Magnuson-Stevens Reauthorization Act

Klamath River Coho Salmon Recovery Plan

Prepared by

The National Marine Fisheries Service

Southwest Region

July 10, 2007
An online version of this report is available at:

http://swr.nmfs.noaa.gov/salmon/MSRA_RecoveryPlan_FINAL.pdf

Literature citation should read as:

National Marine Fisheries Service. 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, Long Beach, CA. 48 pp.

Cover illustration is a work of the National Oceanic and Atmospheric Administration, made

during the course of an employee’s official duties. As works of the U.S. Federal Government, all

NOAA images are in the public domain.
Magnuson-Stevens Reauthorization Act Klamath River 

Coho Salmon Recovery Plan 

Prepared by 

The National Marine Fisheries Service 

Southwest Region 

July 10, 2007 

NATIONAL MARINE FISHERIES SERVICE 

NOAA's National Marine Fisheries Service (NMFS), a division of the Department of Commerce, 

is the federal agency responsible for the stewardship of the nation's living marine resources and 

their habitat. NMFS is responsible for the management, conservation and protection of living 

marine resources within the United States' Exclusive Economic Zone (coastal water 3 to 200 

miles offshore). Using the tools provided by the Magnuson-Stevens Fishery Conservation and 

Management Reauthorization Act (MSRA), NMFS assesses and predicts the status of fish stocks, 

ensures compliance with federal fisheries regulations and works to reduce wasteful fishing 

practices. Under the Marine Mammal Protection Act and the Endangered Species Act (ESA), 

NMFS works to conserve protected marine species (i.e., whales, turtles) and protected 

anadromous species (i.e., salmon) without unnecessarily impeding economic opportunities. 

NMFS is responsible for completing the “Magnuson-Stevens Reauthorization Act Klamath River 

Coho Salmon Recovery Plan” under 2007 amendments included in the MSRA. These new 

amendments also require NMFS to submit within 2 years of enactment, and annually thereafter, a 

report to Congress on: (1) actions taken under the Magnuson-Stevens Reauthorization Act 

Klamath River Coho Salmon Recovery Plan and other laws relating to the recovery of Klamath 

River coho salmon and how those actions are contributing to its recovery; (2) progress made on 

restoration of salmon spawning habitat, including water conditions as they relate to salmon 

health and recovery, with an emphasis on the Klamath River and its tributaries below Iron Gate 

Dam; (3) the status of other Klamath River anadromous fish populations, particularly Chinook 

salmon; and (4) the actions taken by NMFS to address the 2003 National Research Council 

recommendations regarding monitoring and research on Klamath River Basin salmon stocks. 

Working closely with the Pacific Fishery Management Council (PFMC), NMFS is the lead 

federal agency responsible for managing a sustainable west coast salmon fishery, which includes 

approving, implementing and enforcing the salmon fishery management plan, associated 

amendments, and annual regulations, and conducting Essential Fish Habitat consultations under 

the MSRA. Chinook salmon populations from the Klamath River play a key role in the West 

Coast salmon fishery. NMFS’ Southwest and Northwest Fisheries Science Centers (SWFSC and 

NWFSC, respectively) support the NMFS Regional Offices and PFMC process by providing 

salmon harvest management guidance through modeling and focused biological studies. 

NMFS is the lead federal agency in the Klamath River Basin for protecting and recovering the 

threatened coho salmon under the ESA, including: listing determinations, development of 

federal recovery plans, consultations with federal action agencies, and habitat conservation 

planning with private landowners. NMFS listed the Southern Oregon/Northern California Coast 

(SONCC) coho salmon Evolutionarily Significant Unit (ESU), which includes all naturally 

spawning populations of coho salmon between Cape Blanco, Oregon, and Punta Gorda, 

California, as a threatened species under the ESA in 1997 and 2005. NMFS Southwest Region 

initiated ESA recovery planning for SONCC coho salmon in 2002 and is currently preparing 

additional key components of the plan. NMFS works with federal action agencies conducting 

activities in the Klamath River Basin, completing hundreds of ESA section 7 consultations, and 

NMFS is involved in other ESA-related activites, such as providing technical assistance in the 

development of habitat conservation plans, evaluating hatchery practices, and coordinating on 

i 
implementation of improved irrigation practices and water use in important Klamath River Basin 

tributaries. 

