

It is when management activities upon the landscape increase incoming sediment flux within a 

drainage such that it is higher than normal background processes that human-induced impact to 

aquatic resources begin to occur. Depending on the scale considered, effects may be highly 

localized (i.e., at the confluence of two streams) or more diffuse (i.e., multiple miles of increased 

spawning bed embeddedness). Most activities described for the project either occur in the 

uplands outside of riparian reserves, are low impact without ground disturbance, or, when they 

do occur in a riparian reserve, they are distant and do not affect fish-occupied waters.

Parsons, et al. (2006a) summarizes the relationship of erosion and sediment delivery to streams, 

starting with the concept that most sediment transported by streams is delivered from the bed and 

banks of channels and alluvial deposits within the catchment. Therefore, except where a 

landslide intersects a perennial stream channel or other similar unusual circumstances, sediment 

must travel overland before it can contribute to the stream substrate environment. Movement of 

fine sediment, both overland and instream, is dependent upon factors such as slope gradient and 

length, roughness, and precipitation or water; even under ideal modeled or experimental 

circumstances, most sediment does not move very far from its source. For instance, Parsons, et 

al. (2006b) performed a series of controlled experiments, finding that the maximum sediment 

yield was seven meters from a source; this distance is consistent with other models, experiments, 

and observations (Parsons, et al. 2006a). Beyond this point, sediment yield quickly declines.

In the case of timber harvest, increased sediment input to streams is one of many potential 

impacts to aquatic biota (Chamberlin, et al. 1991). However, the distance the soil moves is short

and the use of best management practices, project design features and management actions that 

minimize soil and litter disturbance are effective in containing and controlling overland flow of 

water and sediment (Edwards and Willard 2010; Aust and Blinn 2004).

Vegetated areas adjacent to streams that are as narrow as 10 meters can be effective in 

decreasing sediment from upland timber harvest activities to levels difficult to distinguish from 

background variability (Clinton 2011). However, while narrow vegetated areas (e.g., 15 meters

or less) may be sufficient to preserve physical and chemical stream characteristics, larger widths 

are required to maintain biological components (Castelle, et al. 1994). In regard to effectively 

filtering sediment from upland management activities, 30 meters is a general recommended 

width although other habitat components (e.g., noise reduction, stream shading, large woody 

debris recruitment and retention) should also be taken into account, as well as particular resource 

needs of individual species (Castelle, et al. 1994). Effective width of vegetated area at any given 

location will vary dependent upon the landscape and upslope management activity but eventually 

efficacy will plateau, after which disproportionately large vegetated widths are required for 

incrementally greater sediment removal or biological response (Castelle, et al. 1994; Wong and 

McCuen 1982).
Aquatics Resource Report Craggy Vegetation Management Project

7

Turbidity

This indicator is rated by professional judgment following observation of conditions after high 

water events, the amount of substrate fines, the cumulative watershed effects model results

(universal soil loss equation and geology), and the condition of riparian reserves (Appendices C, 

D). In addition the distance to fish habitat and the likelihood of activities to introduce fine 

sediment into fish-bearing streams will also be incorporated into the effects analysis.

Turbidity describes suspended sediment in the water column. It is generally composed of very 

small particles like silts because larger material is difficult to keep suspended except at high 

flows (Swanston 1991). Because a degree of turbidity is natural in stream systems, often 

observed during spring run-off and storm events, fish are adapted to it (Bjornn and Reiser 1991). 

Outside the laboratory environment, chronic and elevated levels of turbidity considered 

detrimental to aquatic organisms only occur following catastrophic natural incidents such as 

large landslides or extensive wildfires, or where human activities provide an extensive raw 

surface available for continuous stream erosion (Meehan 1991; Neary, et al. 2008).

Instream activities produce both short- and long-term effects in regard to turbidity and suspended 

sediment production. A conceptual model includes two main phases: (1) a pulse of suspended 

sediment associated with construction activities, and (2) continued erosion of fine particles from 

disturbed banks until such time that vegetation stabilizes the soil (Sear, et al. 1998). The initial 

suspended sediment release is expected to be short term, with the amount of suspended sediment 

rapidly dropping to pre-treatment levels both in time and space (Sear, et al. 1998; Madej 2001; 

Brown 2002; Foltz and Yanosek 2005). For example, a study commissioned by the 

Environmental Protection Agency found that turbidity caused by instream suction dredging 

returned to acceptable water quality levels within 250 feet; and no discernible turbidity release 

occurred when dredges were not operating (Royer, et al. 1999). The Forest programmatic 

Facilities Maintenance and Watershed Restoration Biological Assessment included consultation 

on minor instream activities such as culvert replacement, determining that turbidity was 

undetectable beyond a distance of 300 feet (USDA 2004). Residual increases over background 

may remain, however, due to erosion of exposed surfaces and resuspension of settled matter 

(Brown 2002; Foltz and Yanosek 2005). Most erosion occurs in the first few floods following 

channel work, with long-term stabilization occurring once appropriate vegetation grows (Madej 

2001; Sear, et al. 1998).

Large Woody Debris

This indicator is rated using the amount of “large wood” (40 cubic feet or larger) per linear 

length of stream; it is only applicable in 3rd or larger order stream systems (Appendix C, D). The

Forest Plan (standard and guideline 10-56, page 4-113) provides guidelines as to an acceptable 

amount of large wood (20 pieces or as identified at the watershed level). If professional judgment

concludes that guidelines are inadequate or do not capture the nature of the system under 

consideration, the channel width and potential of the site to produce and retain large woody 

debris may be used. Potential for future large woody debris recruitment in both the short and 

long term will also be included in rating the indicator. Recruitment effects will be determined 

using the likelihood of the removal of standing trees that have a high probability of becoming 

large woody debris in the stream channel based on professional judgment and scientific 

literature.
Aquatics Resource Report Craggy Vegetation Management Project

8

For large woody debris to affect fish and fish habitat, it must (1) recruit to the stream and (2) be 

transported to fish-occupied waters. Ninety percent of wood recruitment tends to occur within 30

to 35 meters of the stream (Benda and Bigelow 2011). While debris flows can be an important 

vector in the large-scale exportation of wood from headwaters to fish-bearing reaches, such are 

relatively infrequent in nature (May and Gresswell 2003, 2004) and may be catastrophic in 

extent, scouring channels and banks. Most wood transport that is not due to debris flow tends to 

average a couple hundred feet over the lifetime of the wood in small streams, with the lower 

portion of the headwaters being, therefore, the most important in moving wood to fish-bearing 

areas (Benda and Bigelow 2011).

Disturbance History and Regime

This indicator is primarily rated using all three of the cumulative watershed effects models: 

equivalent roaded area (ERA), universal soil loss equation (USLE), and the geology model 

(GEO) (see Bell 2012 for more information). If professional judgment concludes that these 

models are not fully capturing disturbance risk then road density and location, current impacts 

from past stand-replacing timber harvest and wildfire, fire regime, vegetation regime, and 

development on private property may also be considered (Appendix C, D).

Peak and Base Flows

At the 7th field watershed level, this indicator is rated using elements of equivalent roaded area

and other associated components (Appendix C, D). Any potential effects to flows due to a sitespecific project element are considered individually.

Drainage Network

This indicator is rated by the increase or decrease in the drainage network as it relates to roads, 

ditches, and other similar structures (Appendix C, D).

Change to the drainage network is primarily an aspect of how “connected” an artificial drainage 

feature (road, ditch, or other element) is to the natural hydrologic system. For instance, a road on 

a ridgetop will have less impact to the drainage network than a road adjacent a stream or one 

crossing a stream channel. The more connected a road is to the drainage network, the more it 

potentially influences hydrological regime and inputs of sediment to the stream system. 

Additionally, the gullies and ditches associated with roads can effectively increase the drainage 

length and overall hydrologic connectivity within a basin, with more water flowing through 

channels instead of via normal subsurface or overland routes. Such connectivity can impact local 

hydrologic regimes (Wemple, et al. 1996; Croke and Mockler 2001). The connectivity of 

temporary roads is determined using field review, hillslope placement and distance to a stream 

channel.

Riparian Reserves

This indicator is a consideration of the riparian environs, and it extends into the nearby uplands

(Forest Plan, pages 4-106 to 4-107). For the purposes of analyzing effects to aquatic species, the 

riparian reserve surrounding a body of water (hydrologic riparian reserve) is used. The condition 

of riparian reserves is a synthesis of shade, large woody debris recruitment, and disturbance to

the area surrounding the stream (Appendix C, D). Interim widths of riparian reserves provided 

in the Forest Plan (standard and guidelines MA10-1 and MA10-2, pages 4-107 and 4-108) are 

used for analysis purposes.
Aquatics Resource Report Craggy Vegetation Management Project

9

Spatial and Temporal Bounding of Analysis Area

The analysis area for aquatic resources includes effects at the site-specific and watershed-scale 

extent. Watersheds used in the analysis are at the 5th and 7th field level; the analysis indicators 

retained for analysis will be discussed at these scales.

The site-specific analysis discussion will focus on water drafting within the range of anadromous 

and resident fish. For the remainder of the project area at this scale, project components are 

outside the distribution of analysis species, habitat is not present, or distance to occupied or 

suitable habitat is too distant for an effect to occur.

The temporal analysis timeframe includes effects during implementation, short-term effects 

expected to occur within the first year following implementation, and long-term effects (greater 

than one year).

Background

The location of the project area for the Craggy Project, including watersheds addressed at the 5th

and 7th field scale, is described in Chapter 1 of the environmental impact statement. Several fishbearing streams are potentially affected by the Project: Klamath River, Humbug Creek, Middle 

Fork Humbug Creek, South Fork Humbug Creek, and Sucker Creek.

The analysis area for effects of the Craggy Project on aquatic resources is larger than the project 

area. The portion of the Klamath River within the analysis area has a drainage area of 

approximately 40 square miles. As well as the Klamath River, several fish-bearing streams are 

within the analysis area: Humbug Creek, Middle Fork Humbug Creek, South Fork Humbug 

Creek, and Sucker Creek. Timber harvest, gold mining, roads, recreation, wildfire, and floods are 

some of the primary past and present influences within the 5th and 7th field watersheds, with 

private land comprising about one-third of the ownership. Coho and Chinook Salmon, steelhead, 

resident rainbow trout, and pacific lamprey are present; the upstream limits of each salmonid 

species are restricted by barriers, gradient, discharge, or stream size. Chinook and Coho 

spawning have been observed in the river segment adjacent to the project area, and lamprey 

rearing areas are recorded to be present.

Humbug Creek is a fourth-order perennial tributary to the Klamath River. Generally flowing 

southeast, it drains the north sides of McKinley Mountain, Gunsight Peak, Mahogany Point and 

Deadwood Baldy Peak. It also drains the south side of Craggy Mountain. Humbug Creek is 

approximately 9.5 miles in length, and approximately 3.9 miles of the stream is under private 

ownership. The remaining 5.6 miles is under federal ownership and managed by the Forest. 

Humbug Creek has several named perennial tributaries: Middle Fork Humbug Creek; South Fork 

Humbug Creek; Punch Creek, and Sucker Creek. Past and present influences within the drainage 

include timber harvest, roads, an off-highway vehicle open riding area and trails, recreation, 

grazing, mining, water diversion, wildfire, and flood. Coho, steelhead, resident rainbow trout, 

and pacific lamprey are present in the creek, with the upstream limits of each species (e.g., 

approximately five miles upstream from the mouth of Humbug Creek for Coho Salmon)

restricted by gradient, discharge, stream size, and/or barriers. Klamath River lamprey have a 

potential presence there. Only rainbow trout are present in Sucker Creek, and steelhead have 

thermal refugia there.
Aquatics Resource Report Craggy Vegetation Management Project

10

Middle Fork Humbug Creek is a third-order perennial tributary to Humbug Creek. The creek 

generally flows northeast. It drains the north sides of Gunsight Peak and Mahogany Point. The 

Middle Fork Humbug Creek drainage ownership is Forest Service. Past and present influences

within the drainage include timber harvest, roads, recreation, grazing, mining, wildfire, and 

flood. Steelhead trout and rainbow trout are present in Middle Fork Humbug Creek, with the 

upper limit of anadromous fish migration being a high stream channel gradient beginning at 

about 1.45 miles upstream from the mouth. Above this point, only resident rainbow trout are 

present. Coho and steelhead have thermal refugia in this creek; and both Pacific and Klamath 

River lamprey have a potential presence there.

South Fork Humbug Creek is a third-order perennial of Humbug Creek. Flowing northwest, it 

originates from a ridgeline that is east by northeast of Montana Peak. Except for a 0.7 mile 

section located about 0.4 miles downstream from the source, ownership within the drainage is 

entirely Forest Service. Past and present influences within the drainage include timber harvest, 

roads, grazing, recreation, and flooding. Steelhead and rainbow trout are present within the upper 

limit of anadromous fish migration being the high stream channel gradient that begins about 0.95 

miles upstream from the mouth. Above this point, only resident rainbow trout are present. Coho 

and steelhead have thermal refugia in this creek; both Pacific and Klamath River lamprey have a 

potential presence there. Punch Creek is a second-order perennial tributary to South Fork 

Humbug Creek. Flowing northeast, it originates from the north slope of Montana Peak. Except 

for a 0.1 mile section located about 0.35 miles upstream from the mouth, ownership within the 

drainage is entirely Forest Service. Steelhead and rainbow trout are present with the upper limit 

of anadromous fish migration being a high stream channel gradient beginning about 0.35 miles 

upstream from the mouth. Above this point, only resident rainbow trout are present.

Of particular interest, several of the streams in the project area experienced extensive scouring 

during the 1964 and 1997 flood events. Flood impacts may have been exacerbated due to historic 

mining practices, fire, timber harvest, and roads. Satellite and aerial imagery, such as that 

available from services like GoogleEarth, which date from the years following the 1997 event,

clearly show areas of channel scour in Humbug Creek, as well as track long-term recovery of all 

project area drainages from the earlier event by showing images of the same area at multiple 

dates in a timeline. On the ground, signs of flood impact and on-going system adjustment include 

areas of aggradation and downcutting, streambanks comprised of cobbles and other coarse 

material (i.e., lacking a developed soil covering), riparian forest in early- to mid-seral stage, and 

a general lack of woody debris (because it was transported out of the system). Not all streams 

were affected equally and some systems, or portions within a larger watershed, may have 

experienced little to no impact.

Composition of riparian vegetation within the project area is very diverse, reflecting differences 

between locations in regard to elevation, slope aspect, soil character, timber harvest and wildfire 

history, and local hydrologic condition. Large-scale scouring by recent floods, especially from 

1964 and 1997 as referenced above, has reset the riparian vegetation to an early- to mid-seral 

progression in many tributaries with regrowth retarded due to banks being reduced to cobbles 

and other coarse materials.

As with the riparian, the uplands are varied when considered across the landscape area of the 

project. More information on upland areas is available in the Silviculture (Vegetation) resource 

report.
Aquatics Resource Report Craggy Vegetation Management Project

11

Appendix B includes specifics in regards to the biology of the analysis species, as well as survey 

records. Table 2 provides a summary.

Table 2: Actual and Potential Occupancy by Aquatic Species by 7th and 5th Field Watersheds

Species

7th Field 5th Field

Humbug Creek

Middle Fork 

Humbug Creek

South Fork 

Humbug Creek

Punch Creek

Sucker Creek

Klamath River

Coho X T T X

Chinook X

Steelhead X X, T X, T X T X

Resident Rainbow Trout X X X X X X

Pacific Lamprey X P P X

Klamath River Lamprey P P P X

X - confirmed present

P - potential presence

T - thermal refugia

Affected Environment

Only indicators potentially affected by the project and, therefore, introduced in the 

“Methodology” section, are further discussed here prior to analysis within “Environmental 

Consequences.” Indicators are generally applied only to anadromous systems. A summary of the 

baseline for indicators retained for analysis is presented in Table 3. See Appendix D for a list of 

the remaining indicators and their relationship to baseline conditions.

Temperature

Humbug Creek is 303(d) listed under the Clean Water Act as impaired for water temperature. 

Water temperature on the mainstem is widely recognized as a limiting factor to salmonid 

production in this watershed. Within the project area, recent stream temperature data is available 

for Humbug Creek, and the Klamath River. The Middle Klamath River is “Not Properly 

Functioning” under the Analytical Process framework.

Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek have fish 

habitat, including Coho critical habitat, within project boundaries. Although Sucker Creek only 

supports resident rainbow trout, its confluence outflow at Humbug Creek is an important coolwater thermal refugia area for resident and anadromous fish. Stream temperature monitoring by 

the Forest (starting in 2010), as required by the Regional Water Board for total maximum daily 

load compliance, has determined that the section of Humbug Creek below the confluence with 

Middle Fork Humbug Creek exceeds the state maximum weekly water temperature threshold of 

16 degrees Celsius to support beneficial uses for core juvenile salmonid rearing. However, 
Aquatics Resource Report Craggy Vegetation Management Project

12

stream shade measured in 2011 showed the existing percentage of shade in all three watersheds 

to have no or minimal human-caused reductions (USDA 2011. Therefore, shade in these 

drainages is considered to be in a natural condition, with the caveat that maximum potential may 

not be reached at present due to recovery from past flood scour or fire. There is evidence that, on 

many sites on the Forest where temperatures are observed to be above the State Water Board’s 

beneficial use threshold for juvenile salmonids, higher temperatures are due to natural 

conditions; temperatures in 15 out of 20 reference (non-managed) streams exceed 16 degrees 

Celsius (USDA 2012). Although other Project streams, such as Middle Fork Humbug Creek and 

South Fork Humbug Creek, may exhibit a sufficiently low temperature to consistently meet State 

Water Board’s total maximum daily load requirements, they are considered to be “managed” and 

insufficient stream temperature data has been collected at this time to propose them for removal 

from the 303(d) list.

The lower 4.5 miles of Humbug Creek typically has elevated summer water temperatures that 

are potentially lethal to salmonids; this is seemingly due to cumulative human impacts of water 

diversion on private land, clearing of riparian vegetation, and other factors. During the warm 

summer months when water temperatures in this section of Humbug Creek approach 20 degrees 

Celsius, anadromous and resident fish rely upon cooler water habitat within tributary creeks

upstream and their confluence zones (thermal refugia). Project area creeks of Middle Fork 

Humbug Creek, South Fork Humbug Creek, Sucker Creek, and the upper reaches of Humbug 

Creek provide thermal refugia that juvenile salmonids rely upon when stream temperatures in the 

lower 4.5 miles of Humbug Creek are elevated.

Sediment and Substrate

Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek are all 

considered to be “Properly Functioning”. Although survey specifics have varied over the years, 

all three systems consistently exhibit a low amount of fines when surveyed. Additionally, the 

applicable cumulative watershed effects model results are below critical threshold and road 

densities are low to moderate.

The Middle Klamath River is characterized as “Not Properly Functioning.” No recent substrate 

data is available for the Klamath River mainstem. The Middle Klamath River watershed is 

303(d) listed under the Clean Water Act as impaired for sedimentation. Furthermore, the Coho 

Recovery Plan appraisal of the Middle Klamath River watershed recognized an altered sediment 

supply to be important stressor to fish health (NOAA 2014b). Sources of excessive sediment 

loading were identified as both natural (e.g., granitic geology) and human-caused (e.g., roads or

agriculture) in nature.

Turbidity

Turbidity within the Project area for Humbug Creek, Middle Fork Humbug Creek, and 

South Fork Humbug Creek is “Properly Functioning.” Modeling of soil loss and risk of mass 

wasting in the cumulative watershed effects analysis (provided in the Cumulative Watershed 

Effects modeling) is under the threshold of concern; sediment composition, especially the finest 

elements (less than two millimeters), appears to be functioning properly (see the “Sediment and 

Substrate” indicator discussion). Personal observations following rain events and during spring 

run-off have not raised concerns about lingering turbidity as water in the Project area clears 

quickly, within about three days.
Aquatics Resource Report Craggy Vegetation Management Project

13

Middle Klamath River turbidity is likely “Functioning-at-Risk.” Although substrate data is not 

available, the substrate of the river includes a high percentage of sand and silt, both from 

anthropogenic and natural (e.g., geologic) sources. This type of material is easily mobilized to 

the water column to create turbid conditions. Furthermore, turbidity has been observed to require 

multiple days to clear to its normal baseline following high water events.

Large Woody Debris

All waterways in the Project area (Humbug Creek, Middle Fork Humbug Creek, South Fork 

Humbug Creek, and Middle Klamath River) are “Not Properly Functioning” for large woody 

debris. Both recent and past surveys in the Project area which included a large woody debris 

component found instream wood, as well as potential future recruitment, to not be at desirable 

levels. The lack of large woody debris, and the subsequent detrimental effect to fish habitat, 

including Coho critical habitat, has been repeatedly identified to be of concern (USDA 1993; 

NOAA 2014b). The reason behind the lack of desirable amounts of large woody debris is 

multifaceted and has been attributed to a combination of timber harvest, mining, altered fire 

regime, historic “cleaning” (removal) of wood from stream channels, and scour from large flood 

events.

Disturbance History and Regime

A “Properly Functioning” disturbance regime includes stable natural processes and hydrography, 

where high quality habitat and watershed complexity provide refuge and rearing for all life 

stages or multiple life-history forms; for proper functioning all three cumulative watershed

effects models should be below their thresholds. This description fits all 5th field and 7th field 

watersheds within the project area, except one: the Lower Humbug Creek 7th field watershed. 

Alternately, in an “At-Risk” disturbance regime, the frequency, duration, and magnitude of 

disturbance events have the potential to be moderately departed from the reference condition due 

to human-mediated impacts on the watershed; one or two of the models may be over threshold. 

Upper Humbug Creek and Middle Fork Humbug Creek 7th field watersheds fall under this 

designation. Finally, a “Not Properly Functioning” disturbance regime is described as a 

watershed with disturbance events significantly departed from reference condition as a 

consequence of past or current human activities; all three models are over threshold. See 

Appendix C for additional information in regard to baseline indicator determination.

The Upper Humbug Creek and Middle Fork Humbug Creek 7th field watersheds are elevated 

over threshold in regard to the geology component of the cumulative watershed effects model 

analysis. For further information about these effects see the full geology resource report available 

on the project website.

Peak and Base Flows

The determination of existing condition for peak and base flows is a synthesis of equivalent

roaded area, and vegetation condition.

Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek are “Properly 

Functioning.” The equivalent roaded area model is below critical threshold for all three 7th field 

watersheds, road densities are low to moderate, and roads are generally located outside of 

riparian areas. Effective stream shade is either not or minimally affected by human-caused 

impacts (USDA 2012); while assessment of riparian vegetation is difficult due to on-going 
Aquatics Resource Report Craggy Vegetation Management Project

14

recovery from past flood and fire events, it is generally considered to be in good condition 

(USDA 1993).

Middle Klamath River is best described as “Not Properly Functioning.” While the equivalent 

roaded area model is below critical threshold, other considerations take precedence. In particular, 

base flows have been altered due to releases from Iron Gate Dam. The lack of high winter flow 

and high spring flows resulting from snowmelt runoff from higher in the watershed are identified 

as primary issues of concern in regard to the health of the aquatic ecosystem and its fauna 

(USDA 1993; NOAA 2014b). This impact is of greatest magnitude during periods of drought. 

Furthermore, riparian vegetation condition is considered to be just “fair to good.”

Drainage Network

Due to the complex history of the project area, it is not possible to determine how human-caused 

impacts have increased the drainage network over pre-European conditions. In addition to road 

construction to access mining and timber sites, there are many ditches and other surface 

alterations which conveyed water for mine and residential use. More recently, efforts have been 

expended to improve watershed conditions, primarily through closing unauthorized routes to 

motor vehicle use, rerouting motor vehicle trails, and improving the staging area at the Humbug 

Open Riding area as well as road decommissioning activities on FS Road 45N88 in the Middle 

Fork Humbug Creek 7th field watershed.