Under the Federal Power Act, NMFS developed mandatory prescriptions for the Federal Energy 

Regulatory Commission’s re-licensing of the PacifiCorps’ hydroelectric project on the Klamath 

River and provided significant analytic support related to fish passage and dam decommissioning 

throughout the process. NMFS is a party in the settlement discussions associated with this 

relicensing effort and expects to play an important role in the implementation of any settlement 

agreements. 

In collaboration with a diversity of public, private and non-profit partners, NMFS’s Southwest 

Region works to conserve and protect salmon and steelhead in the Klamath River Basin while 

affording economic opportunities for local communities. NMFS’ Southwest Region is engaged 

in a variety of additional collaborative conservation activities throughout the Klamath River 

Basin, including support to numerous councils and organizations associated with monitoring, 

research and restoration activities. Since 2000, NMFS’ Southwest Region has issued over $13.9 

million (M) to California and $6.2 M to Klamath River Basin indian tribes for salmon restoration 

projects within the Klamath River Basin. 

ii 
PREFACE 

Only a century ago, the people of the Klamath River Basin enjoyed the riches and benefits of a 

healthy and diverse ecosystem,which supported the third largest salmon population in the 

continental United States. The Klamath River and its tributaries provided essential subsistence 

and cultural values to native American indian tribes as well as opportunities for robust 

commercial and recreational fisheries. For generations, rural agricultural and timber communties 

within the Klamath River Basin relied on the availablity of water and land resources for 

economic sustainablity. Today these uses are in serious conflict as salmon runs decline and 

fishing, timber, and agricultural interests compete for limited supplies of water. The restoration 

of the Klamath River ecosystem deserves conscientious stewardship while respecting the 

diversity of interests of affected Basin communities. 

No one public entity has the singular authority, or sufficient funding, to restore Klamath fisheries 

on its own. Today, over a dozen federal and state agencies are working to conserve and manage 

natural resources while maintaining economic opportunities in the Klamath River Basin. Indian 

tribes have unique and recognized rights and interests, self-governance authorities, as well as 

active conservation programs in the Klamath River Basin. Nine county jurisdictions (five in 

California and four in Oregon) occur in the Klamath River Basin, representing additional 

authorities for regulating local programs on county lands. Private landowers play an important 

role in collaborative efforts to develop and implement restoration actions and sustainable landand water-use practices. Finally, conservation organizations and watershed groups work to 

provide outreach, advocacy, and can serve as facilitators of restoration actions. Lasting 

resolution of the Klamath River Basin’s complex natural resource problems will require 

integrated, comprehensive solutions that rely on effective partnerships among the Basin’s diverse 

communities and interests. 

Conflicts over water use in the Klamath River Basin have existed for decades, pitting 

conservationists, tribes, farmers, fishermen and local, state and federal agencies against each 

other. Recently, settlement discussions associated with Federal Energy Regulatory 

Commission’s relicensing of PacifiCorps’ hydroelectric Project have brought these diverse 

interests together for the first time in an effort to develop a comprehensive and lasting solution. 

While seeking to understand each others’ interests and working towards mutually-agreeable 

durable solutions to address these interests, parties to the settlement discussions are defining a 

comprehensive solution that is centered on the restoration of fisheries and sustainabilty of 

affected communities in the Klamath River Basin consistent with environmental laws. 

iii 
iv
TABLE OF CONTENTS 

I. INTRODUCTION...................................................................................................................... 1

II. OVERVIEW OF THE KLAMATH RIVER BASIN................................................................ 2 

A. Geographic Setting of the Basin............................................................................................ 2

III. KLAMATH RIVER BASIN COHO SALMON LIFE HISTORY ......................................... 4 

A. Adult Coho Salmon Freshwater Entry to Spawning.............................................................. 4 

B. Coho Salmon Eggs to Emergence.......................................................................................... 4 

C. Coho Salmon Young-of-Year to Smolts................................................................................ 4 

D. Coho Salmon Smolts ............................................................................................................. 6