South Fork Humbug Creek is considered to be “Functioning-at-Risk.” Although the 

cumulative watershed effects modeling of the equivalent roaded area component is under the 

desired threshold, the area that drains into South Fork Humbug Creek has multiple drainagerelated concerns.

Middle Fork Humbug Creek is considered to be “Properly Functioning.” The cumulative 

watershed effects model of the equivalent roaded area is under the desired threshold and recent 

road decommissioning work has occurred on Forest Service Road 45N88 to reduce the overall 

drainage network.

Humbug Creek is labeled as “Functioning-at-Risk”. Although the watershed effects model of 

the equivalent roaded area component is under the desired threshold and recent stormproofing to 

address road drainage issues has occurred, there are additional factors when considering the 

overall drainage network.

The Middle Klamath River is classified as “Functioning-at-Risk.” The Middle Klamath River 

is a complex system. Roads built upon both private and public land also impart their own impact 

in regard to the drainage network depending upon location, active and potential connectivity to 

adjacent waterways, and how they were (or were not) designed. Due to active undertakings such 

as stormproofing, as well as the natural decades of decay of unused historic ditches and roads, 

the anthropogenic increase in the Middle Klamath River drainage network in and near the project 

area has undoubtedly decreased over time. However, the drainage network remains impacted 

over the natural baseline, and it is the professional opinion of the Fish Biologist that 

“Functioning-at-Risk” best describes the current condition.

Riparian Reserves

Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek are 

characterized to be “Functioning-at-Risk.” Although protocol specifics have varied over the 

years, when shade has been assessed all three systems consistently exhibit a good to excellent 
Aquatics Resource Report Craggy Vegetation Management Project

15

degree of effective shade cover. Furthermore, stream shade measured in 2011 showed existing 

percentage of shade in all three watersheds to have no or minimal human-caused reduction 

(USDA 2011); thus shade in these drainages is considered to be in a natural condition. The 

caveat with the riparian reserve indicator is that other considerations than shade must be taken 

into account. A combination of historic timber harvest (to the streambank in places), altered fire 

regime, flood events, and other natural and anthropogenic events affected the riparian reserves in 

a detrimental manner (USDA 1993; NOAA 2014b). Additionally, there are local impacts to the 

riparian reserve due to roads, recreational residences, and activity on private property. While 

fast-growing alders provide a very good degree of overhead shading and bank stabilization, 

woody debris which originate from this source are less preferred compared to mature conifers 

due to the latter’s larger size and slower decay rate. Future recruitment of large conifers from the 

outer portion of the riparian reserves appeared to be generally poor, likely due to factors such as 

past timber harvest and altered fire frequencies. Recovery of the riparian reserve in the Project 

area is continuing and is a long-term process.

The Middle Klamath River is “Functioning-at-Risk.” The Coho Recovery Plan lists “degraded 

riparian forests” as a primary stressor in the Middle Klamath River drainage (NOAA 2014b). 

Shade in the Middle Klamath River canyon, including the Project area, is still only characterized 

as “fair to good.”

Mining and an altered fire regime (increased understory fuel loading) due to timber extraction 

and long-term fire-suppression practices are described as human-mediated impacts affecting 

riparian forests, particularly along the mainstem of the Middle Klamath River.

Table 3: Baseline for Analysis Indicators for Anadromous Streams in the Project Area

Stream/River

TemperatureSubstrateTurbidityLarge Woody DebrisDist. History/RegimePeak/Base FlowsDrainage NetworkRiparian Reserves

Humbug Creek NF* P P NF FAR P FAR FAR

Middle Fork 

Humbug Creek P P P NF FAR P P FAR

South Fork 

Humbug Creek P P P NF P P FAR FAR

Mid Klamath

River NF NF FAR NF FAR NF FAR FAR

P - "Properly Functioning"

FAR - "Functioning-at-Risk"

NF - "Not Properly Functioning"

*The lower 4.5 miles of Humbug Creek are “Not Properly Functioning, while the rest of Humbug 

Creek is Properly Functioning.
Aquatics Resource Report Craggy Vegetation Management Project

16

Environmental Consequences

Alternative 1

Direct and Indirect Effects

Under Alternative 1, the Craggy Project will not occur and no management actions will be taken. 

See the cumulative watershed effects model results available on the project website for the 

baseline of these models within the analysis area. Legacy sites identified for the Craggy Project 

will not be addressed. The effect to fish and fish habitat from not addressing the legacy sites 

ranges from insignificant to not measurable. While there are several legacy sediment sites 

present throughout the project area, most are distant from fish-occupied waters, and the current 

or potential sediment impact to their respective watershed is minimal. The nearest resident trout 

habitat to a legacy sediment site is 0.30 miles, and anadromous habitat is approximately 0.30

miles from a location with elevated risk. As all major streams, with the exception of the Klamath 

River, in the project area are considered to have good baseline water quality, even with the 

continued existence of the legacy sites, if one or more sites was to experience catastrophic

failure, the impact downstream is likely to be minimal and short-term to fish and fish habitat.

If a fire were to occur in the analysis area the effects to fish and fish habitat would be stream 

shade would be reduced significantly due to loss of riparian vegetation resulting in increased 

stream temperatures. Sediment input into the streams would increase due to loss of riparian and 

upland vegetation, resulting in loss of adult spawning and holding habitat, and juvenile rearing 

habitat.

Cumulative Effects

Past and ongoing actions in the analysis area are reflected in the discussion of the affected 

environment.

The primary consequence to fish and aquatic habitat of Alternative 1 is related to legacy site 

impacts and effects of high intensity wildfire. The legacy site risk is part of the existing baseline; 

because the reasonably foreseeable projects except for the Badger Timber Harvest are not close 

to the fish-bearing streams in the Craggy Project area, adding the effects of their activities to the 

effects of Alternative 1 will neither influence nor exacerbate the existing condition of the 

analysis area. Future foreseeable actions planned at the time of this document include the Yreka 

Flood Hazard Reduction Project, Lower Yreka Creek Full Restoration Project, fuels reduction 

projects on Bureau of Land Management lands, the City of Yreka Wildland Urban Interface

Hazardous Fuels Reduction Project, and the Badger Timber Harvest. The Badger Timber Harvest 

Plan will have minor short-term effects to stream temperature, sediment, and peak-base flow in 

the Lower Humbug Creek 7th field watershed. There may be a slight increase in stream 

temperature in the sections of Humbug Creek downstream of the project activities, and sediment 

input to the stream channel may increase slightly as well. However, the effects are not likely to 

result in any detectable change to stream temperature in fish-bearing reaches or have any 

meaningful impact to fish habitat, including thermal refugia.

The effects of these projects are not likely to have any meaningful impacts to aquatic habitat. 

Effects of future high intensity wildfire on water quality, geology and soil are provided in the 

relevant resource reports and the Cumulative Watershed Effects display on the project website. 

Therefore, without direct effects or a compounding indirect effect, adding the effects of these 
Aquatics Resource Report Craggy Vegetation Management Project

17

projects to the effects of Alternative 1 will not create measurable or significant cumulative 

effects.

Alternative 2

Direct Effects

Direct effects to Coho Salmon (federally-listed as threatened), Forest Service sensitive aquatic 

species, management indicator species and their habitat can result from water drafting activities.

For the project, eight drafting sites are within fish-occupied waters and, therefore, may affect fish 

and their habitat; additional sites may be identified during implementation. Seven of the

identified sites are within anadromous waters (Humbug Creek [three sites]; South Fork Humbug 

Creek [two sites]; and Middle Fork Humbug Creek [one site]); one site is associated with 

resident rainbow trout (Humbug Creek).

Drafting operations can disturb staging or spawning adult fish, as well as impinge on or entrain 

juveniles (Sicking 2003). Additionally, water drafting operations can mobilize suspended 

sediment to downstream aquatic habitat. Suspended sediment increases turbidity, exposing 

juvenile fish to gill damage and reduced oxygen uptake or to reduced vision and compromised 

feeding effectiveness. If water drafting were to occur with eggs present in adjacent redds, 

deposition of suspended sediment could fill in the small spaces of stream bottom substrate; this 

could deprive incubating eggs of dissolved oxygen and result in their mortality.

While screening intakes can reduce effects to fingerlings and fry, minimization of impingement 

requires the use of specific mesh sizes, pumping rates, and screen areas, as outlined in the 

National and Oceanic Atmospheric Administration (NOAA) Fisheries Water Drafting 

Specifications (NOAA 2001; Sicking 2003). As described in Project best management practices 

and project design features, NOAA drafting specifications will be implemented during project 

water drafting at all sites. There is a very low probability of impingement because all locations 

have sufficient room for adult and juvenile to distance themselves from the screens. It is 

anticipated that fish temporarily avoiding water drafting activities are not likely to experience 

reduced feeding success, nor will water drafting result in a significantly higher probability of 

exposure to predators.

For water drafting, the frequency of effects is only during actual operations. Drafting will be 

done in accordance to the NOAA Fisheries Water Drafting Specifications (NOAA 2001) and 

appropriate project best management practices. These water drafting best management practices 

are incorporated into project design features described in chapter 2 of the Craggy Project

environmental impact statement as displayed in Appendix D of that document. By following 

these specifications, and considering the mobility of fish in the river, water drafting in fishbearing areas is likely to have only minor, insignificant direct effects on anadromous fish and 

resident rainbow trout, including habitat, with no long term effects.

There is one site located within an anadromous fish bearing stream (Humbug Creek) where a 

temporary stream crossing will be installed to allow project vehicles to cross the stream. This 

crossing site is where Forest System Road 45N53 crosses Humbug Creek. Therefore, treating 

this site may affect anadromous fish and their habitat. Work at this site could mobilize suspended 

sediment to downstream aquatic habitat. Suspended sediment increases turbidity, exposing 

juvenile fish to gill damage and reduced oxygen uptake or to reduced vision and compromised 

feeding effectiveness. If work at this site were to occur with eggs present in redds downstream, 
Aquatics Resource Report Craggy Vegetation Management Project

18

deposition of suspended sediment could fill in the small spaces of stream bottom substrate, 

depriving incubating eggs of dissolved oxygen and resulting in their mortality. The site work 

will be done in accordance with appropriate Project best management practices and project 

design features described in chapter 2 of the Craggy Project Environmental Impact Statement as 

displayed in Appendix D of that document.

There is a very low probability that fish will be impacted by work at this site since fish will have 

sufficient room to distance themselves from the site work. It is anticipated that fish temporarily 

avoiding legacy site activities are not likely to experience reduced feeding success, nor will this 

work result in a significantly higher probability of exposure to predators.

By following the project best management practices and project design features, and considering 

the mobility of fish in the stream, work at this site is likely to have only minor, insignificant 

direct effects on anadromous fish and resident rainbow trout, including habitat, with no long term 

effects.

No other project elements include instream activities within fish-bearing waters. Fish screens, 

project design features, best management practices, and fish mobility will preclude impingement. 

There will not be direct effects of this alternative to other analysis indicators.

Indirect Effects

Potential indirect effects to aquatic resources may occur as a result of thinning with and without 

product removal, mastication, fuelbreak treatments, prescribed fire, legacy site treatments, and 

water drafting. The indirect effects to indicators which may be affected by project activities are 

as follows:

Temperature

The project could impact stream temperature if vegetation treatments resulted in reductions in 

shade over streams, or by reductions in stream flow due to water drafting.

Thinning with Product Removal

Units planned for thinning with product removal were reviewed in regards to proposed 

equipment and treatment exclusion zones adjacent to stream channels (see map of proposed 

treatments in Appendix B of the Craggy Project environmental impact statement). Vegetation 

treatments next to fish-occupied habitat are at least 150 feet from streams except in three units, 

Units 134-41, 134-248, and 138-23. The bottom of units 134-41 and 134-248 are bounded by 

Forest Road 45N53 which runs parallel to Sucker Creek. The bottom of unit 138-23 is bounded 

by Forest Road 45N43, which runs parallel to Middle Fork Humbug Creek. The closest approach

of Unit 134-41 to Sucker Creek is about 75 feet, and the closest approach of unit 134-248 to 

Sucker Creek is about 100 feet. The closest approach of unit 138-23 to Middle Fork Humbug 

Creek is about 100 feet. Due to the width of Forest Service Roads 45N53 and 45N43, their

location, and general topographic configuration, trees in the units next to these roads are largely 

disconnected from their riparian function, including shade. Elsewhere in the project area, the 

buffer between treatment and streams may be as little as 15 feet in plantation units and 50 feet in 

natural stands. These latter locations are all associated with fishless channels. Review of planned 

treatment units by resource specialists confirmed that habitat elements, including effective 

stream shade, will be maintained. Therefore, because shade will be preserved, there is not likely 

to be any meaningful effect to fish-bearing reaches, including Coho Salmon critical habitat, due 

to this project (Fish Biologist field review).
Aquatics Resource Report Craggy Vegetation Management Project

19

Thinning without Product Removal

No effects to stream temperature are expected from units planned for thinning without product 

removal since vegetation treatments next to fish-occupied habitat would result in trees 

contributing to stream shade being left in place. Therefore, because shade will be preserved, 

there is not likely to be any meaningful effect to fish-bearing reaches, including Coho Salmon 

critical habitat, due to this project.

Mastication

No effects to stream temperature are expected from units planned for mastication since most 

units are outside the 150-foot distance (one “site potential” tree) from fish-occupied habitat and 

treatments outside this distance are not likely to affect fish habitat (see the Large Woody Debris 

section for additional information). There is only one unit within 150 feet of fish-occupied 

habitat (Unit 136-917). Vegetation treatments in this unit would result in trees contributing to 

stream shade being left in place. The remaining units planned for mastication (11 total) are 

located more than 150 feet from fish occupied habitat or are located in 7th field watersheds that 

do not contain any anadromous fish or resident rainbow trout habitat. Therefore, because shade 

will be preserved, there is not likely to be any meaningful effect to fish-bearing reaches, 

including Coho Salmon critical habitat, due to this project.

Fuel breaks

No effects to stream temperature are expected from units planned for fuelbreaks since there is 

only one unit within 150 feet of fish-occupied habitat (Unit FBR4). Vegetation treatments in this 

unit would result in trees contributing to stream shade being left in place. The remaining units 

planned for fuelbreaks (six total) are located more than 150 feet from fish occupied habitat, or 

are located in 7th field watersheds that do not contain any anadromous fish or resident rainbow 

trout habitat. Therefore, because shade will be preserved, there is not likely to be any meaningful 

effect to fish-bearing reaches, including Coho Salmon critical habitat, due to this project.

Prescribed Burning

There are relatively few studies on the effects of prescribed burning on the stream temperature 

analysis indicator that compare the multitude of variables before and after (short- and long-term) 

the action. Two relatively recent studies are:

• Arkle and Pilliod (2010) followed effects to components of riparian and stream habitat 

on an Idaho forest which utilized a spring burn prescription similar to what the Forest

may employ for the Craggy Project. Variables were tracked for three years.

• Beche, et al. (2005) observed riparian impacts within a California research forest using 

an aggressive prescription, including a fall burn with deliberate riparian ignition. 

Variables were tracked for one year.

Both studies included control, pre-fire, and post-fire habitat measurements. Neither reported a 

meaningful effect to overstory riparian vegetation, although the more aggressive prescribed burn 

did observe a significant impact to understory vegetation. With no change to stream cover (and, 

hence, effective shade), no negative alteration to temperature is expected. Arkle and Pilliod 

(2010) included water temperature among observed variables and found no change as a result of 

prescribed burn activities.

Road Crossing Construction and Legacy Sediment Site Treatments
Aquatics Resource Report Craggy Vegetation Management Project

20

No effects to stream temperature are expected from construction of the temporary road crossing 

where FS road 45N53 crosses Humbug Creek and legacy sediment site treatments since these

activities would result in trees contributing to stream shade being left in place.

Water Drafting

Water drafting results in minor short-term reductions in stream flow during operations. 

Implementation of drafting consistent with NOAA specifications (2001) ensures that project 

drafting will not remove greater than 10 percent of stream flow at a site within anadromous 

habitat. Drafting from Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug 

Creek will not have any meaningful impact within the range of anadromous fish migration to 

temperature due to the stream’s flow volume which would render any short-term changes in flow 

(which would be less than 10 percent reduction) due to drafting being insignificant to overall 

stream temperature.

Water drafting in non-anadromous habitat will also follow NOAA drafting specifications (2001), 

which require operations to not reduce flows by more than 10 percent within (downstream) 

anadromous reaches. These sites are perennial and may be fish-bearing or non-fish-bearing, as 

shown in the maps. While the NOAA drafting specifications are designed to safeguard 

anadromous fish, the restrictions will also benefit resident rainbow trout habitat at sites where 

they are present; best management practices and project design features for water drafting that 

are applicable to trout will be used. Local reductions in flow volume will not significantly affect 

stream temperature for the same reasons provided for drafting in anadromous reaches, therefore,

the change in the overall flow volume is short term and minimal compared to the normal 

discharge.

Drafting will not affect thermal refugia. As per the discussion above, changes in stream flow will 

not affect local stream temperature; therefore, there can be no alteration to thermal refugia.

Summary

The project will have minor, short-term effects to stream flow during water drafting operations. 

However, the effects are not likely to result in any detectable change to stream temperature in 

fish-bearing reaches or have any meaningful impact to fish habitat, including thermal refugia. 

There will be no meaningful effects to stream temperature from thinning with product removal, 

thinning without product removal, mastication, fuel-break treatments, construction of the 

temporary stream crossing where Forest System Road 45N53 crosses Humbug Creek, or the 

treatment of legacy sediment sites because effective stream shade will be maintained. Similarly, 

prescribed fire will not impact stream temperature because overstory riparian vegetation will be 

maintained.

Substrate and Sediment

The Craggy Project presents multiple pathways for sediment to potentially affect fish habitat that 

include thinning with and without product removal, prescribed burning, fuelbreak treatments, 

legacy sediment site treatments, and construction of the temporary stream crossing where Forest 

System road 45N53 crosses Humbug Creek. This subsection will discuss each major component 

separately, then summarize the results.

Thinning with Product Removal
Aquatics Resource Report Craggy Vegetation Management Project

21

For all units planned for thinning with product removal, either a variable-width equipment 

exclusion zone, or the edge of the inner gorge whichever is furthest from water, is in place to 

provide a sediment buffer for creeks. Widths are based on (1) the presence of fish, or (2) the 

location of a fishless stream (perennial or intermittent) on the landscape in relation to road 

crossings and fish-bearing waters.

• Fish-occupied stream – minimum equipment exclusion zone of 300 feet (e.g., width of 

two potential site-tree heights).

• Non-fish-occupied stream – minimum equipment exclusion zone of 100 feet applies to 

units or portions of units that are located down-gradient of a road crossing, and no other 

crossing is present between the unit and a fish-occupied waterway.

• Non-fish-occupied stream – minimum equipment exclusion zone of 50 feet applies to 

units or portions of units that are located up-gradient of road crossings.

Equipment which disturbs the ground is not allowed in the equipment exclusion zone. Certain 

classes of machinery such as tractors and skidders, particularly if they are not equipped to have 

low ground-pressure, have a greater negative impact on this indicator than other types of 

equipment. Therefore, the equipment exclusion zone primarily relates to ground-based harvest 

(i.e., “tractor” units). In contrast, skyline units are too steep for tractor harvest, and trees are 

yarded to a road or landing where the skyline equipment is stationed. Equipment which 

processes, stacks, or loads logs to trucks is restricted to landings and roads within the equipment 

exclusion zones. Likewise, equipment associated with units designated for endlining are 

restricted in their movement.

The distance of 100 feet (or more) aligns with the generally recommended widths needed for 

effectively filtering sediment from activities such as logging.

Although equipment is the primary manner by which sediment may be conveyed to waterways, 

skidding or endlining material can also disturb the ground and initiate sediment impacts. 

Therefore, units planned for thinning with product removal also include no-treatment zones to 

minimize near-stream ground disturbance.

• Fish-occupied streams – the no-treatment zone is the same as the equipment exclusion 

zone.

• Non-fish-occupied stream (natural stand unit) – the no-treatment zone is the same as the 

equipment exclusion zone.

• Non-fish-occupied stream (plantation unit) – the minimum no-treatment zone is 15 feet.

To meet the purpose and need of the project, overstocked plantation units will be treated to the 

maximum extent possible, including within riparian reserves and adjacent to stream channels. 

Although no equipment is allowed within a 50-foot or 100-foot equipment exclusion zone, 

manually cut trees can still be endlined or otherwise removed from this area as appropriate. 

Project design features, such as not skidding across stream channels, are in place to maintain the 

integrity of the ground nearest the stream channel and thereby minimize the potential for 

overland sediment movement to streams. The number of locations which may have activity 

within the equipment exclusion zone is minimal, 11 units out of 46.
Aquatics Resource Report Craggy Vegetation Management Project

22

Equipment exclusion zone distances and no-treatment areas for units planned for thinning with 

product removal which include a riparian reserve element are summarized in Table A-1 in

Appendix A.

Thinning without Product Removal

In units of thinning without product removal, the same equipment exclusion zone as described 

for units of thinning with product removal will be used. An equipment exclusion zone or a notreatment zone is not needed where manual treatments are planned because implementation will 

be accomplished with chainsaws and similar equipment (e.g., no ground-based equipment or 

skidding). Because activities within units of thinning without product removal will minimally 

disturb the ground (hand cutting and piling of small diameter trees and brush, cutting limbs, and 

lopping and scattering small material), and there will be no mechanized equipment in these units,

there is no need for a no-treatment zone except as required by certain project design features 

such as not cutting trees rooted in streambanks.

In summary, since most streams within the project area are fishless and, where fish are present 

within the project boundary, they are appropriately buffered from ground-disturbing activities;

planned vegetation treatments have little effect on fish habitat or fish. Existing hydrologic 

function will be maintained throughout the project area. Therefore, sediment will not be 

conveyed to fish-occupied waters in a significant, discernible quantity over the existing 

background variability.

Mastication

In units that will be masticated, a masticator may reach into the equipment exclusion zone with 

its arm to grind trees and brush, but material beyond the machine’s reach will be treated using 

manual means. A biological assessment completed by the Klamath National Forest determined 

that the amount of sediment generated from typical mastication treatments was insignificant and 

was unlikely to have a discernable impact to fish habitat (USDA 2001).

Fuel Breaks

There is only one fuel break unit within 150 feet of a fish-bearing stream, and because activities 

within this unit will minimally disturb the ground (hand cutting and piling of small diameter 

trees and brush, cutting limbs, and lopping and scattering small material), and there will be no 

mechanized equipment in this unit, there is no need for a no-treatment zone; except as required 

by certain project design features such as not cutting trees rooted in streambanks.

In summary, since the activities in this unit will result in minimal ground disturbance, the 

planned project activities will have little effect on fish habitat or fish. The amount of sediment 

generated from these treatments is insignificant and is unlikely to have a discernable impact to 

fish habitat.

Prescribed Burning

Prescribed burning (underburning and pile burning) is expected to impart minimal sedimentassociated effects to fish and fish habitat within the project area. A biological assessment 

completed by the Forest determined that the amount of sediment generated from typical 

prescribed burning activities was insignificant and was unlikely to have a discernable impact to 

fish habitat analysis indicators (USDA 2001). The type of fire with the highest potential for 

sediment impact on aquatic species, an underburn which includes riparian reserves, will be 
Aquatics Resource Report Craggy Vegetation Management Project

23

mitigated with the goal of keeping the fire at a low intensity burn within the riparian reserves, 

and through the implementation of project design features. Pile burning may not remain in a low 

intensity category but effects will also be mitigated with project design features.

Several investigations on the effects of prescribed fire provide support to the view that instream 

sediment impact due to underburn treatments is negligible. A multi-year study of effects to 

riparian and stream habitat following a prescribed fire was conducted on the Payette National 

Forest in Idaho (Arkle and Pilliod 2010). The prescription was for an upslope low-intensity burn 

with no ignition in the riparian area; however, fire was allowed to back into the riparian area.

This prescription, and results, are similar to what is anticipated to occur in the project area. The 

conclusion was that disturbance to the riparian corridor would have to be much greater for 

effects to sediment to be more than negligible. For instance there would have to be higher fire 

intensity, or more riparian area burned, before impacts would be observable beyond which is

expected by natural background variation. A second study looked at the post-fire response to a 

more aggressive fire prescription (Beche, et al. 2005). Located in north-central California, 

treatments included active riparian ignition during an early-fall burn window to produce patches 

of low- to moderate-intensity severity within the riparian corridor. Although understory 

vegetation experienced significant reduction, there was no change in fine sediment input, and the 

riparian reserve continued to act as a functional buffer to the effects of moderate-intensity burn 

on adjacent upland slopes.

Summarized for Alternative 2 for prescribed fire treatments, including underburning and pile 

burning, no measurable effect to fine sediment input or substrate composition is expected. 

Project design features will ensure that riparian reserve fire severity will remain low and patchy 

in extent. Any sediment input resulting from prescribed fire actions will be minimal and not 

discernable over existing background variability.

Construction of the temporary stream crossing

There is one site located within an anadromous fish bearing stream (Humbug Creek) where a 

temporary stream crossing will be installed to allow project vehicles to cross the stream. This 

crossing site is where Forest System Road 45N53 crosses Humbug Creek. Therefore, 

construction of this crossing could mobilize suspended sediment to downstream aquatic habitat. 

However, potential sediment generated from construction of the crossing is likely to be 

undetectable greater than 300 feet downstream of the site and, therefore, any effects to fish or 

their habitat would be localized. Suspended sediment increases turbidity see Turbidity 

Discussion below. The site work will be done in accordance with appropriate Project best 

management practices and project design features described in chapter 2 of the Craggy Project 

Environmental Impact Statement as displayed in Appendix D of that document.

Legacy Sites

Treatment for most legacy sites will require ground disturbance. Except in the case of those 

locations which include an instream component, any sediment impact is expected to remain 

localized to the roadbed and near-slope areas. Only legacy sites with an instream component 

have the potential to affect waterways (eight sites), see Turbidity Discussion below. As part of 

project planning and implementation, members of the interdisciplinary team design and monitor 

the use of project-specific best management practices, ensuring they are employed in crossing 

upgrades, so that short term impacts to fish habitat, especially related to sediment, are 

sufficiently minimized. Additionally, for this project, the remaining legacy site activities occur in 
Aquatics Resource Report Craggy Vegetation Management Project

24

association with stream channels (ephemeral, intermittent, or perennial) that are well above 

habitat occupied by fish, and potential sediment generated from these activities is likely to be 

undetectable greater than 300 feet downstream of the site and, therefore, would not have any 

effect to fish or their habitat.

In the long term, legacy site repair will benefit watersheds in the project area. Because legacy 

sites will be repaired individually and not as a more comprehensive stormproofing package, 

cumulative watershed effect models are unable to show the improvements because the combined 

footprint is below the threshold of what is able to be modeled on the landscape level. However, 

by attending to the legacy sites, risk from human-caused sediment impacts will be reduced. This 

action will contribute to the continued maintenance of project watersheds as properly functioning 

in regard to sediment.

Summary

Most sediment which is mobilized by project activities is expected to remain localized near to 

the site of disturbance. Because there will be no measurable transport of sediment to fishoccupied areas above the background level, indicators which directly or indirectly rely upon this 

metric (turbidity) will not be affected. Due to the location of the project on the landscape, the 

functionality of riparian reserves as areas that protect streams, project design features, and best 

management practices lead to adequate control to overland movement of sediment; neither fish 

nor their habitat will be affected by changes to the sediment regime caused by project activities.

Turbidity

Turbidity will potentially only be created by this project through activities that will occur within 

a stream channel such as work associated with the temporary stream crossing site, legacy site 

repair and water drafting.

There is one temporary stream crossing site located within a stream channel containing 

anadromous fish. This site is located where Forest System road 45N53 crosses Humbug Creek.

There are two legacy sites located within 300 feet of anadromous fish bearing streams and five

sites located within 300 feet of resident fish bearing streams.

The closest legacy site distances (approximate) to anadromous fish-bearing streams are:

• Site 45N08X.1-0.10 (Humbug Creek drainage) – less than 300 feet to resident rainbow 

trout; less than 300 feet to Coho, steelhead, and critical habitat.

• Site 45N08X-0.10 (Humbug Creek drainage) – less than 300 feet to resident rainbow 

trout; less than 300 feet to Coho, steelhead, and critical habitat.

The closest legacy sites distance (approximate) to resident fish bearing streams are:

• Site 45N53-0.40 (Sucker Creek drainage) – less than 300 feet to resident rainbow trout.

• Site 45N53-0.50 (Sucker Creek drainage) – less than 300 feet to resident rainbow trout.

• Site 45N53-0.57 (Sucker Creek drainage) – less than 300 feet to resident rainbow trout.

• Site 45N53-0.72 (Sucker Creek drainage) – less than 300 feet to resident rainbow trout.

• Site 45N53-0.90 (Sucker Creek drainage) – less than 300 feet to resident rainbow trout.
Aquatics Resource Report Craggy Vegetation Management Project

25

The amount of ground disturbance and associated stream turbidity that is likely as a result of 

these crossing upgrades is limited in scope and intensity. The Forest has consulted with NOAA

Fisheries both programmatically and on a project-specific basis on this type of work since the 

Coho Salmon was listed as threatened under the Endangered Species Act in 1997. As part of 

project planning and implementation, members of the interdisciplinary team design and monitor 

the use of project-specific best management practices to ensure crossing upgrades are employed 

so that short-term impacts to fish habitat resulting from crossing upgrade work at the sites listed 

above, especially related to sediment, are sufficiently minimized.

Additionally, for this project, the remaining legacy sites which occur in association with stream 

channels (ephemeral, intermittent, or perennial) are well above habitat occupied by fish, and 

potential sediment generated from these activities is likely to be undetectable greater than 300 

feet downstream of the site and therefore would not have any effect to fish or their habitat.

When drafting from Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug 

Creek, a small plume of suspended sediment is expected during operations, particularly when the

hose is set into and pulled out from the water. As discussed in the direct effects section, turbidity 

will be localized, minimal in extent and duration, with the most likely fish behavior to be one of 

avoidance. No measurable increase in turbidity or bed load is expected beyond the immediate 

area where drafting occurs. Turbidity associated with similar water drafting has been observed to 

be momentary, localized, and quickly dissipating to background conditions (as discussed in the 

description of this analysis indicator earlier in this report). It is unlikely that the small, ephemeral 

plumes of sediment produced in the immediate area where drafting occurs might expose fish, 

including Coho Salmon, to gill damage, reduced oxygen uptake, reduced vision, or compromised 

feeding; because the expected behavioral response of fish is avoidance and their ability to 

sufficiently avoid the disturbance is likely.

Summary

Only work associated with the one temporary stream crossing site, legacy site repair and water 

drafting would occur within a stream channel, potentially creating turbidity. The amount of 

ground disturbance and associated stream turbidity likely as a result of the crossing upgrades is 

limited in scope and intensity. With the legacy site repairs proposed in this alternative, 

approximately 936 less cubic yards of sediment will be available for discharge into streams 

containing anadromous fish and resident rainbow trout habitat, decreasing the amount of 

turbidity possible and thus decreasing negative effects to anadromous fish and resident rainbow 

trout or their habitat. Potential sediment generated from legacy site activities which occur in 

association with stream channels and are well above habitat occupied by fish, is likely to be 

undetectable greater than 300 feet downstream of the site and therefore would not have any 

effect to fish or their habitat.

Where drafting sites are within fish-occupied waters, a small plume of suspended sediment is 

expected during operations but turbidity will be localized and minimal in extent and duration, 

with the most likely fish behavior to be one of avoidance. No measurable increase in turbidity is 

expected beyond the immediate area where drafting occurs.

Large Woody Debris

Thinning with Product Removal
Aquatics Resource Report Craggy Vegetation Management Project

26

Effects to the recruitment and transport of large woody debris of an appropriate size to affect 

habitat attributes of fish-bearing streams is not expected. Creeks with fish and fish habitat 

adjacent to units of thinning without product removal will retain similar rates of current large 

woody debris recruitment due to the width of riparian reserves protecting streams. Where a 

decreased input of smaller debris may affect function of fishless headwater systems, the impact 

will be short-term, localized, and unlikely to be noticeable downgradient within fish-occupied 

reaches. In the long term, benefits are expected throughout the project area via the growth of 

larger trees which may contribute to future large woody debris input.

The project area is “Not Properly Functioning” in regards to large woody debris. Due to this 

existing condition, activities within the riparian reserves, with a focus on units of thinning with 

product removal, were planned to best maintain current and future woody debris input while still 

addressing the purpose of the overall project. Different “no-treatment” zones were devised for 

harvest units, based upon presence or absence of fish in unit waterways, location of culverts, and 

silviculture and fuels needs.

A zone in which there will be no thinning with product removal applies to fish-bearing streams 

traversing or adjacent to all harvest units (plantation or natural stands). The total number of units 

with this treatment is six. The 150-foot distance is one “site potential” tree, which is well beyond 

the 100-foot (about 30 meters) distance that Benda and Bigelow (2011) concluded as being 

where ninety percent of large wood recruits originate. The 150-foot no-treatment buffer width of 

the zone in which no thinning with product removal will occur is also beyond that which is 

modeled by Benda et al. (2015) whereupon two thirds of a tree’s height is suggested to be 

sufficient to maintain wood recruitment at 95 percent (i.e., two thirds of 150-foot tree height 

equates to 112 feet).

Trees thinned from units with product removal that are adjacent to fish-bearing streams are 

expected to be less than 150 feet long. For those stands sampled for this project, the average tree 

height was around 100 feet. Within all project harvest units, trees greater than 150 feet in height 

are very rare and associated diameters for trees of this height are at least 55 inches. Furthermore, 

the stated focus of harvest is on trees 25 inches in diameter and smaller, a size class which is too 

small for a Project area tree to have achieved a 150-foot height. These details further diminish 

the likelihood that thinning will affect existing recruitment because the zone of no thinning with 

product removal is wider than the height of trees that are expected to be available for harvest.

Overall, it is expected that large woody debris recruitment to fish-bearing streams within harvest 

units will remain similar to the rates currently existing.

A 100-foot area on either side of streams traversing or adjacent to natural stand harvest units 

which are located down-gradient of road crossings, and no other crossing is present between the 

unit and a fish-occupied waterway, will have no thinning with product removal. All of these 

stream systems are fishless, and channels may be intermittent or perennial in character. A total of 

six units are identified as falling partially or entirely within this category. Due to the location of 

these units, there is no barrier to movement of woody debris and potential subsequent 

recruitment to fish-bearing waterways. Therefore, a 100-foot (about 30 meters) no-treatment 

zone encompasses the Benda and Bigelow (2011) 90 percent wood recruitment zone for these 

units.
Aquatics Resource Report Craggy Vegetation Management Project

27

Overall, it is expected that large woody debris recruitment to headwater streams within natural 

stand harvest units and subsequent transportation will remain similar to the rates currently 

existing.

An area 50 feet in width from either side of streams will be have no thinning with product 

removal in all natural and plantation stands. This zone of no thinning with product removal

applies to streams traversing or adjacent to units which are located up-gradient of road crossings. 

All of these systems are fishless and the channels may be intermittent or perennial in character. 

A total of eight units are identified as falling partially or entirely within this category. Due to the 

stand locations, there are one or more road crossings between the units and fish-bearing waters. 

The existing condition of woody debris transportation is thus compromised: any large wood 

which gets caught at the crossings is cut up and removed before it can threaten road integrity. 

Therefore, large wood which originates from harvest units upstream of road crossings is not 

expected to recruit to fish-bearing streams.

Overall, there may be a short-term decline in wood debris, but the effect on fish-bearing reaches 

will be minimal. There will be no changes in existing recruitment of larger pieces, such as those 

recognized to benefit habitat in fish-bearing streams, because the presence of culverts below 

harvest units restricts the downgradient movement of these debris. The recruitment rate of small 

wood debris to headwater channels may be decreased, leading to a localized effect, but a 

noticeable impact downstream within fish-bearing reaches is not expected.

Thinning with no Product Removal and Fuelbreaks

To meet objectives, thinning without product removal, and fuelbreaks construction and 

maintenance, will target small trees and brush less than 10 inches in diameter. An equipment 

exclusion zone prevents close approach to stream channels. Therefore, all near-stream activities 

will be accomplished via manual methods. Except for best management practices and project 

design features that prohibit the cutting of trees directly rooted in stream banks, there are no 

treatment exclusion distances from water. Units associated with fish-bearing waterways are 

limited to a few sites; the size material being removed is too small to affect pool formation or 

other habitat attributes at these places. Elsewhere, the potential effect to the upper stream reaches

will be localized and have minimal to no effect to downstream fish-bearing reaches, as 

previously described.

Summary

Effects to the recruitment and transport of large woody debris of an appropriate size to affect 

habitat attributes of fish-bearing streams is not expected. Creeks with fish and fish habitat 

adjacent to harvest units will retain similar rates of current large woody debris recruitment. 

Where a decreased input of smaller debris may affect the function of fishless headwater systems, 

the impact will be short term, localized, and unlikely to be noticeable downgradient within fishoccupied reaches. In the long term, benefits are expected throughout the Project area via the 

growth of larger trees which may contribute to future large woody debris input.

Disturbance History and Regime

Ground disturbance within the project area will include the following activities: landing 

construction, thinning with and without product removal, development and maintenance of 

fuelbreaks, and prescribed burning elements consisting of pile-burning and underburning. 

Prescribed burning will occur within thinning units as well as on the general landscape. 
Aquatics Resource Report Craggy Vegetation Management Project

28

Additional ground disturbance will occur in conjunction with legacy sediment site activities, 

such as repairing culvert crossings where new temporary roads are established, and where 

temporary roads are re-established on existing roadbeds. All temporary roads will be closed and 

hydrologically stabilized at the completion of the project.

The ERA indices will increase in the Lower Humbug Creek, Upper Humbug Creek and Middle 

Fork Humbug Creek 7th field watersheds as a result of project implementation (Tables 5-6; 

USDA 2017; Craggy Project Hydrology Resource Report). The greatest increase will be 

associated with the Upper Humbug Creek 7th field watershed where the bulk of grounddisturbing activities will occur: thinning with and without product removal, development and 

maintenance of fuelbreaks, prescribed burning, and temporary road use. The Lower Humbug 

Creek and Middle Fork Humbug Creek 7th field watersheds will see small increases in the ERA 

indices. All three 7th field watersheds are below threshold for ERA and will not cross the 

threshold of concern as a result of project actions. The Upper Humbug Creek 7th field watershed 

will maintain an elevated geology model (GEO) risk rating, but the project will not noticeably 

increase the existing risk. It decreases from 1.37 to 1.29 in Upper Humbug Creek and in Middle 

Fork Humbug Creek it goes below threshold of concern from 1.10 to 0.89. The GEO risk rating 

for the Lower Humbug Creek 7th field watershed decreases from 0.53 to 0.47. There are very 

slight increases in the USLE risk ratings for Upper Humbug Creek and Middle Fork Humbug 

Creek 7th field watersheds. There is a very slight decrease in the USLE risk rating in the Lower 

Humbug Creek 7th field watershed. None of these watersheds are over threshold for USLE.

Summary

While there are increases in the ERA and USLE cumulative watershed effects model estimates as 

a result of this project, there will be no significant effects to aquatic habitat from any project 

activities (see the cumulative watershed effects model results on the project website). Model 

estimates for the equivalent roaded area and the universal soil loss equation remain below the 

threshold, and this analysis concludes that the functional level of this indicator will not change. 

Model estimates for GEO, while over threshold in Upper Humbug Creek, do decrease as a result 

of the project. Additionally, because all other models remain below threshold, indicators which 

directly or indirectly use this metric will not be measurably affected: peak or base flows, 

substrate and turbidity.

Peak and Base Flows

At the site level, water drafting will occur in the following anadromous streams: Humbug Creek, 

Middle Fork Humbug Creek, and South Fork Humbug Creek. Therefore, there is the potential for 

short-term indirect effects downstream. Watering drafting at upslope sites where no fish are 

present will also result in localized changes in flows but these will not be measurable or 

discernable at occupied habitat downstream. This is because, at all project drafting sites, the 

pumping rate will not exceed 350 gallons per minute or 10 percent of the flow of any 

anadromous stream and pumping will be done in short periods. Water drafting will result in only 

slight temporary decreases in flow which will be undetectable at both a short distance 

downstream and further downstream in fish-occupied habitat. In large systems, flows are not 

measurably affected by typical short-term drafting operations such as those required to fill a 

water tender (Sicking 2003). Additionally, as analyzed in the Facility Maintenance and the 

Facilities Maintenance and Watershed Restoration Biological Assessment, the effects of water 

drafting are considered to be insignificantly small (USDA 2004).
Aquatics Resource Report Craggy Vegetation Management Project

29

There will be no watershed-scale changes to peak or base flows as a result of project activities 

due to treatment unit location on the landscape, minimal and localized impacts, and functioning 

buffering capacity of intervening riparian reserve habitat. This is reflected in the equivalent 

roaded area model output which remains below the threshold of concern (see Table 4).

Drainage Network

The construction or reoccupation of existing landings and skid trails will create a temporary 

increase in the local drainage network while the commercial element of the project is active. Any 

effects will be short term and confined to treatment units in upslope areas. Project design features 

will help ensure that drainage impacts are short-term and localized. This is because skid trails 

will not cross perennial streams, and intermittent streams will only be crossed while dry and at 

pre-approved locations. In the long term, there will be no increase in the drainage network from 

these timber harvest-related activities because landings and skid trails will be rehabilitated.

Roads can have a major impact on the drainage network. The project will affect no change in 

miles of National Forest Transportation System (system) roads on the landscape and there will be 

no authorized public motorized vehicle use of currently closed or decommissioned roads. About 

12 miles of existing roadbeds will be used as temporary roads. Three new temporary roads will 

be constructed to access landings; the total length of these will be small (about two miles). After 

their use for the project, all temporary roads will be hydrologically stabilized. This includes such 

treatments as removing materials used for any stream channel crossings, outsloping road prisms 

if appropriate, and obliterating access to the road. Overall, these actions are expected to eliminate 

or minimize negative effects that are due to treatments; this is because these temporary road 

segments will be left in a hydrologic state that is similar to or better than their pre-project 

condition. Because the pre- and post-project conditions will be similar on the landscape scale, 

any long-term beneficial effects are too small to be accounted for in the equivalent roaded area

model analysis. Additional localized benefits are expected at legacy sites which correct 

conditions that may cause adverse instream hydrologic issues.

Summarizing, in the short term, there will be an insignificant increase in the drainage network 

from landing and skid trail construction, with these impacts being neutral in the long term due to 

subsequent rehabilitation and natural stabilization. In the long term, there will be an insignificant 

decrease in the drainage network following the hydrologic stabilization of temporary roads and 

legacy site repair.

Riparian Reserves

Project activities within riparian reserves include thinning with and without product removal, 

mastication, developing and maintaining fuelbreaks, prescribed burning (underburning), and 

water drafting. New landings will not be constructed within riparian reserves, although some 

existing ones may be reoccupied. Where existing riparian reserve landings are used, they will be 

stabilized after the project and project design features will be implemented so that riparian 

reserve character will not be detrimentally altered by project activities. In some treatment units, a 

long term benefit may occur via the promotion of the growth of larger trees.

Thinning with and without Product Removal

Best management practices and project design features minimize project-associated impacts from

disturbance, the use and maintenance of system roads, and changes to temperature (i.e., shade) 

within the riparian reserves. Therefore, the focus of discussion for riparian reserve character as 
Aquatics Resource Report Craggy Vegetation Management Project

30

potentially affected by thinning treatments is on elements of in-stream wood production in the 

short and long term.

The Craggy Project thinning treatments may have a short-term negative effect to riparian 

reserves but are expected to impart a long-term benefit. Short-term effects to separate elements 

which comprise riparian reserves have been discussed in prior subsections, including “substrate

and sediment”, “disturbance history and regime”, and “large woody debris.” Long-term benefits 

to the riparian and near-riparian uplands within the riparian reserve will require decades to 

become noticeable. Additionally, stand-specific gains in riparian health are expected to be 

greatest in thinning units associated with fishless headwaters. This is because the larger riparian 

reserve widths adjacent to fish-occupied creeks will maximize the retention of existing 

conditions including stand density, and current and future wood recruitment. Vegetation-related 

benefits beyond the first site-potential tree width are likely to remain insignificant to negligible 

in regards to adjacent fish habitat. Instead, the no-treatment portion of these riparian reserves 

must either rely on natural processes to move toward desired conditions, or else on assistance via 

the introduction of prescribed fire (discussed below). On the landscape scale, the long-term 

benefit to riparian reserves includes increased resiliency to permutations; flood, fire, and climate 

change; in sustaining overall riparian functionality.

Mastication and Fuelbreaks

In units that will be masticated, a masticator may reach into the equipment exclusion zone with 

its arm to grind trees and brush, but material beyond the machine’s reach will be treated using 

manual means. Fuelbreaks construction and maintenance, will target small trees and brush less 

than 10 inches in diameter. While mastication treatments and fuelbreak construction will have 

some utility in removing undergrowth and excess fuels, these treatments are expected to impart 

minimal effects to aquatic habitat, including Coho Salmon and their critical habitat.

Although construction of handpiles or pile burning may occur in riparian reserves at least 30 feet 

from perennial or fish bearing streams, and will aid in removing excess fuels, the piles will be 

evenly spaced and will, therefore, not significantly alter effective canopy shade in riparian 

reserves. There will be no long-term effects to riparian reserves from pile burning because the 

effects associated pile burning will be localized, short term, and occur where only the piles are 

placed. Therefore, pile burning may have insignificantly small localized effects but will not 

affect the functional level of the riparian reserve indicator.

Prescribed Burning

Prescribed fire will be used within the project area. Treatments will include handpile burning and 

underburning, both of which have the potential to affect riparian reserve condition. Potential 

impacts of prescribed burning (both underburning and pile-burning) to the individual indicators 

which comprise riparian reserves have already been discussed in their respective subsections. 

Instead, the focus here is on the riparian condition as a whole.

Prescribed fire in the riparian reserve is expected to impart minimal effects to aquatic habitat, 

including Coho Salmon and their critical habitat. While treatments will undoubtedly have some 

utility in removing undergrowth and excess fuels, overall underburning behavior within the 

riparian corridor is expected to be minimal.

In the outer edges of the riparian reserve, where riparian vegetation transitions to upslope 

species, and along drier headwater channels, treatments are expected to be more successful. 
Aquatics Resource Report Craggy Vegetation Management Project

31

Because the project is unlikely to re-establish the natural fire regime, or profoundly decrease fuel 

loading, within riparian corridors, the fire regime component contributing toward riparian 

reserve degradation on the landscape scale within the project area is expected to remain 

unchanged or be insignificantly benefitted.