IV. KLAMATH RIVER BASIN COHO SALMON ABUNDANCE........................................... 6 

A. Adult Coho Salmon Abundance ............................................................................................ 7 

B. Juvenile Coho Salmon Abundance ........................................................................................ 9 

C. Summary of Coho Salmon Abundance Information ........................................................... 10 

D. Influence of Ocean Conditions on Coho Salmon Abundance ............................................. 10 

V. ONGOING KLAMATH RIVER BASIN CONSERVATION AND MANAGEMENT 

EFFORTS ..................................................................................................................................... 11 

A. Conservation Efforts............................................................................................................ 11 

B. Management Efforts............................................................................................................. 17 

VI. THREATS TO COHO SALMON HABITAT AND RECOMMENDED RESTORATION 

ACTIVITIES................................................................................................................................. 23 

A. Klamath River HU............................................................................................................... 24 

B. Salmon River HU................................................................................................................. 30 

C. Scott River and Shasta Valley HUs ..................................................................................... 31 

D. Trinity River HUs................................................................................................................ 34 

VII. CONCLUSIONS.................................................................................................................. 38 

VIII. LITERATURE CITED ....................................................................................................... 41

IX. APPENDIX I: THREATS TABLE ORGANIZED AT THE HSA LEVEL ........................ 49

X. APPENDIX II: CDFG’S IMPLEMENTATION SCHEDULE FOR KLAMATH 

WATERSHED RECOMMENDATIONS .................................................................................... 50

v 

I. INTRODUCTION 

Coho salmon (Oncorhynchus kisutch) have experienced a significant decline in abundance over 

the past century along the west coast of North America. Their reliance on coastal streams and 

off-channel wintering habitats has made coho salmon vulnerable to the effects of poor water 

quality conditions and barriers to fish passage from coastal development and land-use, including 

dams. Since the 1960s, coho salmon abundance has declined at least 70 percent in California 

(Weitkamp et al. 1995). In the Klamath River, little information exists on the historical 

abundance of coho salmon. Data associated with canneries of the early 1900s indicate hundreds 

of thousands of adult coho salmon returned to the Klamath River annually (Weitkamp et al.

1995). Monitoring data suggest a marked decline in abundance of adult coho salmon returning 

to the Klamath River to spawn by the 1950s. By the early 1980s, the annual escapement of adult 

coho salmon to the Klamath River ranged from an estimated 15,000 to 20,000 fish, including 

hatchery fish. 

In 1995, NOAA’s National Marine Fisheries Service (NMFS) determined that the Southern 

Oregon/Northern California Coast (SONCC) coho salmon Evolutionary Significant Unit (ESU), 

composed of populations inhabiting coastal streams between Punta Gorda, California and Cape 

Blanco, Oregon, and including coho salmon that inhabit the Klamath River, constitutes a 

“distinct population segment” under the Endangered Species Act (ESA). Although in the 1940s 

SONCC coho salmon populations ranged from 150,000 to 400,000 naturally spawning fish, by 

the late 1990s NMFS found that SONCC coho salmon populations were “greatly diminished and 

... composed largely of hatchery fish,” with only approximately 10,000 naturally-spawning coho 

salmon in the California portion of the SONCC ESU (Weitkamp et al. 1995). In 1997, NMFS 

listed the SONCC coho salmon ESU as a threatened species under the ESA due to a variety of 

factors, including habitat degradation, harvest, artificial propagation, drought, floods, and poor 

ocean conditions (Weitkamp et al. 1995). NMFS also concluded that existing regulatory 

mechanisms across the ESU were inadequate and existing conservation efforts were insufficient 

to conserve SONCC coho salmon. NMFS re-evaluated the status of coho salmon in 2001 and 

determined that it should remain a threatened species under the ESA. In 2005, the California 

Fish and Game Commission found that coho salmon warranted listing as a threatened species 

from Punta Gorda, California north to the California-Oregon border under the California 

Endangered Species Act (CESA). In Oregon, under Oregon’s Native Fish Conservation Policy 

adopted in 2002 and revised in 2003 (Oregon Department of Fish and Wildlife (ODFW) 2005), 

ODFW considers the status of salmon populations in Oregon that overlap with the SONCC ESU 

as either “critical,” or, in the case of the upper Klamath River watershed, a “no status” rating is 

given since coho salmon have been excluded from the upper basin since the construction of 

impassible dams in the mainstem Klamath River. 