Water Drafting

Water drafting will involve the use of existing access roads and approaches. Brushing, grading, 

and rocking of existing access roads and approaches will have effects on riparian reserves that 

remain confined to road prisms and vegetation that is immediately adjacent to roads. Brushing of 

approaches will only provide for vehicle passage and will, therefore, not significantly alter 

effective canopy shade in riparian reserves. There will be no long-term effects to riparian 

reserves from drafting because all effects associated with the use of drafting sites will be 

localized, short term, and occur at only eight existing sites. Therefore, water drafting may have 

insignificantly small localized effects but will not affect the functional level of the riparian 

reserve indicator.

Summary

Project activities will have both short-term and long-term effects to riparian reserves. In the short

term, individual components which comprise the riparian reserve indicator will impart 

insignificant, mostly localized, negative effects which will not alter the functional level of the 

riparian reserve in the project area. In the very long term, harvest and silviculture treatments are 

expected to provide a landscape-scale benefit to riparian reserves in the form of larger trees and 

increased size of in-stream wood. However, this positive effect may be offset by prescribed fuels 

treatments which are insufficiently aggressive to fundamentally modify the existing riparian 

condition of an altered fire regime. Therefore, it is the professional judgment of the Fish 

Biologist that the long-term effect to riparian reserves is neutral.

Table 4: Summary of the Effects on Salmonid Fish for Action Alternatives in the Craggy Project by Indicator 

and Project Element

Indicators

Thinning with 

Product Removal

(Tractor, Skyline, 

Endline)

Thinning 

without 

Product 

Removal

Fuelbreak 

Treatments Comments

Temperature -/0 0 0

Insufficient change in effective stream shading 

(vegetation treatments) or flow (drafting) to 

affect fish-occupied waters; see text for further 

discussion

Turbidity 0 0 0

No change in sediment input to fish-occupied 

streams; CWE models remain below threshold 

or do not contribute to over threshold; further 

analysis provided for drafting and legacy 

treatments

Sediment 

and 

Substrate

-/0 0 0

No measurable sediment impacts to fishoccupied streams from Project activities; see 

text for further discussion

Large 

Woody 

Debris

-/0 -/0 -/0

No removal of large woody debris within 

Riparian Reserves; application of project design 

features to burn prescriptions. Further 

discussion is required concerning wood 

recruitment and transportation, especially in 

regard to units of thinning with product removal
Aquatics Resource Report Craggy Vegetation Management Project

32

Indicators

Thinning with 

Product Removal

(Tractor, Skyline, 

Endline)

Thinning 

without 

Product 

Removal

Fuelbreak 

Treatments Comments

Change in 

Peak and 

Base Flows

0 0 0

Insufficient change in Equivalent Roaded Area

to affect flows; further analysis provided for 

drafting

Increase in 

Drainage 

Network

-/+ 0 0

Landing/skid trail construction, temporary 

road/trail rehabilitation, and legacy site 

rehabilitation - analysis provided. Other Project 

elements will not affect the drainage network

Disturbance 

History and 

Regime

-/0 0 0 Increase in disturbance and erosion indices; 

further analysis provided

Riparian 

Reserves -/+ 0/+ 0

While long-term desired Riparian Reserve 

character will not be detrimentally altered, there 

may be short-term effects from multiple Project 

activities; see text for further analysis

Effects and indicators apply to both anadromous and resident fish unless noted.

0 = Neutral effects

- = Insignificant or discountable negative effects

+ = Insignificant or discountable positive effects

S-= Significant negative effects

S+ = Significant positive effects

*/* = Short-term/long-term effects
Aquatics Resource Report Craggy Vegetation Management Project

33

Table 5: Summary of the Effects on Salmonid Fish for Action Alternatives in the Craggy Project by Indicator 

and Project Element

Indicators Prescribed 

Underburn

Water 

Drafting

Temporary Road 

Crossing and

Legacy Treatments

Comments

Temperature -/0 -/0 0

Insufficient change in effective stream 

shading (vegetation treatments) or flow 

(drafting) to affect fish-occupied waters; see 

text for further discussion

Turbidity 0 -/0 -/0

No change in sediment input to fish-occupied 

streams; CWE models remain below 

threshold or do not contribute to being over 

threshold; further analysis provided for 

drafting and legacy treatments

Sediment 

and 

Substrate

-/0 0 -/+

No measurable sediment impacts to fishoccupied streams from Project activities; see 

text for further discussion

Large 

Woody 

Debris

0 0 0

No removal of large woody debris within 

Riparian Reserves; application of project 

design features to burn prescriptions.

Further discussion is required concerning 

wood recruitment and transportation, 

especially in regard to commercial harvest 

units.

Change in 

Peak and 

Base Flows

0 -/0 0

Insufficient change in Equivalent Roaded 

Area risk ratio to affect flows; further 

analysis provided for drafting

Increase in 

Drainage 

Network

0 0 +/+

Landing/skid trail construction, temporary 

road/trail rehabilitation, and legacy site 

rehabilitation - analysis provided. Other 

Project elements will not affect the drainage 

network

Disturbance 

History and 

Regime

0 0 0 Increase in disturbance and erosion indices; 

further analysis provided

Riparian 

Reserves -/0 -/0 0

While long-term desired Riparian Reserve 

character will not be detrimentally altered, 

there may be short-term effects from multiple 

Project activities; see text for further 

analysis

0 = Neutral effects

- = Insignificant or discountable negative effects

+ = Insignificant or discountable positive effects

S-= Significant negative effects

S+ = Significant positive effects

*/* = Short-term/long-term effects

Cumulative Effects

Within the project area, there is one foreseeable non-Federal (e.g., private or State) action 

planned or undergoing implementation at the time of this document: the Badger Timber Harvest 

Plan (THP).
Aquatics Resource Report Craggy Vegetation Management Project

34

The Badger THP will have minor short-term effects to stream temperature, sediment, and peakbase flow in the Lower Humbug Creek 7th field watershed. There may be a slight increase in 

stream temperature in the sections of Humbug Creek downstream of the project activities, and 

sediment input to the stream channel may increase slightly as well. However, the effects are not 

likely to result in any detectable change to stream temperature in fish-bearing reaches or have 

any meaningful impact to fish habitat, including thermal refugia.

Cumulative impact occurs when the effect of one project overlaps in time and space with or 

compounds the effects of another. Adding the effects on aquatic species and habitat of 

Alternative 2 to the effects of the Badger THP would constitute cumulative effects of this 

alternative. The primary consequence to fish and aquatic habitat of Alternative 2 is related to 

legacy sediment site impacts.

A reasonable foreseeable future action planned at the time of this document that coincides with 

the watersheds that are analyzed in this document for effects to aquatic habitat includes the City 

of Yreka Wildland Urban Interface Project on private land which is noted in Appendix C of the 

Craggy Project Environmental Impact Statement. This project shares the Middle Fork Humbug 

Creek 7th field watershed and the Humbug-Klamath River 5th field watershed for which this 

report includes and analysis. Since this project proposes fuel reduction treatment, including 

thinning of small material without product removal, the previous discussion of the effects of 

these treatments are not expected to add negative effects to aquatic species.

There are three additional foreseeable future actions planned at the time of this document that 

coincide with the watersheds that were excluded from analysis since they do not have any fish 

resources, and thus there is no chance for effects to fish resources in them.

(1) Yreka Flood Hazard Reduction Project

(2) Lower Yreka Creek Full Restoration Project and Side Channel Project

(3) Fuel Reduction on lands managed by the Bureau of Land Management

While past events within the project area (e.g., mining, timber harvest, road building, grazing, 

flood, and fire) contribute to the existing condition, this project will not cumulatively add 

significant effects in the analysis area for the applicable analysis indicators for aquatic species.

In summary, there will be minimal cumulative impacts to aquatic species from current and 

reasonably future foreseeable projects within the vicinity of the Craggy Project. Model estimates 

for GEO, while over threshold in Upper Humbug Creek, do decrease as a result of the project. In 

Middle Fork Humbug Creek the pre-project model estimates for GEO are over threshold, but 

decrease below threshold as a result of the project. Cumulative watershed effects models for 

watersheds that are currently below threshold remain below the threshold of concern when 

effects of Alternative 2 are added to the effects of other past, current and reasonable foreseeable 

actions so there are no significant cumulative effects of aquatic species and their habitat.

Alternative 3

Direct Effects

Direct effects for Alternative 3 are the same as direct effects for Alternative 2 because the 

number and likely location of water drafting sites is the same in both action alternatives.
Aquatics Resource Report Craggy Vegetation Management Project

35

Indirect Effects

Temperature

The effects of Alternative 3 are the same as for Alternative 2 with the following exceptions:

Commercial harvest units were reviewed in regards to proposed equipment and treatment 

exclusion zones adjacent to stream channels. Vegetation treatments next to fish-occupied habitat 

are at least 150 feet from streams except in four units, Units 134-41, 134-248, 138-23, and 138-

501 (see Table A-1 in Appendix A). The bottom of units 134-41 and 134-248 are bounded by 

Forest Road 45N53, which runs parallel to Sucker Creek. The bottom of units 138-23 and 138-

501 are bounded by Forest Road 45N43, which runs parallel to Middle Fork Humbug Creek. The 

closest approach of Unit 134-41 to Sucker Creek is about 75 feet, and the closest approach of 

unit 134-248 to Sucker Creek is about 100 feet. The closest approach of units 138-23 and 138-

501 to Middle Fork Humbug Creek is about 100 feet. Due to the width of Forest Service Roads 

45N53 and 45N43, their location, and general topographic configuration, trees in the units next 

to these roads are largely disconnected from their riparian function, including shade. Elsewhere 

in the project area, the treatment buffer may be as little as 15 feet in plantation units and 50 feet 

in natural stands. These latter locations are all associated with fishless channels. Commercial 

treatment units have been reviewed by resource specialists and confirmed that habitat elements, 

including effective stream shade, will be maintained. Therefore, because shade will be preserved, 

there is not likely to be any meaningful effect to fish-bearing reaches, including Coho Salmon 

critical habitat, due to this project (Fish Biologist field review).

Substrate and Sediment

The difference of treatments in Alternative 3 compared to Alternative 2 is negligible in terms of 

their effects upon this indicator and, therefore, effects are similar to Alternative 2.

Turbidity

Effects of Alternative 3 will be the same as for Alternative 2 in terms of water drafting, the 

temporary stream crossing where Forest System Road 45N53 crosses Humbug Creek, and legacy 

sites since the same number and location of sites is the same in both action alternatives.

(see the Craggy Project Hydrology Resource Report for additional information).

Large Woody Debris

The effects of Alternative 3 will be the same as for Alternative 2 with the following exceptions:

There will be five thinning with product removal units in which there will be a no-treatment zone 

of one potential site tree (150 feet) on either side of fish-bearing streams (compared to six units 

in Alternative 2). There will be five thinning with product removal units in which a no-treatment 

zone of 100 feet in width on either size of fish-bearing streams (compared to six in Alternative 

2); and seven such units in which the no-treatment zone is 50 feet from either side of a stream 

(compared to eight in Alternative 2). There would be negligible differences between the action 

alternatives in terms of large woody debris recruitment.

Disturbance History and Regime

The effects of Alternative 3 on disturbance history and regime would be the same as for 

Alternative 2 with the following exception:
Aquatics Resource Report Craggy Vegetation Management Project

36

The increase over the baseline in equivalent roaded area (ERA) for Alternative 3 is slightly less 

than for Alternative 2 (see the Craggy Project Cumulative Watershed Effects Model results 

available on the project website). There is a very slight decrease in the geology (GEO) model 

results for Alternative 3 than for Alternative 2 in Upper Humbug Creek 7th field watershed and 

the results are the same as for Alternative 2 in Lower Humbug Creek and Middle Fork Humbug 

Creek 7th field watersheds. The universal soil loss equation (USLE) models show very slight 

decreases in all three 7th field watersheds for Alternative 3 than for Alternative 2. These models 

do not capture the effects of treating legacy sediment sites, as discussed above under Turbidity 

and in the Hydrology resource report.

Peak and Base Flow

The difference of treatments in Alternative 3 compared to Alternative 2 is negligible in terms of 

their effects on this indicator. There is no discernible difference between the action alternatives 

in terms of effects on peak and base flow.

Riparian Reserves

The difference of treatments in Alternative 3 compared to Alternative 2 is negligible in terms of 

their effects upon this indicator. There is no discernible difference between the action 

alternatives in terms of effects on riparian reserves.

Cumulative Effects

The difference of treatments in alternative 3 compared to alternative 2 is negligible in terms of 

their cumulative effects and therefore they are similar to Alternative 2. See the cumulative 

effects discussion for Alternative 2.

Comparison of Alternatives

Although there will be no long-term change in the baseline functionality of analysis indicators

with implementation of the Craggy Project, there will be some long-term benefits of taking 

action. The benefits to water quality displayed in the Hydrology resource report are likely to 

have some beneficial effect on aquatic species. Negative effects of action alternatives are 

primarily short term and are eliminated or minimized by implementation of best management 

practices and project design features. There will be a small benefit for the drainage network 

indicator under action alternatives compared to Alternative 1 but it will not likely be sufficient to 

change the existing condition.

Table 6: Indicator Summary for Craggy Project Alternatives

Indicator Alternative 1 Alternative 2 Alternative 3

Temperature 0 -/0 -/0

Substrate/Sediment 0 -/+ -/+

Turbidity 0 -/0 -/0

Large Woody Debris 0 -/0 -/0

Disturbance History/Regime 0 -/0 -/0

Peak and Base Flow 0 -/0 -/0
Aquatics Resource Report Craggy Vegetation Management Project

37

Indicator Alternative 1 Alternative 2 Alternative 3

Drainage Network 0/- -/+ -/+

Riparian Reserves 0 -/+ -/+

0 = Neutral effects

- = Insignificant or discountable negative effects

+ = Insignificant or discountable positive effects

S-= Significant negative effects

S+ = Significant positive effects

*/* = Short-term/long-term effects

Potential indirect impact to aquatic resources will occur as a result of harvest and silviculture 

activities, prescribed fire, fuelbreaks, the one temporary stream crossing site where Forest 

System road 45N53 crosses Humbug Creek, legacy site treatments, and water drafting. Most 

effects will be localized, insignificant, and short term and will impart no meaningful impact to 

fish or fish habitat, including Coho and Coho critical habitat. The majority of project activities 

are mid-slope, on ridges, or adjacent to fishless streams distant from fish-occupied waters. The 

use of project design features and best management practices, along with set buffer distances, 

will mitigate most potential impactors to aquatic resources to non-detectability from background 

natural variation. While cumulative watershed effects models will be affected by project actions, 

they will either remain below critical threshold or not contribute to over-threshold risks. Finally, 

there will be insignificant beneficial effects due to treatment of legacy sediment sites and postproject rehabilitation of temporary roads; and riparian reserve condition in some locations may 

also benefit in the long term in the growth of larger trees and the increased size of in-stream 

wood.

Since the action alternatives are so similar, the fish biologist has reached the following 

determinations on the effects of action alternatives as outlined in Table 7.

Table 7: Summary of Determinations for Action Alternatives for the Craggy Project

Species Special 

Status

1

Determination

Fish Species

Coho Salmon (and critical habitat) Federally-listed 

as Threatened NLAA

Chinook Salmon (Spring/Fall runs)

(Upper Klamath-Trinity Rivers) FSS NE

Steelhead Trout

(Klamath Mountains Province) FSS, MIS MANL

Rainbow Trout (resident) MIS MANL

Pacific Lamprey FSS MANL

Klamath River Lamprey FSS MANL

Other Habitat
Aquatics Resource Report Craggy Vegetation Management Project

38

Species Special 

Status

1

Determination

Essential Fish Habitat 

(Coho/Chinook) N/A Will Not Effect 

1

Federally Listed Species

NE - Will not affect the species or its Critical Habitat

NLAA - May affect, not likely to adversely affect the species or its Critical Habitat

LAA - May affect, likely to adversely affect the species or its Critical Habitat

Forest Sensitive Species (FSS) / Management Indicator Species (MIS)

NE - No effect to the species (FSS and MIS)

MANL - May affect individuals, but is not likely to lead to a trend towards listing (FSS); and/or

 May affect individuals, but is not likely to lead to a decreasing population trend (MIS)

MALT - May affect individuals, and is likely to result in a trend towards listing (FSS); and/or

 May affect individuals, and is likely to lead to a decreasing population trend (MIS)

Compliance with law, regulation, policy, and the Forest Plan

All alternatives will meet Forest Plan standards and guidelines, the Endangered Species Act, the 

Magnuson-Stevens Fishery Conservation and Management Act, and all other relevant 

regulations, laws, and policies. Section 7 consultation will be completed with the National 

Marine Fisheries Service for a preferred alternative.
Aquatics Resource Report Craggy Vegetation Management Project

39

Literature Cited

Arkle, R.S., and D.S. Pilliod. 2010. Prescribed fires as ecological surrogates for wildfires: a 

stream and riparian perspective. Forest Ecology and Management 259: 893-903

Aust, W.M., and C.R. Blinn. 2004. Forestry best management practices for timber harvesting and 

site preparation in the eastern United States: an overview of water quality and 

productivity research during the past 20 years (1982-2002). Water, Air, and Soil 

Pollution: Focus 4: 5-36.

Beche, L.A., Stephens, S.L., and V.H. Resh. 2005. Effects of prescribed fire on a Sierra Nevada 

(California, USA) stream and its riparian zone. Forest Ecology and Management 218: 37-

59.

Bell, A. 2012. Cumulative Watershed Effects Modeling: The Abridged Version. Prepared for the 

Klamath National Forest.

Benda, L., and P. Bigelow. 2011. Recruitment, storage, transport and function of wood in 

Northern California streams. A report submitted to the California Board of Forestry and 

Fire Protection. 49 p.

Benda, L.E., Litschert, S.E., Reeves, G., and R. Pabst. 2015. Thinning and in-stream wood 

recruitment in riparian second growth forests in coastal Oregon and the use of buffers and 

tree tipping as mitigation. Journal of Forestry Research, 1-16. doi:10.1007/s11676-015-

0173-2

Bjornn, T.C., and D.W. Reiser. 1991. Habitat requirements of salmonids in streams. In:

Influences of forest and rangeland management on salmonid fishes and their habitat 

(W.R. Meeham, ed.). American Fisheries Society Special Publication 19, pp. 83-138.

Brown, T.M. 2002. Short-term total suspended-solid concentrations resulting from stream 

crossing obliteration in the Clearwater National Forest, Idaho. MS Thesis. Seattle, WA: 

University of Washington, College of Forest Resources, Division of Management and 

Forestry.

Castelle, A.J., A.W. Johnson, and C. Conolly. 1994. Wetland and stream buffer requirements – a 

review. Journal of Environmental Quality 23: 878-882.

Chamberlin, T.W., R.D. Harr, and F.H. Everest. 1991. Timber harvesting, silviculture, and 

watershed processes. In: Influences of forest and rangeland management on salmonid 

fishes and their habitat (W.R. Meeham, ed.). American Fisheries Society Special 

Publication 19, pp 181-206.

Clinton, B.D. 2011. Stream water responses to timber harvest: riparian buffer width 

effectiveness. Forest Ecology and Management 261: 979-988.

Croke, J., and S. Mockler. 2001. Gully initiation and road-to-stream linkage in a forested 

catchment, southeastern Australia. Earth Surface Processes and Landforms 26: 205-217.
Aquatics Resource Report Craggy Vegetation Management Project

40

Edwards, P.J., and K.W.J. Willard. 2010. Efficiencies of forestry best management practices for 

reducing sediment and nutrient losses in the eastern United States. Journal of Forestry

108: 245-249.

Foltz, R.B., and K.A. Yanosek. 2005. Effects of road obliteration on stream water quality in

Managing watersheds for human and natural impacts (Moglen, G.E., ed.). Proceedings of 

the 2005 Watershed Management Conference (July 19-22), American Society of Civil 

Engineers, Williamsburg, Virginia. 12 p.

Madej, M.A. 2001. Erosion and sediment delivery following removal of forest roads. Earth 

Surface Processes and Landforms 26: 175-190.

May, C., and R. Gresswell. 2003. Large wood recruitment and redistribution in headwater steams 

in southern Oregon Coast Range, USA. Canadian Journal of Forest Research 33: 1352-

1362.

May, C., and R. Gresswell. 2004. Spatial and temporal patterns of debris-flow deposition in the 

Oregon Coast Range, USA. Geomorphology 57: 135-149.

Meehan, W.R. (ed.). 1991. Influences of forest and rangeland management on salmonid fishes 

and their habitats. American Fisheries Society Special Publication 19.

National Oceanic and Atmospheric Administration (NOAA). 2001. NOAA Fisheries Water 

Drafting Specifications. National Marine Service, Southwest Region.

National Marine Fisheries Service (NOAA). 2014a. Final Recovery Plan for the Southern 

Oregon/Northern California Coast Evolutionarily Significant Unit of Coho Salmon 

(Oncorhynchus kisutch) (Chapters 1-6). National Marine Fisheries Service. Arcata, CA.

National Marine Fisheries Service (NOAA). 2014b. Chapter 33 of the Final Recovery Plan for 

the Southern Oregon/Northern California Coast Evolutionarily Significant Unit of Coho 

Salmon (Oncorhynchus kisutch). National Marine Fisheries Service. Arcata, CA.

Neary, D.G., K.C. Ryan, and L.F. DeBano, eds. 2005. (Revised 2008). Wildland fire in 

ecosystems: effects of fire on soils and water. Gen. Tech. Rep. RMRS-GTR-42-vol. 4. 

USDA Forest Service, Rocky Mountain Research Station, Ogden, UT. 250 p.

Parsons, A.J., J. Wainwright, R.E. Brazier, and D.M. Powell. 2006a. Is sediment delivery a 

fallacy? Earth Surface Processes and Landforms 31: 1325-1328.

Parsons, A.J., R.E. Brazier, J. Wainwright, and D.M. Powell. 2006b. Scale relationships in 

hillslope runoff and erosion. Earth Surface Processes and Landforms 31: 1384-1393.

Rosgen, D. 1996. Applied River Morphology. 1st Edition. Wildland Hydrology. Pagosa Springs, 

CO.

Royer, T.V., A.M. Prussian, and G.W. Minshall. 1999. Impact of suction dredging on water 

quality, benthic habitat, and biota in the Fortymile River and Resurrection Creek, Alaska. 

Prepared for Environmental Protection Agency, Region 10, Seattle, WA. 72 p.
Aquatics Resource Report Craggy Vegetation Management Project

41

Sear, D.A., A. Briggs, and A. Brookes. 1998. A preliminary analysis of the morphological 

adjustment within and downstream of a lowland river subject to river restoration. Aquatic 

Conservation: Marine and Freshwater Ecosystems 8: 167-183.

Sicking, L.P. 2003. Anadromous fish strainers for use in wildland drafting operations. USDA 

Forest Service, San Dimas Technology and Development Center, San Dimas, CA. 24 p.

Swanston, D.N. 1991. Natural processes. In: Influences of forest and rangeland management on 

salmonid fishes and their habitat (W.R. Meeham, ed.). American Fisheries Society 

Special Publication 19, pp 139-180.

USDA Forest Service. 1995. Klamath National Forest Land and Resource Management Plan. 

Updated 2010. Klamath National Forest, Yreka, CA.

USDA Forest Service. 1993. Klamath National Forest Humbug Landscape Analysis and Design. 

Klamath National Forest, Yreka, CA. 70 pp. + appendices.

USDA Forest Service. 2004. Biological Assessment/Evaluation for Threatened, Endangered, 

Proposed, Petitioned and Sensitive Species that may be affected by Facility Maintenance 

and Watershed Restoration. Klamath National Forest, Yreka, CA. 45 pp + appendices.

USDA Forest Service, Klamath National Forest. 2011. Stream Shade Monitoring on the Klamath 

National Forest 2010. Yreka, CA.

USDA Forest Service, Klamath National Forest. 2012. Stream temperature monitoring on the 

Klamath National Forest: 2010 - 2011. Yreka, CA.

USDI Fish and Wildlife Service. 2017. Memorandum: List of threatened and endangered species 

that may occur in the Craggy proposed project area. Consultation Code 08EYRE00-2017-

SLI-0141 (from ECOS-IPaC) June 20, 2017.

USDI, USDA, and NOAA. 2004. Analytical process for developing biological assessments for 

federal actions affecting fish within the Northwest Forest Plan area. November 2004. 17 

pp. + appendices.

Wemple, B.C., J.A. Jones, and G.E. Grant. 1996. Channel network extension by logging roads in 

two basins, western Cascades, Oregon. Water Resources Bulletin 32: 1195-1207.

Wong, S.L., and R.H. McCuen. 1982. The design of vegetative buffer strips for runoff and 

sediment control. A technical paper developed as part of a study of stormwater 

management in coastal areas funded by the Maryland Coastal Zone Management 

Program. Civ. Eng. Dep., University of Maryland, College Park, MD.
Aquatics Resource Report Craggy Vegetation Management Project

42

Appendix A: Riparian Reserve Treatments

Units within riparian reserves mentioned in this table have been assessed by a district hydrologist 

and determined that these riparian reserves could benefit from project activities: thinning or fuel 

reduction. Aquatic conservation strategy objectives would be maintained or restored in these 

riparian reserves, and there will be no negative effect to shade if buffer width is applied as 

indicated in this table.

Not all activities currently being proposed within riparian reserves (RRs) have currently been 

assessed by a district hydrologist. In these cases, either standard Forest Plan riparian reserve 

widths will be applied (300 feet for fish-bearing perennial streams, 150 feet for non-fish-bearing 

perennial streams and intermittent streams), or if it is determined that treatment within outer 

portions of these riparian reserves will be beneficial to aquatic conservation strategy objectives 

and have no effect to shade, modified riparian reserve buffer and equipment exclusion zones will 

be fully divulged in the application for Water Board Waiver coverage under the 2015 Waiver

(North Coast Regional Water Quality Control Board 2015). Such site specific recommendations 

will only decrease treatment unit size.

Table A-1: Riparian Reserve Treatments

Unit Prescription System Stand type Water 

feature Shade

Riparian 

Reserve 

Buffer

Equipment 

exclusion Comments

137-6 Thin from 

below Skyline Natural Intermittent 

streams 86% 100' 100'

Middle intermittent stream 

in unit is not a stream, no 

annual scour or 

deposition. Buffered 

intermittent streams on 

either side of middle

134-145 Thin from 

below

Ground 

Based Plantation

Perennial 

and 

intermittent 

stream

98% 100' 100'

134-240 Thin from 

below

Ground 

Based 

and PCT

Plantation

Perennial 

and 

intermittent 

stream

91%

100' 

intermittent, 

150' perennial 

stream

100'

134-39 Thin from 

below

Skyline 

and PCT Natural

Intermittent 

stream to 

Humbug 

Creek

96% 100' 100'

134-38 Thin from 

below Skyline Natural Intermittent stream 90% 100' 100' Intermittent stream is the boundary on one side

134-83 Thin from 

below

Skyline 

and 

Ground 

Based

Plantation Headwaters 95% 100' 100'

134-33 Thin from 

below Skyline Natural Intermittent 

headwaters NA NA NA

Could not find a channel, 

only found inner gorges, 

no riparian reserve 

restrictions
Aquatics Resource Report Craggy Vegetation Management Project

43

Unit Prescription System Stand type Water 

feature Shade

Riparian 

Reserve 

Buffer

Equipment 

exclusion Comments

134-34 Thin from 

below Skyline Plantation Intermittent stream 88% 75' 75'

Elmo Gulch headwaters75' riparian reserve 

buffer, not less than 50' 

or break in slope.

134-2 Thin from 

below Skyline Natural Intermittent 

stream 92% 50' 50'

134-83 Thin from 

below

Skyline 

and 

Ground 

based

Plantation Intermittent 

stream 91% 100' 100'

Intermittent stream North 

and South, both with 100' 

riparian reserve buffer 

and 100' equipment 

exclusion zone.

134-41 Thin from 

below

Ground 

Based Plantation Perennial 

Stream 89% 100' 50'

136-18 Thin from 

below

Ground 

Based Plantation Intermittent 

stream 95% 50' 50'

136-57 Thin from 

below

Ground 

Based Plantation Intermittent stream 91% 50' 50'

136-24 Thin from 

below

Ground 

Based Plantation Intermittent 

stream 88% 50' 50'

136-26 Thin from 

below

PCT and 

Ground 

Based

Natural NA NA NA NA

No stream channel found, 

no riparian reserve 

restriction

138-12 Thin from 

below

Ground 

Based Natural

Perennial 

and 

intermittent 

stream

90%

100 

intermittent 

150' Perennial

100'

Riparian reserve buffer 

for intermittent channel is 

100' and 150' for 

perennial

138-1 Thin from 

below

Ground 

Based Natural Intermittent 

stream 91% 100' 100'

138-151 Thin from 

below

Ground 

Based natural Intermittent stream 93% 100' 100'

138-532 Thin from 

below

Ground 

Based Plantation Intermittent stream 40' currently

134-70

Manual Thin, 

Handpile 

Brush and 

Trees <10"

PCT Plantation Intermittent 

stream

0' on southern 

stream, 20' on 

northern by 

maps

134-250 Thin from 

below

Ground 

Based Plantation Perennial 

Stream 60' then 0'

134-29

Manual Thin, 

Handpile 

Brush and 

Trees <10"

PCT Plantation

Not mapped 

as 

intermittent 

stream 

(ephemeral) 

but has 

riparian 

reserve

0
Aquatics Resource Report Craggy Vegetation Management Project

44

Unit Prescription System Stand type Water 

feature Shade

Riparian 

Reserve 

Buffer

Equipment 

exclusion Comments

134-27 Thin from 

below Skyline Natural

Not mapped 

as 

intermittent 

stream 

(ephemeral) 

but has 

riparian 

reserve

0

134-244

Manual Thin, 

Handpile 

Brush and 

Trees <10"

PCT Plantation Intermittent 

stream 0

134-31 Thin from 

below

Ground 

Based Plantation Perennial Stream 70' on map

136-22 Thin from 

below

Ground 

Based Plantation Intermittent stream 0

136-47 Thin from 

below

Ground 

Based Plantation Intermittent stream 0'-50' on map

136-146 Thin from 

below

Ground 

Based Plantation Perennial 

Stream

County road is 

boundary (50-

75')

Likely no effect to shade 

because unit is on the cut 

bank side of a county 

road.

136-145 Thin from 

below

Ground 

Based Plantation Perennial 

Stream

County road is 

boundary (50-

75') mostly 75'

Likely no effect to shade 

because unit is on the 

other side of a county 

road.

138-53

Manual Thin, 

Handpile 

Brush and 

Trees <10"

PCT Natural Perennial 

Stream

50'-100' on 

map Probably mis-mapped

Literature Cited

North Coast Regional Water Quality Control Board. 2015. Order No. R1-2015-0021, Waiver of 

Waste Discharge Requirements for Nonpoint Source Discharges on Federal Lands. Santa 

Rosa, CA.
Aquatics Resource Report Craggy Vegetation Management Project

45

Appendix B: Life history and biological 

requirements of Pacific salmonids and 

lamprey

Coho Salmon

General life history information and biological requirements of Southern Oregon/Northern California 

Coastal (SONCC) Coho salmon have been described in various documents (Hassler 1987; 

Sandercock 1991; Weitkamp, et al. 1995) as well as NOAA-Fisheries’ final rule listing SONCC 

Coho salmon (May 6, 1997; 62 FR 24588) and the subsequent Recovery Plan (NOAA 2014a).

Coho salmon enter the mainstem of the Klamath River for spawning typically in their third year, 

primarily between September and December, with a peak in October (NFMS 2007). Over most of this 

interval, mainstem flows below Iron Gate Dam often are high (ca. 2500-3000 cfs: NMFS 2001). 

Thus, standard methods for observing and counting spawning fish are not easily applied, and the size 

of the spawning population is unknown. Approximations put the entire ESU at about 10,000 

spawning Coho salmon of non-hatchery origin per year (Weitkamp, et al. 1995), of which only a 

small portion is associated with the Klamath Basin, where several important tributary runs have been 

reduced to a handful of individuals (NMFS 2001, 2007). Although a minor amount of spawning and 

growth may occur in the mainstem, the mainstem serves adults primarily as a migration route (NFMS 

2007).

Spawning occurs from November to January (Hassler 1987) in the tributaries to the Klamath River, 

but occasionally as late as February or March (Weitkamp, et al. 1995). Coho salmon eggs incubate 

for 35-50 days between November and March. Successful incubation depends on several factors 

including dissolved oxygen levels, temperature, substrate size, amount of fine sediment, and water 

velocity. Fry start emerging from the gravel two to three weeks after hatching and move into shallow 

areas with vegetative or other cover. As fry grow larger, they disperse up or downstream. In summer, 

Coho salmon fry prefer pools or other slower velocity areas such as alcoves, with woody debris or 

overhanging vegetation. Juvenile Coho salmon over-winter in slow water habitat with cover as well. 

Juveniles may rear in fresh water for up to 15 months then migrate to the ocean as smolts from March 

to June (Weitkamp, et al. 1995). Coho salmon adults typically spend two years in the ocean before 

returning to their natal streams to spawn as three-year olds.

Available historical and most recent published Coho salmon abundance information are summarized 

in the NOAA-Fisheries coast-wide status review (Weitkamp, et al. 1995). The rivers and tributaries in 

the California portion of this ESU were estimated to have average recent runs of 7,080 natural 

spawners and 17,156 hatchery returns, with 4,480 identified as native fish occurring in tributaries 

having little history of supplementation with non-native fish. However, limited information exists 

regarding Coho salmon abundance in the Klamath River basin. What information exists [NOAA 

2014b; CDFW unpublished data; U.S. Fish and Wildlife Service (USFWS) unpublished data] 

suggests adult populations are small to nonexistent in most years. The decline of SONCC Coho 

salmon across the ESU is not the result of one single factor, but rather a number of natural and 

anthropogenic factors that include dam construction, instream flow alterations; land use activities 

coupled with large flood events, fish harvest and hatchery effects.
Aquatics Resource Report Craggy Vegetation Management Project

46

Humbug Creek – Coho Surveys

Coho are not present in Humbug Creek above private land beginning in T46N, R7W, Section 31. 

Juvenile Coho surveys were conducted in the summer of 2011/12, from the confluence with 

Sweetwater Gulch to the Middle Fork Humbug Creek confluence, but nothing was observed. Juvenile 

Coho presence in the lower 3.6 miles of Humbug Creek has been confirmed by surveys conducted by 

the Forest from 2002 to 2006 (unpublished data and/or field notes from 2002-2006). A 

comprehensive review of datasets originating from multiple agencies/entities was conducted by 

CDFW, with the conclusion that Coho presence in upper Humbug Creek was not substantiated 

(Garwood 2012).

Water diversions and human made barriers in a 1 mile long section of Humbug Creek located on 

private land beginning in T46N, R7W, Section 31 and Section 6 NW 1⁄4 block adult Coho migration. 

No adult or juvenile Coho have been observed in Humbug Creek above this section.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

South Fork Humbug Creek – Coho Surveys

No surveys targeting Coho have been completed in South Fork Humbug Creek. This stream is above 

the upstream limit of Coho migration in the Humbug Creek drainage noted above.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

Middle Fork Humbug Creek – Coho Surveys

No surveys targeting Coho have been completed in Middle Fork Humbug Creek. This stream is 

above the upstream limit of Coho migration in the Humbug Creek drainage noted above.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

Chinook Salmon

The following information was excerpted or summarized from NMFS status review of Chinook

salmon (Meyers, et al. 1998). Chinook salmon mature between 2 and 6+ years of age (Meyers, et al.

1998). Fall-run Chinook salmon enter freshwater at an advanced stage of maturity, move rapidly to 

their spawning areas on the mainstem or lower tributaries of the rivers, and spawn within a few days 

or weeks of freshwater entry (Healey 1991). Incubation temperature for eggs is 5.0 to 14.4°C, with 

below 13.0°C preferred for optimal development in most stocks (McCullough 1999). Emerging fry 

generally do not develop normally above 12.8°C (McCullough 1999). Post-emergent fry seek out 

shallow, nearshore areas with slow current and good cover, and begin feeding on small terrestrial and 

aquatic insects and aquatic crustaceans. Once feeding, the optimal growth range for juveniles is 10.0 

to 15.6°C, with fingerlings preferring to hold at 12 to 14°C (McCullough 1999). In preparation for 

their entry into a saline environment, juvenile salmon undergo physiological transformations known 

as smoltification that adapt them for their transition to salt water. For Chinook salmon, the 

recommended maximum temperature to maintain migratory response and seaward adaptation is 

12.0°C; and at temperatures greater than 13.0°C, some physiological processes of smolting may be 

delayed, and, in extreme cases, reversed (McCullough 1999). Chinook salmon spend between one 

and four years in the ocean before returning to their natal streams to spawn (Meyers, et al. 1998). 

Chinook salmon addressed in this document exhibit an ocean-type life history, and smolts out-
Aquatics Resource Report Craggy Vegetation Management Project

47

migrate predominantly as subyearlings, generally during April through July. Chinook salmon spend 

between 2 and 5 years in the ocean (Healey 1991), before returning to freshwater to spawn. Some 

Chinook salmon return from the ocean to spawn one or more years before full-sized adults return.

The UKT ESU includes fall- and spring-run Chinook salmon in the Klamath and Trinity River Basin 

upstream of the confluence of the Klamath and Trinity rivers. Historically, spring-run Chinook

salmon were probably the predominate run. This ESU still retains several distinct spring-run 

populations, albeit at much reduced abundance levels. Fish from this ESU exhibit an ocean-type life 

history; however genetically and physically, these fish are quite distinct from coastal and Central 

Valley Chinook salmon ESUs. Genetic analysis indicated that this ESU form a unique group that is 

quite distinctive compared to neighboring ESUs. The majority of spring- and fall-run fish emigrate to 

the marine environment primarily as subyearlings, but have a significant proportion of yearling 

smolts. Recoveries of coded wire tags indicate that both runs have a coastal distribution off the 

California and Oregon coasts. The 2014 fall-run Chinook salmon run into the Klamath River system, 

as compiled by CDFW, was estimated to be 182,792 fish (160,444 adult and 22,348 grilse) (CDFW 

2015). Of the 112,599 basin-wide natural spawners (i.e., not of hatchery origin), 3,233 were from the 

Salmon River and 12,470 from the Scott River. The Klamath River run in 2015 was projected to be 

average to below average compared to recent historical average (KRTT 2015).
Aquatics Resource Report Craggy Vegetation Management Project

48

Humbug Creek – Chinook Surveys

Chinook are not present in Humbug Creek. No surveys targeting Chinook have been completed. The 

lower 1⁄4 mile of this stream is dry during the time that adult Chinook salmon are migrating and 

spawning in the Klamath River.

Steelhead

Biologically, steelhead can be divided into two basic run-types, based on the state of sexual maturity 

at the time of river entry and duration of spawning migration (Moyle 2002). The stream-maturing 

type, or summer steelhead, enters fresh water in a sexually immature condition and requires several 

months in freshwater to mature and spawn. The ocean-maturing type, or winter steelhead, enters fresh 

water with well-developed gonads and spawns shortly after river entry (August 9, 1996, 61 FR 

41542; Barnhart 1986). South of Cape Blanco, Oregon, summer steelhead are known to occur in the 

Rogue, Smith, Klamath, Trinity, Mad, and Eel rivers, and in Redwood Creek (Busby, et al. 1996).

Winter steelhead in California enter fresh water after rivers rise in response to fall/winter rains, 

typically from December through March, with a peak in January and February, with spawning soon 

after reaching the breeding grounds (Moyle 2002). In contrast, summer steelhead enter systems as 

flows taper off in the spring, then spawn the following winter (Moyle 2002). Steelhead require a 

minimum depth of 0.18 m and a maximum velocity of 2.44 m/s for active upstream migration (Smith 

1973). Spawning and initial rearing of juvenile steelhead generally take place in small, moderategradient (generally 3-5%) tributary streams (Nickelson, et al. 1992). A minimum depth of 0.18 m, 

water velocity of 0.30-0.91 m/s, and clean substrate 0.6-10.2 cm are required for spawning. Steelhead 

spawn in 3.9-9.4°C water (Bell 1991). Depending on water temperature, steelhead eggs may incubate 

for 1.5 to 4 months (August 9, 1996, 61 FR 41542) before hatching, generally between February and 

June (Bell 1991). After two to three weeks, in late spring, and following yolk sac absorption, alevins 

emerge from the gravel and begin actively feeding. After emerging from the gravel, fry usually 

inhabit shallow water along banks of perennial streams. Fry occupy stream margins (Nickelson, et al.

1992). Summer rearing takes place primarily in the faster parts of pools, although young-of-the-year 

are abundant in glides and riffles. Winter rearing occurs more uniformly at lower densities across a 

wide range of fast and slow habitat types. Productive steelhead habitat is characterized by complexity,

primarily in the form of large and small wood. Some older juveniles move downstream to rear in 

larger tributaries and mainstem rivers (Nickelson, et al. 1992). Steelhead prefer water temperatures 

ranging from 12-15°C (Reeves et al. 1987). Juveniles live in freshwater from one to four years 

(usually two years in the California ESUs), then smolt and migrate to the ocean in March and April 

(Barnhart 1986). Winter steelhead populations generally smolt after two years in fresh water (Busby, 

et al. 1996).

The KMP steelhead ESU occurs in coastal river basins between the Elk River in Oregon and the 

Klamath River in California, inclusive. The KMP steelhead ESU contains populations of both winter 

and summer steelhead. The Rogue and Klamath River basins are distinctive in that they are two of the 

few basins producing “half-pounder” steelhead. In 2001, NOAA-Fisheries reconsidered the status of 

KMP steelhead under the ESA (66 FR 17845, April 4, 2001) and determined that KMP steelhead do 

not warrant listing as threatened or endangered at this time.

In California, the largest proportions of naturally spawning hatchery fish are believed to occur in the 

Trinity River, where estimates from 1990s range from 20-70 percent hatchery. These estimates apply 

to fall-run fish. Because the hatchery program in the Trinity River basin propagates mostly fall-run 

fish, natural spawners in this basin that return at other times are believed to be predominantly of 
Aquatics Resource Report Craggy Vegetation Management Project

49

natural origin. Counts at Willow Creek weir provide an estimate of about 2000 natural origin fall-run 

spawners per year. The Willow Creek weir samples steelhead only over a period of about 3 months 

during the fall run and thus provides no information about other runs in the basin. CDFW biologists 

estimated natural escapement in the California portion of the ESU to be approximately 30,000-50,000 

adults per year.

Rainbow Trout

Rainbow trout are native to Pacific slope drainages from the Kuskokwim River in Alaska to Baja 

California, Mexico (Moyle 2002). However their distribution has expanded significantly, including 

previously fishless streams and lakes, due to introductions. Rainbow trout is a Management Indicator 

Species (MIS) in on the Klamath National Forest.

Rainbow trout inhabit a wide variety of habitats. However, stream dwelling rainbows tend to prefer 

waters with a higher percentage of riffles than pools. Optimal habitat conditions include temperatures 

between 15 and 18o

C, slightly alkaline water (pH 7-8), and oxygen concentrations close to saturation. 

Temperatures above 28oC are known to be lethal to rainbow trout; and for large fish, lethal 

temperatures may be around 23-25oC. In summer, where water temperatures begin to approach the 

upper range of tolerance, trout will seek cooler microhabitats (Moyle 2002).

Adult forage and dispersal patterns appear to vary with local conditions, environmental factors, and 

the presence of other fish species (Meehan and Bjornn 1991, Moyle 2002). Rainbow trout are 

typically diurnal, opportunistic feeders. They are carnivores that feed in a rover-predator style. The 

majority of their diet consists of aquatic insects, although they will eat crayfish, grasshoppers, winged 

bugs, worms, salamanders, and other fish (including other trout). They occasionally feed on benthic 

invertebrates when the benthic food supply is great and/or when there is increased competition for 

prey form the water column (Behnke 2002).

Rainbow trout usually spawn between the ages of 2 to 4 years old. Age of first spawn can vary 

greatly depending on size and genetics (Behnke 2002). Female fecundity ranges from 1,200-3,200 

eggs per kilogram of body weight (Behnke 2002). Rainbow trout spawning behavior typically begins 

during the spring but can begin as early as in December and varies due to temperature and water flow 

conditions. Temperatures of 3-6o

C often initiate spawning behavior, although actual spawning does 

not usually occur until temperatures reach 6-9o

C (Behnke 2002). In lakes, this often means moving 

from the lake into their natal stream. If the lake is not stream-fed, rainbow trout will move into nearshore shallow waters (Moyle and Cech 2000). In rivers, rainbow trout will migrate from feeding areas 

into smaller, cool-water tributaries (Moyle and Cech 2000). Both rainbow and steelhead trout are 

iteroparous, meaning that they can spawn more than once throughout their lifetime
Aquatics Resource Report Craggy Vegetation Management Project

50

Humbug Creek – Steelhead/Rainbow Trout Surveys

Both steelhead and resident rainbow trout are present in Humbug Creek. Humbug Creek was visited 

in 2011 and 2012 to check for steelhead spawning. One redd was observed in the section of Humbug 

Creek just above the county road 8J002 bridge (T45N, R8W, Sec 1 SW 1⁄4). Except in the case of 

obvious barriers to anadromous fish, snorkel surveys generally do not make distinction between small 

resident trout and steelhead due to the impossibility to differentiate the two; and larger sizes are also 

rarely separated. Snorkel or electrofishing surveys conducted by Forest Service and/or cooperators in 

2002-2006, 2011, and 2012 reported steelhead/rainbow trout (unpublished data and/or field notes 

from 2011-12).

Steelhead distribution in Humbug Creek extends further upstream in the system compared to Coho 

(see respective discussion). Anadromy is officially considered to end ~1.5 miles upstream from the 

confluence with Rider Gulch. Boulder/bedrock barriers and steep gradient prevent anadromy above 

this point.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

Middle Fork Humbug Creek – Steelhead/Rainbow Trout Surveys

Both steelhead and resident rainbow trout are present in Middle Fork Humbug Creek. Except in the 

case of obvious barriers to anadromous fish, snorkel surveys generally do not make distinction 

between small resident trout and steelhead due to the impossibility to differentiate the two; and larger 

sizes are also rarely separated. Snorkel or electrofishing surveys conducted by Forest Service and/or 

cooperators in 2002-2006, 2011, and 2012 reported steelhead/rainbow trout.

Steelhead distribution in Middle Fork Humbug Creek extends approximately 1.5 miles upstream from 

the confluence with Humbug Creek. Boulder/bedrock barriers and steep gradient prevent anadromy 

above this point.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

South Fork Humbug Creek – Steelhead/Rainbow Trout Surveys

Both steelhead and resident rainbow trout are present in South Fork Humbug Creek. Except in the 

case of obvious barriers to anadromous fish, snorkel surveys generally do not make distinction 

between small resident trout and steelhead due to the impossibility to differentiate the two; and larger 

sizes are also rarely separated. Snorkle or electrofishing surveys conducted by Forest Service and/or 

cooperators in 2002-2006, 2011, and 2012 reported steelhead/rainbow trout.

Steelhead distribution in South Fork Humbug Creek extends approximately 0.9 miles upstream from 

the confluence with Middle Fork Humbug Creek. Boulder/bedrock barriers and steep gradient prevent 

anadromy above this point.

*CalFish query performed on 02/11/2016

• No live/dead fish nor redd counts available

Sucker Creek – Steelhead/Rainbow Trout Surveys
Aquatics Resource Report Craggy Vegetation Management Project

51

Resident rainbow trout are present in Sucker Creek. Steep channel gradient and boulder barriers near 

the mouth prevent anadromy above this point. Rainbow trout occupy about 0.5 miles of stream, with 

upstream extent limited by gradient and natural barriers.

Middle Klamath River – Steelhead/Rainbow Trout Surveys

Steelhead and resident rainbow trout are present in the Klamath River in the general project area.

Specifics concerning suitability of the river in this location for spawning is poorly known due to often 

hazardous discharge conditions which are present in spring.

*Location restricted, where possible, to general Project area 

*CalFish query performed on 02/11/2016

• No redd counts available

• Steelhead distribution maps include the Klamath River in the Project area
Aquatics Resource Report Craggy Vegetation Management Project

52

Critical Habitat for Coho Salmon (and)

Essential Fish Habitat for Coho/Chinook Salmon

Designated Critical Habitat (CH) for Coho salmon encompasses accessible reaches of all rivers 

(including estuarine areas and tributaries) between the Mattole River in California and the Elk River 

in Oregon, inclusive (May 5, 1999, 64 FR 24049). The area described in the final rule represented the 

current freshwater and estuarine range of Coho salmon. Land ownership patterns within the Coho 

salmon ESU analyzed in this document and spanning southern Oregon and northern California are 

53% private lands; 36% Federal lands; 10% State and local lands; and 1% Tribal lands. The Forest 

Service manages about 1,680,000 acres (90.6%) of land within the Forest boundaries and about 

200,000 acres (9.4%) of land are within the Forest boundaries but in other ownership (Forest Plan, 

page 3-12). Essential Fish Habitat (EFH) is considered for both Coho and Chinook salmon, with 

consultation occurring under 305 (b) (4) (A) of the Magnuson-Stevens Fishery Conservation and 

Management Act. The definition of Coho/Chinook EFH components and extent is described by 

Amendment 14 (Appendix A, pages 12-35 [adopted year 2000]) of the 1978 Pacific Fisheries 

Management Council Salmon Fisheries Management Plan.

Conclusions regarding CH and EFH occurrence are based on field review of habitat suitability, 

professional judgment, District fish survey records, and California Department of Fish and Wildlife 

(CDFW) information. In general, the Forest Coho Presence (GIS) layer defines CH, and Coho or 

Chinook distribution (whichever is of maximal extent) defines EFH. As appropriate, the California 

state information in Calfish.org may also be utilized. Where information on Coho or Chinook is 

lacking (e.g., no/few surveys have been completed), else it is the professional judgment of the Fish 

Biologist that neither Forest nor Calfish.org range maps fully capture CH/EFH extent, the Forest

Steelhead Trout Distribution (GIS) layer may be used as a proxy for maximum range of anadromous 

fishes. This dataset is recognized as a conservative approach for assessment of effects to anadromous 

fish habitat because Coho and Chinook salmon may not occupy the same waters as steelhead due to 

differences in jumping abilities. The maximum jumping height (under ideal conditions) for Coho is 

2.2 meters; Chinook salmon is 2.4 meters; and steelhead is 3.4 meters (Meehan 1991). Therefore, 

steelhead trout can access more habitat than Coho or Chinook salmon (i.e., steelhead trout can make a 

3-meter jump to migrate up a stream, but Coho and Chinook salmon cannot). Additionally, 

differences in spawn timing may also affect actual distribution. As an example, steelhead spawn in 

the spring, encountering higher discharge conditions than Chinook, which spawn in the fall. In 

consequence, Chinook may be denied access to streams, or segments thereof, due to the presence of 

low-water barriers that are passible to steelhead during spring flows.

In all cases, field review and site-specific surveys may refine the location of CH or EFH.

Figure B-1 shows the distribution of CH and EFH in the Action Area and Analysis Area in relation to 

proposed treatments in the alternative with the greatest number of acres proposed for treatment 

(Alternative 3). This map is based on fish distribution with site-specific changes made per 

professional fisheries biologist knowledge, stream surveys, or CDFW data. Field review, survey 

history, and CalFish.org agree that Coho presence is appropriately reflected by the existing Forest 

Service map database for the Project area. Fish surveys have occurred in Humbug Creek, defining 

Coho distribution and locating barriers to anadromy. Therefore, Coho distribution (and, thus, CH) 

will not follow steelhead distribution in the Project area, instead utilizing the Klamath National Forest 

and CalFish.org maps. Elsewhere in the Project area, barriers, such as those at the mouth of Sucker

Creek, low stream discharge, and/or steep gradients lacking pool habitat control distribution of 
Aquatics Resource Report Craggy Vegetation Management Project

53

Steelhead, both adults and juveniles. Since Chinook salmon are not present in Humbug Creek, EFH 

in the project area is confined to the Klamath River only.

Figure B-1: Craggy Project Fish Distribution Map
Aquatics Resource Report Craggy Vegetation Management Project

54

Lamprey

Pacific Lamprey (Entosphenus tridentata)

Pacific lamprey are found in north Pacific coast streams from Japan, through Alaska, and down the 

North America continent coast, potentially as far as southern California or Baja California (USDI

2012; Moyle 2002). This species has many derivative forms, including anadromous (the most 

common), resident, and landlocked; and the relationship between E. tridentata and its multiple forms, 

as well as similar species, is not fully resolved (Moyle 2002). Pacific lamprey is a Sensitive species 

for the Klamath National Forest.

Pacific lamprey are usually anadromous, with two distinct parts of their complex life cycle. 

Following is a generalized life cycle description, as summarized from Moyle (2002), Close, et al. 

(2010), and USFWS (2012). After hatching in freshwater in the late spring and early summer, larvae 

(ammocoetes) leave the nest and passively drift until suitable substrate – sand/silt – is encountered. 

Once a site is colonized, the blind larvae filter feed upon detritus for an extended period of time. 

Length of in-stream residence is uncertain, an individual may retain a larval form between three to 

seven years, with four to six years typical. Time to metamorphosis is dependent upon how long it 

takes to grow to a particular size. At 14-16 centimeter total length, larvae begin metamorphosis to the 

ocean-going adult form. Metamorphosis occurs over multiple months, and requires physiological 

changes from sessile filter-feeder to active predator, including changes in sensory system (such as 

growing eyes), digestive system, and tolerance to sea water. Downstream migration appears 

correlated with high flow events of winter and spring. Adults spend up to four years in the ocean 

where feeding is by parasitism: an individual latches to its prey (usually fish, but sometimes marine 

mammals), rasps a hole through the skin, extracts body fluids and flesh, and finally drops off once 

full. Upmigration from the ocean occurs from winter through early summer, although lamprey may 

hold in a river up to a year before the final migration into spawning streams. Once the spawning 

migration starts, lamprey stop eating. Pacific lamprey do not appear to home to a natal stream, instead 

following the smell of pheromones produced by ammocoetes to find suitable spawning habitat. In late 

spring through early summer, nests are constructed, and while some adults may survive to return to 

the ocean, most die soon after spawning.

Specifics of the general Pacific lamprey life cycle as applied to the Klamath River system, much less 

its individual tributaries, are largely uncertain. Initial movement of spawners from the ocean into the 

river may occur at any time of the year, but is primarily late winter and into spring (Larson and 

Belchik 1998, Close, et al. 2010). Additionally, there is evidence of at least two distinct runs: a spring 

run that spawns shortly after entering freshwater, and a fall run that holds over and spawns the 

following spring (Anglin 1994). Downstream emigration of lamprey occurs year-round, with final 

outmigration to saltwater of transformed adults in late fall through spring (Anglin 1994; Close, et al. 

2010). Other particulars, such as details about the ammocoete stage and spawning specifics (i.e., 

months, locations) for the various Klamath River tributaries, are unknown.

Habitat for Pacific lamprey ammocoetes is very important due to the long in-stream residence. Sands 

and silts are the preferred habitat of larvae, with larger substrate sizes utilized by larger (older) 

individuals (Sugiyama and Goto 2002; Stone and Barndt 2005). Finer particles are endemic of lower 

velocity environments such as stream margins, backwaters, eddies, and pools. Although ammocoetes 

are often considered to be sedentary, they will actively seek new habitat if a particular site becomes 

unsuitable (Moyle 2002; USFWS 2010). Most important is that the stream velocity has to be fast 

enough to allow filter feeding, yet sufficiently slow to retain the preferred sediments (Torgensen and 

Close 2004). For poorly known reasons, distribution of lamprey larvae in a stream tends to be patchy 

– not all suitable habitats are utilized – but it may be a function of microhabitat, variation between 
Aquatics Resource Report Craggy Vegetation Management Project

55

stream reaches, and seasonal movement to take advantage of different habitat (Sugiyama and Goto 

2002; Torgensen and Close 2004). Optimal temperature requirements for ammocoetes, as well as 

other water quality parameters, needs further study. However, it is known that eggs will successfully 

hatch from 10° to 22°C, with highest survival 10° to 18°C; and that local spawning peaks are likely 

tied with water temperatures most advantageous for embryo development (Meeuwig, et al. 2005).

Pacific lamprey spawning habitat is very similar to that required by salmonids. Redds are generally 

built in gravel and cobble substrates, with moderate velocity flowing water. Of the 125 Pacific 

lamprey nests surveyed in the Smith River, Oregon, most were observed in low gradient riffles, pool 

tailouts and lateral scour pools (Gunckel, et al. 2009). Most of these nests were associated with cover, 

including gravel and cobble substrates, vegetation and woody debris. Likewise, most nests observed 

in Cedar Creek, Washington, were observed in pool-tail outs, low gradient riffles and runs (Stone 

2005). Upstream extent of spawning Pacific lamprey is often considered synonymous with salmonid 

anadromy, although there are indications that this assumption may not always be true – under natural 

conditions, lamprey may be able to pass traditional barriers to upmigrating steelhead and salmon, 

such as waterfalls (USFWS 2012). Research is on-going on this topic. Until consensus is reached 

within the scientific community, it is appropriate to continue to utilize salmonid anadromy as Pacific 

lamprey extent.

Pacific lamprey numbers in the Klamath River appear to be decreasing. While there is no estimate of 

the current population, oral history taken from tribal fishers indicates a long-term decline in adult 

catch (Larson and Belchik 1998; USFWS 2012). A downward trend is suggested for out-migrating 

juveniles caught in rotary screw traps in the Klamath River basin between 1997 and 2004 (USFWS 

2004).

Klamath River Lamprey (Entosphenus similis)

Klamath River lamprey are found in the upper and lower Klamath River system, including its 

tributaries (Moyle 2002). This species is non-migratory and can be found within both rivers and lakes 

(Moyle 2002. Klamath River lamprey is a Sensitive species for the Klamath National Forest.

Specifics concerning the life history and habitat needs of the Klamath River lamprey are few, but it is 

presumed to be broadly similar to the Pacific lamprey. One primary difference is that this species is 

limited to freshwater (i.e., is not anadromous), and therefore adults feed on prey such as salmonids, 

suckers, and cyprinids throughout their life (Moyle 2002). Downstream of Iron Gate Dam, the 

distribution of Klamath River lamprey is presumed to be similar to anadromous salmonids, its 

primary food source.

All Locations – Lamprey Surveys

Understanding of the full extent of distribution of Sensitive lamprey species within Project area 

waterways is unknown. In the Klamath River, Pacific lamprey and Klamath river lamprey are 

annually captured in the CDFW rotary screw trap located just upstream of the I-5 bridge, the former 

appearing to comprise a larger proportion of the population than the latter. The extent of lamprey in 

Humbug Creek, Middle Fork Humbug Creek, and South Fork Humbug Creek is unknown.
Aquatics Resource Report Craggy Vegetation Management Project

56

References

Anglin, D.R. 1994. Lower Klamath River instream flow study: scoping evaluation for the Yurok 

Indian Reservation. Completed under interagency agreement No: AG1J520003. U.S. Fish and 

Wildlife Service Lower Columbia River Fishery Resource Office, Vancouver, WA. 46 p.

Barnhart, R.A. 1986. Species profiles: life histories and environmental requirements of coastal fishes 

and invertebrates (Pacific Southwest) – steelhead. U.S. Fish and Wildlife Service Biological 

Report 82 (TR-EL-82-4/82-11-60). 27 p.

Behnke, R.J. 2002. Trout and Salmon of North America. (George, S., ed.). The Free Press, New 

York, New York. 359 p.

Bell, M.C. 1991. Fisheries handbook of engineering requirements and biological criteria, 3rd edition. 

U.S. Army Corps of Engineers, Portland, Oregon.

Busby, P.J., T.C. Wainwright, G.J. Bryant, L.J. Lierheimer, R.S. Waples, F.W. Waknitz, and I.V. 

Lagomarsino. 1996. Status review of west coast steelhead from Washington, Idaho, Oregon, 

and California. Technical Memorandum NMFS-NWFSC-27. National Marine Fisheries 

Service, Northwest Fisheries Science Center, Seattle, Washington. Available 

online: https://www.nwfsc.noaa.gov/publications/scipubs/techmemos/tm27/tm27.htm

California Department of Fish and Wildlife (CDFW). 2017. Klamath River basin fall Chinook salmon 

spawner escapement, in-river harvest and run-size estimates, 1978-2016.

Close, D., Docker, M., Dunne, T., and G. Ruggerone. 2010. Scientific assessment of two dam 

removal alternatives on lamprey – Klamath River Expert Panel. Final report prepared for U.S. 

Fish and Wildlife Service, Washington, D.C. 56 p + appendices.

Garwood, J. 2012. Historic and recent occurrence of Coho salmon (Onchorhynchus kisutch) in 

California streams within the Southern Oregon/Northern California Evolutionarily Significant 

Unit. Fisheries Branch Administrative Report, 2012-03. California Department Fish and 

Wildlife, Arcata, CA. 77 p.

Gunckel, S.L., Jones, K.K., and S.E. Jacobs. 2009. Spawning distribution and habitat use of adult 

Pacific and western brook lampreys in Smith River, Oregon. American Fisheries Society 

Symposium 72: 173-189.

Hassler, T.J. 1987. Species profiles: life histories and environmental requirements of coastal fishes 

and invertebrates (Pacific Southwest). Coho Salmon. U.S. Fish and Wildlife Service 

Biological Report 82(11.70). 26 p. Available 

online: https://www.nwrc.usgs.gov/wdb/pub/species_profiles/82_11-070.pdf

Healey, M.C. 1991. Life history of Chinook salmon (Oncorhynchus tshawytscha). Pages 313-393 in

Pacific Salmon Life Histories (C. Groot and L. Margolis, editors). University of British 

Columbia Press, Vancouver, BC.

Klamath River Technical Team (KRTT). 2017. Ocean abundance projections and prospective harvest 

levels for Klamath River Fall Chinook, 2017 Season. Pacific Fishery Management Council.

Larson, Z.S., and M.R. Belchik. 1998. A preliminary status review of eulachon and Pacific lamprey 

in the Klamath River Basin. Yurok Tribal Fisheries Program, Klamath, CA. 24 p.

McCullough, D.A. 1999. A review and synthesis of effects of alterations to the water temperature 

regime on freshwater life stages of salmonids, with special reference to Chinook salmon. 

Report EPA 910-R-99-010. U.S. Environmental Protection Agency, Seattle, Washington.
Aquatics Resource Report Craggy Vegetation Management Project

57

291 p. Available online: http://www.krisweb.com/biblio/gen_usepa_mccullough_1999.pdf

Meehan, W.R. (ed.). 1991. Influences of forest and rangeland management on salmonid fishes and 

their habitats. American Fisheries Society Special Publication 19.

Meehan, W.R. and T.C. Bjornn. 1991. Salmonid distribution and life histories in Influences of forest 

and rangeland management on salmonid fishes and their habitats (Meehan, W.R., ed.). 

American Fisheries Society Special Publication 19:47-82.

Meeuwig, M.H., Bayer, J.M., and J.G. Seelye. 2005. Effects of temperature on survival and 

development of early life stage Pacific and western brook lampreys. Transactions of the 

American Fisheries Society 134: 19-27.

Meyers, J.M., R.G. Kope, G.J. Bryant, D. Teel, L.J. Lierheimer, T.C. Wainwright, W.S. Grant, F.W. 

Waknitz, K. Neely, S.T. Lindley, and R.S. Waples. 1998. Status review of Chinook salmon 

from Washington, Idaho, Oregon, and California. Technical Memorandum NMFS-NWFSC35. National Marine Fisheries Service, Northwest Fisheries Science Center, Seattle, 

Washington. Available online: https://www.fws.gov/yreka/HydroDocs/Myers_etal_1998.pdf

Moyle, P.B. 2002. Inland Fishes of California. University of California Press, Berkeley, California. 

502 p.

Moyle, P.B., and J.J. Cech, Jr. 2000. Fishes: an introduction to ichthyology. 4th edition. Prentice-Hall, 

Saddle River, New Jersey.

National Marine Fisheries Service (NOAA). 2014a. Final Recovery Plan for the Southern 

Oregon/Northern California Coast Evolutionarily Significant Unit of Coho Salmon 

(Oncorhynchus kisutch) (Chapters 1-6). National Marine Fisheries Service. Arcata, CA.

National Marine Fisheries Service (NOAA). 2014b. Chapter 33 of the Final Recovery Plan for the 

Southern Oregon/Northern California Coast Evolutionarily Significant Unit of Coho Salmon 

(Oncorhynchus kisutch). National Marine Fisheries Service. Arcata, CA.

National Marine Fisheries Service (NMFS). 2007. Magnuson-Stevens Reauthorization Act Klamath 

River Coho Salmon Recovery Plan. Prepared by Rogers, F. R., I. V. Lagomarsino and J. A. 

Simondet for the National Marine Fisheries Service, Southwest Region Long Beach, 

California. 48 p.

National Marine Fisheries Service (NMFS). 2001. Biological Opinion. Ongoing Klamath Project 

Operations. National Marine Fisheries Service, Southwest Region, Long Beach, California.

Nickelson, T.E., J.D. Rodgers, S.L. Johnson, and M.F. Solazzi. 1992. Seasonal changes in habitat use 

by juvenile coho salmon (Oncorhynchus kisutch) in Oregon coastal streams. Can. J. Fish. 

Aquat. Sci. 49: 783-789.

Reeves, G.H., F.H. Everest, and J.B. Hall. 1987. Interactions between the redside shiner 

(Richardsonius balteatus) and the steelhead trout (Salmo gairdneri) in western Oregon: the 

influence of water temperatures. Canadian Journal of Fish and Aquatic Science 44: 1603-

1613.

Sandercock, F.K. 1991. Life history of Coho salmon (Oncorhynchus kisutch). Pages 397-446 in

Pacific Salmon Life Histories (C. Croot and L. Macolis, eds.). UBC Press, University of 

British Columbia, Vancouver, BC.

Smith, A.K. 1973. Development and application of spawning velocity and depth criteria for Oregon 

salmonids. Transactions of the American Fisheries Society 102: 312-316.
Aquatics Resource Report Craggy Vegetation Management Project

58

Stone, J., and S. Barndt. 2005. Spatial distribution and habitat use of Pacific lamprey (Lampetra 

tridentata) ammocoetes in a western Washington stream. Journal of Freshwater Ecology 20: 

171-185.

Sugiyama, H. and A. Goto. 2002. Habitat selection by larvae of a fluvial lamprey, Lethenteron 

reissneri, in a small stream and an experimental aquarium. Icthyological Research 49: 62-68.

Torgensen, C.E., and D.A. Close. 2004. Influence of habitat heterogeneity on the distribution of 

larval Pacific lamprey (Lampetra tridentata) at two spatial scales. Freshwater Biology 49: 

614-630.

U.S. Fish and Wildlife Service (USFWS). 2012. Pacific lamprey (Entosphenus tridentatus) –

assessment and template for conservation measures in California. U.S. Fish and Wildlife 

Service, Pacific Southwest Region, Sacramento, CA. 117 p.

U.S. Fish and Wildlife Service (USFWS). 2010. Best management practices to minimize adverse 

effects to Pacific lamprey. U.S. Fish and Wildlife Service, Pacific Region, Portland, OR. 25 p.

U.S. Fish and Wildlife Service (USFWS). 2004. 90-day finding on a petition to list three species of 

lamprey as threatened or endangered. Federal Register 69: 77158-77167.

Weitkamp, L.A., T.C. Wainwright, G.J. Bryant, G.B. Milner, D.J. Teel, R.G. Kope, and R.S. Waples. 

1995. Status review of Coho salmon from Washington, Oregon, and California. Technical 

Memorandum NMFS-NWFSC-24. National Marine Fisheries Service, Northwest Fisheries 

Science Center, Seattle, Washington. Available 

online: https://www.nwfsc.noaa.gov/publications/scipubs/techmemos/tm24/tm24.htm
Aquatics Resource Report Craggy Vegetation Management Project

59

Appendix C: Table of Pathway and Indicators

Klamath National Forest Matrix: Table of Population and Habitat Indicators for Use on the 

Klamath National Forest in the Northwest Forest Plan Area

Aquatic Habitat Conditions Analysis Guidelines

AP = Analytical Process for Developing Biological Assessments for Federal 

Actions Affecting Fish within the Northwest Forest Plan Area (USDI, USDA, 

and NOAA 2004).

The table(s) within this Appendix show criteria used to determine baseline conditions in 7th and 5th

field watersheds within the Forest boundaries that contain anadromous fish habitat. The criteria in 

the Table and footnotes are used to describe the current condition of Klamath Mountain watersheds, 

and to determine if projects are likely to affect anadromous salmonids via effects on salmonid habitat 

components. Current conditions of watershed(s) are assessed and documented in the Table of Habitat 

Indicators; effects to Indicators from proposed actions are discussed in the narrative and summarized 

in the Table of Habitat Indicators.

The initial Klamath National Forest and National Marine Fisheries Service (NMFS) Level 1 review 

of the Table criteria was completed by Perrochet, Thomas, and Flickinger in April 2007. Edits to 

large woody debris (LWD) were made in March 2009 to reflect Forest Plan EIS values (USDA 1994, 

pages 3-68 to 3-69). The Table was updated as part of the Analytical Process for ESA consultation 

with NMFS. In May 2012 Grunbaum and Meneks provided updates and edits to this document and 

the Table of Habitat Indicators.

The Table, as designed in the 2004 Analytical Process, and in earlier versions (1997 NMFS 

Biological Opinion for the Forest Plan), suggests values to determine a level of functioning for 

anadromous fish bearing streams. A note about rigid values to assess level of functioning: in addition 

to fixed habitat parameters not allowing for natural variability, fixed habitat parameters set standards 

that may be geomorphically inappropriate (Bisson et al. 1997). Variability is an inherent property of 

aquatic ecosystems in the Pacific Northwest and habitats at any given location will change from year 

to year, decade to decade, and century to century (Bisson et al. 1997). Healthy lotic ecosystems 

require different parts of the channel system to exhibit very different in-channel conditions and that 

those conditions change through time (Reid and Furniss 1998). Also, data may not be available for 

the stream being assessed. Therefore, a conclusion of function must be evaluated with professional 

judgment recognizing the streams capability to perform within rigid values. In some cases, a stream’s 

morphology, aspect or size may not support “Properly Functioning” criteria values for one or more 

habitat Indicators. If an Indicator for a particular stream is determined to be functioning at its 

capability (due to morphology, aspect, or size), it is rated as Properly Functioning even if it doesn’t 

meet Table criteria values. In the absence of available data, table and associated footnotes suggest 

factors that should be considered when evaluating indicators.
Aquatics Resource Report Craggy Vegetation Management Project

60

Table C-1: Klamath National Forest Tributaries Table of Pathways and Indicators

Pathways Indicators Properly Functioning At Risk Not Properly 

Functioning

Habitat: Non Watershed Condition Indicators

Water Quality:

Temperature (1)

1st - 3rd Order 

Streams 

[instantaneous]

69 F degrees (~ 20.5 C) or less > 69 to 70.5 degrees F 70.5 F degrees (~ 21.3 C) or more

4th-5th Order 

Streams

[Maximum Weekly 

Maximum 

Temperature]

70.5 F degrees (~ 21.4 C) or less > 70.5 to 73.5 degrees F 73.5 F degrees (~ 23.0 C) or more

Suspended 

Sediment/Turbidity 

Little to no quantitative turbidity 

data exists for streams on the 

Klamath National Forest. Use the 

following criteria to infer condition 

of turbidity Indicator: (1) 

professional judgment from years of 

direct observation of tributary 

streams; (2) amount of fines in 

substrate from stream survey data, 

(3) CWE modeled level of 

watershed surface erosion and mass 

wasting, and (4) condition of stream 

buffer RR and channel (particularly 

if there has been recent debris flows 

that altered the channel).

Professional judgment of turbidity 

is based on observations of water 

clarity after peak flows in 

tributaries to the mainstems of the 

Klamath, Scott, and Salmon Rivers 

that have watersheds with varying 

degrees of disturbance from nearly 

pristine to highly disturbed.

Properly Functioning: Water clarity 

returns quickly (within three days) 

following peak flows.

Water clarity slow (four to six days) to 

return following peak flows, moderate 

to high fines in substrate, moderate 

modeled surface erosion and mass 

wasting, and riparian reserves are not 

fully functioning. 

Water clarity poor for long periods of 

time (one week or more) following 

peak flows. Some suspended 

sediments occur even at low flows or 

base flow. High fines in substrate, 

stream buffers in poor condition, 

high modeled surface erosion and 

mass wasting, and riparian reserves 

are in poor condition.

Chemical/Nutrient

Contamination (2)

Scott, Salmon, and Klamath River 

mainstems: Low levels of 

contamination from agriculture, 

industrial, and other sources; no 

excess nutrients. No CWA 303d 

designated reaches. 

Scott, Salmon, and Klamath River 

tributaries: None or low levels of 

chemical and/or nutrient 

contamination from agriculture, 

industrial, and other sources; no 

excess nutrients.

Scott, Salmon, and Klamath River

mainstems: Moderate levels of 

contamination from agriculture, 

industrial, and other sources; some 

excess nutrients. One or more CWA 

303d designated reaches 

Scott, Salmon, and Klamath River 

tributaries: Moderate levels of 

contamination from agriculture,

industrial, and other sources and/or 

moderate excess nutrients.

Scott, Salmon, and Klamath Rivers: 

mainstems: High levels of 

contamination from agriculture, 

industrial, and other sources; high 

levels of nutrients. One or more CWA 

303d designated reaches 

Scott, Salmon, and Klamath River 

tributaries: High levels of 

contamination from agriculture, 

industrial, and other sources and/or 

moderate to high excess nutrients.

Habitat 

Access:

Physical Barriers 

(AP) 

Any man-made barriers present in 

watershed allow upstream and 

downstream passage at all flows.

One or more human -made barriers 

present in watershed do not allow 

upstream and/or downstream passage 

at base/low flows.

Human-made barriers present in 

watershed do not allow upstream 

and/or downstream passage at a range 

of flows for at least one life history 

stage.

Substrate 

character (3)

Use stream survey data for determining substrate character. In addition, use USLE and GEO models to determine 

functioning level of Indicator and potential effects of sediment delivery to streams that may affect anadromous 

fish and their habitat. Can also infer substrate character functioning level from other factors such as high road 

density and hydrologic connection, recent large intense wildfires, and recent (last 20 years) altered channel.
Aquatics Resource Report Craggy Vegetation Management Project

61

Pathways Indicators Properly Functioning At Risk Not Properly 

Functioning

Habitat 

Elements:

Less than 15% fines (<2 mm) in 

spawning habitat (pool tail-outs, 

low gradient riffles, and glides) and 

cobble embeddedness less than 

20%.

Additional desired conditions, as 

per TMDL/NCRWB water quality 

compliance, include:

*Pool sediment vol (V*): ≤21%

*Subsurface, <0.85 mm: ≤14%

*Subsurface, <6.4 mm: ≤30%

15% or greater fines (<2 mm) in 

spawning habitat (pool tail-outs, low 

gradient riffles, and glides) and/or 

cobble embeddedness is 20% or 

greater.

Greater than 20% fines (<2 mm) in 

spawning habitat (pool tail-outs, low 

gradient riffles, and glides) and 

cobble embeddedness greater than 

25%.

Large Woody 

Debris (4)

See Forest Plan EIS Chapter 3, text 

and tables on Pages 3-68 and 3-69. 

For stream reaches on the Westside 

of the Forest, manage for an 

average of 20 pieces of large wood 

per 1,000 ft in 3-5th order streams 

(Forest Plan Page 4-143). Large 

wood is defined as a minimum 

length of 50 feet and diameter of 24 

inches on the Westside. However, 

site potential and channel width 

must be considered rather than 

using strict numbers. Also consider 

the potential for future LWD 

recruitment in both the short- and 

long-term.

Current levels are being maintained at 

minimum levels desired for “properly 

functioning” but potential sources for 

long term woody debris recruitment are 

lacking to maintain these minimum 

values.

Current levels are not at those desired 

levels for “properly functioning” and 

potential sources of woody debris for 

short and/or long term recruitment 

are lacking.

Pool Quality and 

Frequency (5)

At least one primary pool every 

three to seven bankfull channel 

widths. In 1st through 3rd order 

streams, a primary pool must have a 

maximum depth of two feet or 

greater. In 4th and 5th order streams, 

a primary pool must have a 

maximum depth of three feet or 

greater. In 6th order and larger 

streams, a primary pool must have a 

maximum depth of four feet or 

greater.

At least one pool every three to seven 

bankfull channel widths. At least half 

of the pools are primary pools. At least 

half the pools have a maximum depth 

of at least 24 inches (1st- 3rd order 

streams) or 36 inches (4th order and 

greater).

There is less than one pool every 

three to seven bankfull channel 

widths and/or less than half the pools 

have maximum depth of at least 24 

inches (1st-3rd order streams) or 36 

inches (4th order and greater).

Off-Channel 

Habitat

Fish have unrestricted access to offchannel habitats (such as oxbows, 

off-channel ponds, backwaters, and 

areas of low flow velocity and 

cover) in unconstrained reaches 

during high flows and flooding 

events in winter. And these offchannel areas are relatively 

undisturbed by dikes, levees, dredge 

tailings, roads, excavations, fills, 

flow diversions, development, 

vegetation clearing, wood removal, 

poor water quality, etc.

Fish access to off-channel habitats, and 

the quantity and quality of off-channel 

habitats, in unconstrained reaches, is 

diminished due to dikes, levees, dredge 

tailings, roads, excavations, fills, flow 

diversions, development, vegetation 

clearing, wood removal, poor water 

quality, etc.

Fish access to off-channel habitats in 

unconstrained reaches is severely 

restricted or impossible due to dikes, 

levees, dredge tailings, roads, 

excavations, fills, flow diversions, 

development, etc., and/or the quality 

of the off-channel habitats is poor 

due to vegetation clearing, wood 

removal, poor water quality, and the 

other factors listed above.
Aquatics Resource Report Craggy Vegetation Management Project

62

Pathways Indicators Properly Functioning At Risk Not Properly 

Functioning

Habitat 

Elements:

Refugia (important 

remnant habitat for 

sensitive aquatic 

species)

Critical habitats necessary for 

successful completion of all 

anadromous salmonid life history 

phases (spawning, incubation, 

emergence, freshwater rearing, and 

migration) are functioning, 

accessible, and well-distributed. 

Critical summer refugia in Klamath 

Mountain streams include: (1) 

thermal refugia and (2) anadromous 

stream reaches with intact riparian 

reserves, cool clean water, pools 

that are not filled-in or partially 

filled-in with excess sediment, 

adequate stream flows, and good 

water quality. Critical winter habitat 

for anadromous salmonids includes 

side channels, off-channel habitats, 

and floodplain habitats.

Not all critical habitats necessary for 

successful completion of all 

anadromous salmonid life history 

phases are functioning and/or 

accessible for salmonids and/or welldistributed. Habitat quality and/or 

accessibility is diminished due to 

dikes, levees, dredge tailings, other 

fills, roads, excavations, flow 

diversions, development, vegetation 

clearing, wood removal, poor water 

quality, etc.

Many of the critical habitats 

necessary for successful completion 

of all anadromous salmonid life 

history phases are not functioning 

and/or not accessible for salmonids, 

and are thus are poorly distributed 

across the stream network and not 

providing adequate biological 

connectivity.

Channel 

Condition and 

Dynamics:

Width/Depth 

Ratio (6)

Width-to-Depth ratio < 12 on all 

reaches that could otherwise best be 

described as 'A', 'G', and 'E' channel 

types. Width-to-Depth ratio > 12 on 

all reaches that could otherwise best 

be described as 'B', 'F', and 'C' 

channel types. No braided streams 

formed due to excessive sediment 

loads.

Lacking data, width-to-depth ratio 

should be evaluated considering the 

following factors: (1) recent (last 20 

years) history of debris flows that 

have scoured channel and resulted 

in aggradation or degradation of the 

stream bed, (2) recent history of 

mass wasting that delivered large 

volumes of sediment to the stream 

that may have filled in pools, (3) 

pool frequency and depth 

information from stream surveys, 

(4) watershed disturbance as 

estimated with CWE modeling for 

mass wasting (GEO) and peak 

flows (ERA/TOC), and (5) 

frequency of large woody debris in 

the stream channel. For properly 

functioning, stream crossing density 

is low, there have been few mass 

wasting events caused by 

management actions, there are 

numerous deep pools, modeled 

mass wasting and surface erosion is 

low, and there is adequate LWD. If 

there is no or little management 

disturbance legacy in a watershed, 

then width-to-depth ratio is 

assumed to be properly functioning.

More than 10% of the reaches are 

outside of the ranges given for 

Width/Depth ratios for the channel 

types specified in "Properly 

Functioning" block. Braiding has 

occurred in some alluvial reaches as a 

result of excessive aggradation due to 

high sediment loads.

For at-risk, stream crossing density is 

moderate to high, there have been 

some mass wasting events caused by 

management actions, pool frequency 

and quality is at-risk, modeled mass 

wasting and surface erosion is 

moderate to high, and there is 

inadequate LWD. 

More than 25% of the reaches are 

outside of the ranges given for 

Width/Depth ratios for the channel 

types specified in "Properly 

Functioning" block. Braiding has 

occurred in many alluvial reaches as 

a result of excessive aggradation due 

to high sediment loads.

For not properly functioning, stream 

crossing density is high, there have 

been some large mass wasting events 

caused by management actions, pool 

frequency and quality is poor, 

modeled mass wasting and surface 

erosion is moderate to high, and there 

is inadequate LWD.
Aquatics Resource Report Craggy Vegetation Management Project

63

Pathways Indicators Properly Functioning At Risk Not Properly 

Functioning

Streambank 

Condition (AP)

> 80% of any stream reach has >

90% stability. Most watersheds 

have no bank stability surveys data 

so the level of streambank stability 

should be evaluated by considering: 

(1) density of road-stream crossings 

per stream or stream reach, (2) 

amount of inner gorge road, (3) 

other clearing and/or compaction 

directly adjacent to the stream, (4) 

artificial banks created by pushing 

up berms, and (5) recent (since 

1996) channel altering debris flows.

For properly functioning: Stream 

crossing density is low to moderate, 

there is little to no inner gorge road, 

there is no or only minor 

disturbance next to the stream 

channel, there are few or no berms, 

dikes, or levees constraining the 

channel, and/or there has been no or 

minor channel alteration/filling due 

to debris flows/landslides related to 

past management actions.

50-80% of any stream reach has > 90% 

stability.

For at-risk: Stream crossing density is 

moderate to high, there is some inner 

gorge road, there is some disturbance 

next to the stream channel, there are 

some berms, dikes, or levees 

constraining the channel, and/or there 

has been some channel 

alteration/filling due to debris 

flows/landslides related to past 

management actions.

< 50% of any stream reach has >90% 

stability

For not properly functioning: Stream 

crossing density is high, there is over 

a mile of inner gorge road, there is 

significant disturbance next to the 

stream channel, berms, dikes, or 

levees constrain over a mile of 

channel; and/or there has been 

significant channel alteration/filling 

due to debris flows/landslides related 

to past management actions.

Floodplain 

Connectivity (AP) 

Off-channel areas are frequently 

hydrologically linked to main 

channel; overbank flows occur and 

maintain wetland functions, riparian 

vegetation, and succession.

Reduced linkage of wetland, 

floodplains, and riparian areas to main 

channel; overbank flows are reduced 

relative to historic frequency, as 

evidenced by moderate degradation of 

wetland function, riparian 

vegetation/succession.

Severe reduction in hydrologic 

connectivity between off-channel, 

wetland, floodplain, and riparian 

areas; wetland area drastically 

reduced and riparian 

vegetation/succession altered 

significantly.

Flow / 

Hydrology:

Change in 

Peak/Base 

Flows (7)

Properly functioning watersheds for 

peak flow have low modeled 

ERA/TOC, low road density, few 

large clearings in the rain-snow 

transition zone, and vegetation 

close to reference condition.

Properly functioning watersheds for 

base flow have low modeled 

ERA/TOC, low road density and 

hydrologic connectivity, and 

vegetation close to reference 

condition. 

Watersheds at-risk for change in peak 

flow have moderately high to high 

modeled ERA/TOC, moderate to high 

road density, and/or some large recent 

clearings in the rain-snow transition 

zone.

Watersheds at-risk for change in base 

flow have denser vegetation compared 

to reference conditions, several water 

diversions, and moderate density of 

roads that have hydrologic 

connectivity.

Watersheds not properly functioning 

or change in peak flow have high 

modeled ERA/TOC, high road 

density, and may have large recent 

clearings in the rain-snow transition 

zone.

Watersheds not properly functioning 

for change in base flow have much 

denser vegetation compared to 

reference conditions, numerous or 

large water diversions, and high 

density of roads that have hydrologic 

connectivity.

Increase in 

Drainage Network 

(AP)

Zero or minimum increases in 

active channel length correlated 

with human caused disturbance 

(e.g., trails, ditches, compaction, 

impervious surface, etc.). The 

primary cause of drainage network 

increase in Klamath Mountain 

watersheds is hydrologic 

connectivity between the road 

system and the stream network.

Low to Moderate increases in active 

channel length correlated with human 

caused disturbance (e.g., trails ditches, 

compaction, impervious surface, etc.).

Greater than moderate increase in 

active channel length correlated with 

human caused disturbance (e.g., trails 

ditches, compaction, impervious 

surface, etc.).

Watershed Condition Indicators

Road Density and 

Location (AP) Less than 2 miles per square mile. Two to three miles per square mile. Over 3 miles per square mile.
Aquatics Resource Report Craggy Vegetation Management Project

64

Pathways Indicators Properly Functioning At Risk Not Properly 

Functioning

Watershed 

Conditions:

Riparian Reserves 

– NW Forest Plan 

(AP) (8)

The riparian reserve system 

provides adequate shade, large 

woody debris recruitment, and 

habitat protection and connectivity 

in all subwatersheds, and buffers or 

includes known refugia for sensitive 

aquatic species (> 80% intact), 

and/or for grazing impacts; percent 

similarity of riparian vegetation to 

the potential natural 

community/composition > 50%. 

Moderate loss of connectivity or 

function (shade, LWD recruitment, 

etc.) of riparian reserve system, or 

incomplete protection of habitat and 

refugia for sensitive aquatic species 

(approx. 70-80% intact), and/or for 

grazing impacts; percent similarity of 

riparian vegetation to the potential 

natural community/composition 25-

50% or better. Some past standreplacement timber harvest or intense 

fire in RR, moderate road and landing 

density in RR, minor to moderate level 

of mining in RR, vegetation/fuels 

moderately departed from historic fuels 

conditions, species diversity and 

vegetation structure in stream buffers 

moderately altered from reference 

condition due to fire suppression and 

past timber harvest, and moderate 

modeled CWE values.

Riparian reserve system is 

fragmented, poorly connected, or 

provides inadequate protection of 

habitat and refugia for sensitive 

aquatic species (approx. less than 

70% intact), and/or for grazing 

impacts; percent similarity of riparian 

vegetation to the potential natural 

community/composition is 25% or 

less. Extensive past standreplacement timber harvest or intense 

fire in RR, high road and landing 

density in RR, moderate to high 

intensity of mining in RR, 

vegetation/fuels greatly departed 

from historic fuels conditions, 

species diversity and vegetation 

structure in stream buffers 

significantly altered from reference 

condition due to fire suppression and 

past timber harvest, and high 

modeled CWE values.

Disturbance 

History/Regime 

Frequency, duration, and magnitude 

of stochastic disturbance events are 

close to reference condition. The 

following factors should be 

considered in rating the Watershed 

Disturbance/Regime indicators: (1) 

overall watershed disturbance as 

determined through CWE 

modeling, (2) road density and 

location, (3) current impacts from 

past stand-replacing forestry, 

mining, and intense fires, (4) 

departure from historic fire regime, 

(5) departure from historic 

vegetation structure and 

composition, and (6) character of 

development on private property.

For properly functioning, a 

watershed should have low CWE 

and road density (all models under 

“1” threshold), few impacts from 

past stand-replacement forestry or 

intense fire, are not significantly 

departed from historic 

vegetation/fuels condition and fire 

regime, and/or have low 

disturbance on private property. 

In at-risk watersheds, frequency, 

duration, and magnitude of stochastic 

disturbance events are moderately 

departed from reference condition. Atrisk watersheds have moderate to high 

CWE and road density (one or two 

models over “1” threshold), some 

significant impacts from past standreplacement forestry or intense fire, are 

moderately departed from historic 

vegetation/fuels condition and fire 

regime, and/or have moderate 

disturbance on private property.

In not properly functioning 

watersheds, frequency, duration, and 

magnitude of stochastic disturbance 

event is significantly departed from 

reference condition. Not properly 

functioning watersheds have high 

CWE and road density (all models 

over “1” threshold), significant 

impacts from past stand-replacement 

forestry or intense fire, are 

significantly departed from historic 

vegetation/fuels condition and fire 

regime, and/or have significant 

disturbance on private properties. 

Summary 

Integration of all 

species and 

habitat 

indicators effects

How do the effects to indicators affect each fish species and their habitat? Describe by species and by 7th

and 5th field watersheds. See Analytic Process guidance. In addition to the narrative summary, use a 

summary table.
Aquatics Resource Report Craggy Vegetation Management Project

65

Footnotes to Table Above: Table of Population and Habitat Indicators for Use on the Klamath National 

Forest in the Northwest Forest Plan Area, as adjusted from Appendix A in the Analytical Process.

1) (Temperature) Proper Functioning criteria for 4th -5th Order streams is derived from 

temperature monitoring near the mouth of streams of relatively undisturbed watersheds (Clear, 

Dillon, and Wooley Creeks). –Maximum Weekly Maximum Temperatures (MWMT) as high as 

70.5 degrees F have been recorded on these streams (EA Engineering, 1998 Salmon River and 

Dillon Creek Watershed Fish Habitat and Channel Type Analysis, Appendix 2). At-Risk criteria 

for 4th/5th order streams is derived from monitoring in streams that support populations of 

anadromous fish, although temperatures in this range (70.5 to 73.5 degrees F) are considered 

sub-optimal. The Not Properly Functioning criterion is sustained temperatures above 73.5 

degrees F - that causes cessation of growth and approach lethal temperatures for salmon and 

steelhead. Properly Functioning criteria for 1st - 3rd order streams is derived from Desired 

Future Conditions (DFC) values given in the Forest Plan EIS, page 3-68. At Risk and Not 

Properly Functioning criteria for 1st – 3rd order streams are assigned on a temperature continuum 

with values given for 4th/5th order streams, with the maximum instantaneous temperature of At 

Risk 1st - 3rd order streams coinciding with the minimum MWMT of 4th/5th order At Risk 

streams. [Stream Order according to Strahler (1957).]

(2) (Chemical/Nutrient Contamination) For projects within the river corridors of the mainstem 

Scott, Salmon, and Klamath Rivers the criteria is unchanged from AP Table. For tributaries to 

the Scott, Salmon, and Klamath Rivers use the criteria from the AP table. Although these 

tributaries have CWA 303d designation, Klamath National Forest tributaries are typically 

properly functioning for dissolved oxygen, nutrients, and microcystin, and because temperature 

and sediment is assessed in the Temperature and Substrate Character Indicators. Chemical 

contamination and nutrients should be assessed for Scott, Salmon, and Klamath River tributaries.

(3) (Substrate Character) Use recent stream survey data where available. Properly Functioning 

criteria for % fines in gravel is from the Forest Plan EIS, p 3-68. Additional Forest-wide desired 

conditions for sediment (pool sediment, subsurface sediment) are described by Laurie and Elder 

(2012) in relation to monitoring for TMDL and NCRWB water quality standards. When 

location-specific information is unavailable, use the following as best appropriate: use USLE and 

GEO models to determine functioning level of Indicator and potential effects of sediment 

delivery to streams that may affect anadromous fish and their habitat, infer substrate character 

functioning level from other factors such as high road density and degree of hydrologic 

connection, recent large intense wildfires, and recent (last 20 years) debris flows that altered 

channels, and lastly use professional judgment to describe existing conditions and to estimate 

effects based upon model output interpretation, research results, or other information. The Forest

CWE modeling procedure describes the risk (probability) of project-caused sediment production 

(see 2004 CWE process paper by Elder and Reichert). For existing condition and effects of the 

action:

1. Properly Functioning: USLE and GEO values are less than 1.0

2. At Risk: USLE and GEO values are between 1.0-1.20

3. Not Properly Functioning: USLE and GEO values are greater than 1.20

(4) (Large Woody Debris) See Forest Plan EIS Chapter 3, text and tables on Pages 68-69. For 

stream reaches on the Westside of the Forest, manage for an average of 20 pieces of large wood 

per 1,000 ft in 3-5th order streams (USDA 1995, page 4-143). Large wood is defined as a 
Aquatics Resource Report Craggy Vegetation Management Project

66

minimum length of 50 feet and diameter of 24 inches on the Westside. However, site potential 

and channel width must be considered rather than using strict numbers. Also consider the 

potential for future LWD recruitment in both the short- and long-term.

Criteria for length of LWD for larger streams may be based on average bankfull channel width of 

the reach: in streams larger than 3rd order a piece of woody debris may qualify as large woody 

debris in a stream reach if its length is 1.5 times the average bankfull channel width, or if it has a 

rootwad attached and its length is 11⁄4 times the average bankfull channel width. Stable pieces of 

woody debris remain stationary during normal to high flows. Channel width and depth largely 

determines whether large woody debris recruited into a stream reach will be stable, and largely 

determines the average size of wood retained in streams (Bilby and Ward 1989, 1991; Robison 

and Beschta 1990). As channels become wider and deeper, the average size of a stable piece of 

wood increases. Pieces shorter than bankfull width and with a diameter less than bankfull depth 

are more likely to be transported out of a reach by streamflow (Bilby 1984, Braudrick et al. 

1997). Length of woody debris appears to be most important to its stability where stream 

discharge is sufficient to float large diameter stems (Bilby 1985, Swanson et al. 1984). Branches 

and/or rootwads, if still attached, add to the stability of woody debris. Therefore, criteria for 

length of LWD for larger streams may be based on average bankfull channel width of the reach: 

in streams larger than 3rd order a piece of woody debris may qualify as large woody debris in a 

stream reach if its length is 1.5 times the average bankfull channel width, or if it has a rootwad 

attached and its length is 11⁄4 times the average bankfull channel width.

(5) (Pool Quality and Frequency) A measurable pool is an area of channel which (1) shows clear 

signs that the pool was created by scour at high flows and/or that the pool is the result of the 

channel being dammed at the downstream end; (2) has a significant residual depth - the deepest 

part of the pool must be at least twice as deep as the water flowing out of the pool at the riffle 

crest; (3) has an essentially flat water surface during low flow - water surface slope <0.05 

percent; and (4) includes most of the channel - it must include the thalweg and occupy at least 

half of the width of the low-flow channel. “Primary” pools are defined by their maximum depth 

in relationship to size or stream order. As the order or size of the stream increases the required 

minimum depth for a primary pool increases. In 1st through 3rd order streams, a primary pool 

must have a minimum depth of two feet or greater. In 4th and 5th order streams, a primary pool 

must have a minimum depth of three feet. In 6th order and larger streams, a primary pool must 

have a minimum depth of four feet.

(6) (Width/Depth Ratio) The Width-to-Depth ratio for various channel types is based on 

delineative criteria of Rosgen (Rosgen 1996). Properly Functioning means that Width-to-Depth 

ratio falls within expected channel type as determined by the other four delineative factors 

(entrenchment, sinuosity, slope, and substrate). Aggradation on alluvial flats causing braiding is 

well known phenomenon that often accompanies changes in Width-to-Depth ratio as watershed 

condition deteriorates. Stream width is a function of streamflow occurrence and magnitude, size 

and type of transported sediment, and the bed and bank materials of the channel (Rosgen 1996). 

Channel widths generally increase with flow volume downstream. Channel widths can be 

modified by changes in riparian vegetation, landslides particularly debris flows, changes in 

streamflow regimes, and changes in sediment supply. The AP Table indicates that confined or 

entrenched channel types (such as A, G, and E types) are Properly Functioning when Width-toDepth ratios are <12, and wider channel types (such as B, C, and F types) are Properly 
Aquatics Resource Report Craggy Vegetation Management Project

67

Functioning when Width-to-Depth ratios are >12. To meet the Properly Functioning criteria 

channels must also have no or minimal braiding due to excessive sediment.

(7) (Peak/Base Flows) In most cases, sufficient hydrograph data is not available to determine 

comparative changes in peak flows as suggested in the AP. Infer changes in peak flows when no 

hydrograph data is available by considering the following factors: (1) CWE runoff model 

(ERA/TOC) outputs, (2) road density and the degree of hydrologic connectivity between the road 

system and the stream network, and (3) number, size, and vintage of openings in the forest 

canopy resulting from past stand-replacement forestry in the snow-rain transition zone where 

increased openings can result in elevated runoff from rain-on-snow events. The potential for 

decreased base flows in the Project HUC7 watersheds should be evaluated by considering the 

following factors: (1) increased/decreased evapotranspiration due to denser/sparser vegetation 

than reference condition that has resulted from stand-replacement forestry and/or fire 

suppression, (2) number and size of water diversions, and (3) degree of hydrologic connectivity 

between the road system and the stream network (watersheds with high road density likely have 

reduced base flows due to impervious surfaces and groundwater interception in road cuts).

(8) (Riparian Reserves) The following factors should be considered in determining the condition 

of stream buffer (hydrologic) RR: (1) amount and age of past stand-replacement forestry or 

intense fire in stream buffers, (2) road and landing density in stream buffers, (3) mining in stream 

buffers, (4) departure from historic fire regime, (5) condition of riparian vegetation for providing 

shade, large woody debris, sediment-filtering, and nutrient cycling, and (6) the amount of overall 

disturbance in the watershed particularly as estimated by the peak flow (ERA) and mass wasting 

(GEO) models. The following two factors should be considered in determining the condition of 

geologic RR: (1) amount and age of past stand-replacement timber harvest and/or recent intense 

wildfire on geologic RR and (2) road and landing density on geologic RR.

Literature Cited

Bilby, R.E. 1984. Removal of Woody Debris May Affect Stream Channel Stability. Journal of 

Forestry, October 1984, pp. 609-613.

Bilby, R.E. 1985. Contributions of Road Surface Sediment to a Western Washington Stream. 

Forest Science, Vol. 31, No. 4, 1985, pp. 827-838.

Bilby, R.E. and J. W. Ward. 1989. Changes in Characteristics and Function of Woody Debris 

with Increasing Size of Streams in Western Washington, Transactions of the American 

Fisheries Society, 118:4, 368-378.

Bilby, R.E. and J. W. Ward. 1991. Characteristics and Function of Large Woody Debris in 

Streams Draining Old-Growth, Clear-Cut, and Second-Growth Forests in Southwestern 

Washington. Can. J. Fish. Aquat. Sci.

Bisson, P.A., G.H. Reeves, R.E. Bilgy, and R.J. Naiman. 1997. Watershed Management and 

Pacific Salmon: Desired Future Conditions, in D. J. Stouder et al. (eds.), Pacific Salmon 

& Their Ecosystems. Chapman & Hall 1997.
Aquatics Resource Report Craggy Vegetation Management Project

68

Braudrick, C.A., G.E. Grant, Y. Ishikawa, and H. Ikeda. 1997. Dynamics of Wood Transport in 

Streams: A Flume Experiment. Earth Surface Processes and Landforms, Vol. 22, pp. 669-

683.

Elder, D. and M. Reichert. 2004. Cumulative Watershed Effects Analysis. Klamath National 

Forest, February 9, 2001. Quantitative Models for Surface Erosion, Mass Wasting and 

ERA/TOC. Unpublished document.

Reid, L.M. and M.J. Furniss. 1998. On the use of regional channel-based indicators for 

monitoring. Staff Report, 1998.

Robison, G.E. and R.L. Beschta .1990. Characteristics of Coarse Woody Debris for Several 

Coastal Streams of Southeast Alaska, USA. Can. J. Fish. Aquat. Sci. Vol. 47, pp. 1684-

1693.

Rosgen, D. 1996. Applied River Morphology. 1st Edition. Wildland Hydrology. Pagosa Springs, 

CO.

Strahler, A.N. 1957. Quantitative Analysis of Watershed Geomorphology. Transactions, 

American Geophysical Union, Vol. 38, No. 6, pp. 913-920.

Swanson, F.J., M.D. Bryant, G.W. Lienkaemper and J.R. Sedell. 1984. Organic Debris in Small 

Streams, Prince of Wales Island, Southeast Alaska. USDA Forest Service, Pacific 

Northwest Forest and range Experiment Station. General Technical Report PNW-166. 

June 1984.

USDA Forest Service. 1994. Final Environmental Impact Statement for the Klamath National 

Forest Land and Resource Management Plan, Chapter 3. Klamath National Forest, Yreka, 

CA.

USDA Forest Service. 1995. Klamath National Forest Land and Resource Management Plan. 

Klamath National Forest, Yreka, CA.

USDI, USDA, and NOAA. 2004. Analytical process for developing biological assessments for 

federal actions affecting fish within the Northwest Forest Plan area. November 2004. 17 

pp. + appendices.
Aquatics Resource Report Craggy Vegetation Management Project

69

Appendix D: Environmental Baseline and 

Proposed Effects Checklist

Checklists for documenting environmental baseline and effects of proposed actions(s) on 

relevant indicators for

CRAGGY VEGETATION MANAGEMENT PROJECT

Legend For Reference Information Used to Determine Baseline Conditions:

ND: No data

N/A: Not applicable

PJ: Professional judgment (B. Thomas – Project Fish Biologist)

CDFW 2017: Salmon Spawner Escapement, In-river Harvest and Run-size Estimates (CDFW 

2017)

Sed 2013: Sediment monitoring, Klamath National Forest – 2009 to 2013 (USDA 2013)

WQ 2012: Stream temperature monitoring, Klamath National Forest – 2010 and 2011 (USDA

2012)

LAD 1993: Humbug Landscape Analysis and Design (USDA 1993)

Coho-Mid Kla 2014: SONC Coho Recovery Plan (2014a), Chapter 33 – Middle Klamath River

(NOAA 2014b)

CWE (2017): CWE data by watershed (see the Cumulative Watershed Effects report on the 

project website)

Temps: Summer temperature data (2010-2014) – Humbug Creek

CA-EPA: http://www.swrcb.ca.gov/northcoast/water_issues/programs/tmdls/303d/
Aquatics Resource Report Craggy Vegetation Management Project

70

Table D-1: Pathway and Indicators for 7th Field Watershed: Lower Humbug Creek (for Humbug Creek)

DIAGNOSTIC OR 

PATHWAY

and

INDICATOR

Environmental Baseline Effects of the Action

PROPERLY 

FUNCTIONING

FUNCTIONINGAT RISKNOT PROP. 

FUNCT. RESTORE MAINTAIN DEGRADE

HABITAT:

Habitat Quality

Temperature

WQ 2012; 

Temps-Humbug X

Suspended Sediment -

Intergravel DO/Turbidity 

PJ; CWE; Sed 

2013 X

Chemical Contamination/ 

Nutrients PJ X

Habitat Access

Physical Barriers PJ; FishPass 2001 X

Habitat Elements

Substrate Character and 

Embeddedness 

CWE; Sed 2013; 

LAD 1993 X

Large Woody Debris PJ; LAD 1993 X

Pool Frequency and 

Quality PJ; USDA 2012; 

LAD 1993 X

Large Pools

Off-channel Habitat N/A Not Present X

Refugia PJ X

Channel Cond & Dyn

Average Wetted 

Width/Maximum Depth

PJ X

Streambank Condition PJ X

Floodplain Connectivity PJ X

Flow/Hydrology

Change in Peak/Base 

Flows

PJ; CWE X

Increase in Drainage 

Network PJ X

Watershed Conditions

Road Density & Location LAD 1993; GIS X

Disturbance History & 

Regime PJ; CWE X

Riparian Reserves -

Northwest Forest Plan 

PJ; Coho-Mid Kla

2014; LAD 1993 X

SPECIES AND HABITAT:

Species and Habitat:

Summary/Integration of 

all Species and Habitat 

Indicators

X X

Due to lack of data, specific trend for anadromous fish in this 

subdrainage is unknown. 

Recent trends for Coho are unclear, but overall the run is 

considered to be depressed.

See Life History section for additional information

See Environmental Consequences and Table 

6 for an Indicator effects summary. The 

Environmental Consequences section also 

describes effects to fish and their habitat. 

Project will not cause adverse effects.
Aquatics Resource Report Craggy Vegetation Management Project

71

Table D-2: Pathway and Indicators for 7th Field Watershed: Upper Humbug Creek (for Humbug Creek 

above the Confluence with Middle Fork Humbug Creek)

DIAGNOSTIC OR 

PATHWAY

and

INDICATOR

Environmental Baseline Effects of the Action

PROPERLY 

FUNCTIONIN

G

FUNCTIONINGAT RISKNOT PROP. 

FUNCT. RESTORE MAINTAIN DEGRADE

HABITAT:

Habitat Quality

Temperature PJ X

Suspended Sediment -

Intergravel 

DO/Turbidity 

PJ; CWE; Sed 

2013 X

Chemical 

Contamination/ 

Nutrients

PJ X

Habitat Access

Physical Barriers

PJ; FishPass 

20011 X

Habitat Elements

Substrate Character and 

Embeddedness 

CWE; Sed 2013; 

LAD 1993 X

Large Woody Debris PJ

LAD 1993; 

X

Pool Frequency and 

Quality PJ; USFS 2012; 

LAD 1993; 

X

Large Pools

Off-channel Habitat N/A Not Present X

Refugia PJ X

Channel Cond & Dyn

Average Wetted 

Width/Maximum Depth

PJ X

Streambank Condition PJ X

Floodplain Connectivity PJ X

Flow/Hydrology

Change in Peak/Base 

Flows

PJ; CWE X

Increase in Drainage 

Network PJ X

Watershed Conditions

Road Density & 

Location

PJ; LAD 1993; 

GIS X

Disturbance History & 

Regime PJ; CWE X

Riparian Reserves -

Northwest Forest Plan 

PJ; Coho-Mid Kla

2014; LAD 1993 X

SPECIES AND HABITAT:

Species and Habitat:

Summary/Integration of 

all Species and Habitat 

Indicators

X X

Due to lack of data, specific trend for anadromous fish in 

this sub-drainage is unknown. Recent trends for Coho are 

unclear, but overall the run is considered to be depressed.

 See Life History section for additional information

See Environmental Consequences and Table 6 for 

an Indicator effects summary. The 

Environmental Consequences section also 

describes effects to fish and their habitat. Project 

will not cause adverse effects.
Aquatics Resource Report Craggy Vegetation Management Project

72

Table D-3: Pathway and Indicators for 7th Field Watershed: Middle Fork Humbug Creek (for Middle Fork 

Humbug Creek and South Fork Humbug Creek)

DIAGNOSTIC OR 

PATHWAY

and

INDICATOR

Environmental Baseline Effects of the Action

PROPERLY 

FUNCTIONING

FUNCTIONINGAT RISKNOT PROP. 

FUNCT. RESTORE MAINTAIN DEGRADE

HABITAT:

Habitat Quality

Temperature PJ X

Suspended Sediment 

– Inter-gravel 

DO/Turbidity 

PJ; CWE; Sed 

2013 X

Chemical 

Contamination/ 

Nutrients

PJ X

Habitat Access

Physical Barriers

PJ; FishPass 

20011 X

Habitat Elements

Substrate Character 

and Embeddedness 

CWE; Sed 2013 X

Large Woody Debris PJ, LAD 1993 X

Pool Frequency and 

Quality

USFS 2012; PJ X

Large Pools

Off-channel Habitat N/A - Not present

Refugia PJ X

Channel Cond & 

Dyn

Average Wetted 

Width/Maximum 

Depth

PJ X

Streambank 

Condition PJ X

Floodplain 

Connectivity PJ X

Flow/Hydrology

Change in Peak/Base 

Flows

PJ; CWE X

Increase in Drainage 

Network PJ X

Watershed 

Conditions

Road Density & 

Location

PJ; GIS X

Disturbance History 

& Regime PJ; CWE 2015 X

Riparian Reserves -

Northwest Forest 

Plan 

PJ; Coho-Mid Kla

2014 X

SPECIES AND HABITAT:

Species and 

Habitat:

Summary/Integration 

of all Species and 

Habitat Indicators

X X

Coho are not present in Middle Fork Humbug Creek or South 

Fork Humbug Creek See other matrices for general basin-wide 

conditions for steelhead.

See Environmental Consequences and Table 6 for 

an Indicator effects summary. The 

Environmental Consequences section also 

describes effects to fish and their habitat. Project 

will not cause adverse effects.
Aquatics Resource Report Craggy Vegetation Management Project

73

Table D-4: Pathway and Indicators for 5th Field Watershed: Humbug Creek-Klamath River (for mainstem 

Middle Klamath River)

DIAGNOSTIC OR 

PATHWAY

and

INDICATOR

Environmental Baseline Effects of the Action

PROPERLY 

FUNCTIONING

FUNCTIONINGAT RISKNOT PROP. 

FUNCT. RESTORE MAINTAIN DEGRADE

HABITAT:

Habitat Quality

Temperature Temps-Klamath R X

Suspended Sediment 

- Intergravel 

DO/Turbidity 

PJ1,2 X

Chemical 

Contamination/ 

Nutrients

CA-EPA X

Habitat Access

Physical Barriers Coho-Sct 2014 X

Habitat Elements

Substrate Character 

and Embeddedness 

PJ1,2; Coho-Mid 

Kla 2014

X

Large Woody Debris Coho-Mid Kla

2014; LAD 1993 X

Pool Frequency and 

Quality ND - likely altered due to historic mining practices and from 

alterations in flow due to Iron Gate Dam X

Large Pools

Off-channel Habitat PJ1

; Coho-mid 

Kla 2014

X

Refugia PJ1 X

Channel Cond & 

Dyn

Average Wetted 

Width/Maximum 

Depth

ND - likely altered due to historic mining practices and from 

alterations in flow due to Iron Gate Dam X

Streambank 

Condition PJ1,2 X

Floodplain 

Connectivity

PJ1

; Coho-Sct 

2014

X

Flow/Hydrology

Change in Peak/Base 

Flows

PJ1

; Coho-Mid Kla

2014

X

Increase in Drainage 

Network PJ1 X

Watershed 

Conditions

Road Density & 

Location

PJ; Coho-Mid Kla 

2014 X

Disturbance History 

& Regime

PJ1

; Coho-Mid 

Kla 2014

X

Riparian Reserves -

Northwest Forest 

Plan 

PJ; Coho-Mid Kla 

2014 X

SPECIES AND HABITAT:

Species and 

Habitat:

Summary/Integration 

of all Species and 

Habitat Indicators

X X

Sources available to examine the general Mid Klamath River 

condition for anadromous fish include: 

(1) Screw trap data since 2000 suggests a steady to upward 

trend for Chinook smolts and steady to slightly down for 

steelhead smolts; and 

(2) Run size estimate for spawning Chinook since 1978 is 

steady to slightly down (CDFW 2017).

Recent trends for Coho are unclear, but overall the run is 

considered to be depressed.

 See Life History section for additional information

See Environmental Consequences and Table 6 for 

an Indicator effects summary. The 

Environmental Consequences section also 

describes effects to fish and their habitat. Project 

will not cause adverse effects.
Aquatics Resource Report Craggy Vegetation Management Project

74

DIAGNOSTIC OR 

PATHWAY

and

INDICATOR

Environmental Baseline Effects of the Action

PROPERLY 

FUNCTIONING

FUNCTIONINGAT RISKNOT PROP. 

FUNCT. RESTORE MAINTAIN DEGRADE

1

This 5th field watershed includes extensive private property within/without the Forest boundary. Historic resource use throughout the

drainage, including dredging, has impacted the watershed, and agriculture and timber extraction continue on private. Therefore, while Forest 

Service, or inholdings within the boundary, may show properly functioning condition - for instance, all ERA and USLE CWE models under 

"1" threshold (CWE 2017) - the consideration of the whole 5th-field watershed suggest lower ratings. Data is largely lacking for private 

properties.

2

Due to size of middle Klamath River and extreme difficulty to survey, comprehensive datasets for physical attributes are not available.
Aquatics Resource Report Craggy Vegetation Management Project

75

References:

California Department of Fish and Wildlife (CDFW). 2017. Klamath River basin fall Chinook 

salmon spawner escapement, in-river harvest and run-size estimates, 1979-2016.

National Marine Fisheries Service (NOAA). 2014a. Final Recovery Plan for the Southern 

Oregon/Northern California Coast Evolutionarily Significant Unit of Coho Salmon 

(Oncorhynchus kisutch) (Chapters 1-6). National Marine Fisheries Service. Arcata, CA.

National Marine Fisheries Service (NOAA). 2014b. Chapter 33 of the Final Recovery Plan for 

the Southern Oregon/Northern California Coast Evolutionarily Significant Unit of Coho 

Salmon (Oncorhynchus kisutch). National Marine Fisheries Service. Arcata, CA.

Rosgen, D. 1996. Applied River Morphology. 1st Edition. Wildland Hydrology. Pagosa Springs, 

CO.

USDA Forest Service. 1993. Klamath National Forest Humbug Landscape Analysis and Design. 

Klamath National Forest, Yreka, CA. 70 pp. + appendices

USDA Forest Service, Klamath National Forest. 2012. Stream temperature monitoring on the 

Klamath National Forest: 2010 - 2011. Yreka, CA.

USDA Forest Service 2013. Stream sediment monitoring on the Klamath National Forest, 2009-

2012. Klamath National Forest, Yreka, CA. 18 p.
Aquatics Resource Report Craggy Vegetation Management Project

76

Appendix E: Distance between Fish Habitat 

and Treatments

Table E-1: Summary of Closest Distance between Project Activities and Anadromous Fish and Their Habitat 

(Including Critical Habitat) in 7th and 5th Field Watersheds

Watershed Stream Name Distance to Habitat occupied by Steelhead trout, Coho Salmon and Coho 

Salmon Critical Habitat (in miles)

7th field watersheds

Lower 

Humbug 

Creek

Humbug 

Creek

The closest treatment is the same for all species, except for Chinook which is 

not present in Humbug Creek.

<0.05 - Fuel break [via Humbug Creek]

0.25 - Unit 138-13 (skyline) [via intermittent drainage]

0.15 - Unit 136-400 Mast (mastication) [via intermittent drainage]

<0.05 - Underburn [via Humbug Creek]

0.2 – Unit 138-532 (Ground-based) [via intermittent drainage] 

1.8 – Unit 136-21-(noncommercial thinning) [via Whites Gulch]

0.10 – Legacy treatment [overland via Forest Service road 45N39]

0.00 - Water drafting [via Humbug Creek]

Middle 

Fork 

Humbug 

Creek

Middle Fork 

Humbug 

Creek and 

South Fork 

Humbug 

Creek

Closest treatment same for all species except for Chinook

0.25 - Fuel break [overland]

0.10 - Unit 134-21 (skyline) [Middle Fork Humbug Creek]

<0.05 - Unit 138-23 (noncommercial thinning) [overland]

1.0 - Underburn [overland]

0.35 – Unit 134-44 (Ground-based) [overland]

0.10 – Legacy treatment [South Fork Humbug Creek]

0.00 - Water drafting [via Middle Fork Humbug Creek]

Upper 

Humbug 

Creek

Humbug 

Creek

Closest treatment same for all species except for Chinook

0.15 - Fuel break[overland]

0.35 - Unit 134-28 (skyline) [overland]

0.10 - Unit 134-23 (noncommercial thinning) [overland]

<0.05 - Underburn [Humbug Creek]

0.4 Unit 134-248 (Ground-based) [via Sucker Creek]

0.00 – Legacy treatment [via Humbug Creek]

0.00 - Water drafting [via Humbug Creek]
Aquatics Resource Report Craggy Vegetation Management Project

77

Watershed Stream Name Distance to Habitat occupied by Steelhead trout, Coho Salmon and Coho 

Salmon Critical Habitat (in miles)

5th field watershed

Humbug 

CreekKlamath 

River 

Humbug 

Creek, Middle 

Fork Humbug 

Creek, South 

Fork Humbug 

Creek, and

Klamath River

Closest treatment same for all species except Chinook 

<0.05 - Fuel break[via Humbug Creek]

0.10 - Unit 134-21 (skyline) [Middle Fork Humbug Creek]

0.10 - Unit 134-23 (noncommercial thinning) [overland]

~100' – underburn [Humbug Creek]

0.20 – Unit 138-532 (ground-based) [via intermittent drainage]

0.15 – Unit 136-400-Mast (mastication) [via intermittent drainage]

0.00 – Humbug Creek

0.00 - Water drafting [via Humbug Creek]

Closest treatment for Chinook (Klamath River)

3.8 – (Fuel break) [via Humbug Creek]

3.65 – Unit 137-8 (skyline) [via Trail Gulch/Humbug Creek]

2.15 – Unit 136-926 (noncommercial thinning) [via intermittent 

drainage/Clear Creek/Humbug Creek]

3.8 – (Underburn) [via Humbug Creek]

4.4 – Unit 138-42 (ground-based) [via intermittent drainage/Humbug 

Creek]

4.10 – Unit 137-74 -Mast (mastication) [via intermittent drainage/Humbug 

Creek] 

5.60 – Legacy treatment [South Fork Humbug Creek]

4.62 - Water drafting [via Humbug Creek]