On January 12, 2007, President Bush signed into law the Magnuson-Stevens Fishery 

Conservation and Management Reauthorization Act (MSRA). The updated MSRA includes 

several new requirements related to salmon in the Klamath River Basin. In particular, within six 

months after the enactment of the MSRA, NMFS must complete a recovery plan for Klamath 

River coho salmon and make it available to the public. Given the statutory deadline, NMFS 

relied on the foundation of data currently in existence for Klamath River Basin coho salmon to 

complete this recovery plan. 

1
NMFS has compiled and synthesized the best available information on coho salmon in the 

Klamath River in a cohesive framework to develop the Magnuson-Stevens Reauthorization Act 

Klamath River Coho Salmon Recovery Plan (MSRA Recovery Plan). NMFS has primarily 

relied on published information in this synthesis. The MSRA Recovery Plan draws heavily from 

existing recovery and restoration plans developed with substantial stakeholder participation (e.g., 

Northwest Forest Plan (NFP), U.S. Department of Agriculture – Forest Service (USFS) and U.S. 

Department of Interior – Bureau of Land Management (BLM) 1994; Klamath River Basin 

Fishery Resources Restoration Act of 1986; and the California Department of Fish and Game 

(CDFG) Recovery Strategy for California Coho Salmon (CDFG 2004)), as well as various subbasin restoration and management plans. 

The MSRA Recovery Plan presents long-range guidance for various agencies, organizations and 

individuals to use as they consider taking actions or pursuing projects that may affect Klamath 

River coho salmon.

II. OVERVIEW OF THE KLAMATH RIVER BASIN 

A. Geographic Setting of the Basin 

The Klamath River Basin encompasses over 10 million acres of south-central Oregon and northcentral California (Figure 1). Today, the region includes about 96,000 acres of tribal trust lands, 

four million acres of private lands, and six million acres of public lands. The Klamath River 

Basin includes six National Wildlife Refuges (Bear Valley, Clear Lake, Klamath Marsh, Lower 

Klamath, Tule Lake, and Upper Klamath), a National Park (Crater Lake), five National Forests 

(Fremont-Winema, Klamath, Shasta-Trinity, Modoc, and Six Rivers), two National Monuments 

(Lava Beds and Cascade Siskiyou), three Wild and Scenic River designations (Klamath River 

from J.C. Boyle Powerhouse to the California-Oregon border, North Fork Sprague River, and the 

Sycan River), and other public lands. The basin also includes four federally-recognized tribes, 

including the Yurok Tribe (lower Klamath River), the Hoopa Tribe (lower Trinity River), the 

Karuk Tribe of the middle Klamath, and several tribes located in the Upper Klamath River Basin 

in Oregon (collectively referred to as the Klamath Tribes). 

The Klamath River originates in south-central Oregon, east of the Cascade Mountain range, and 

flows 263 miles, generally in a southwesterly direction, through southern Oregon and northern 

California, bisecting the Cascade and Coast ranges. The Wood, Williamson, Sprague and Sycan 

Rivers are the significant headwater tributaries that flow into Upper Klamath Lake. Water flows 

from Upper Klamath Lake into the short Link River (about 1.2 miles long), and then into Lake 

Ewauna near Klamath Falls, Oregon. The Klamath River officially begins at the downstream 

end of Lake Ewauna. Iron Gate Dam, at river mile (rm) 190, is a commonly recognized dividing 

2
Figure 1: Map of the Klamath River Basin, Northern California and Southern Oregon. 

3
point between what is referred to as the upper and lower river basins. Major tributaries of the 

lower Klamath River are the Shasta, Scott, Salmon, and Trinity Rivers. The Klamath River 

enters the Pacific Ocean about 22 miles south of the California-Oregon border. 

III. KLAMATH RIVER BASIN COHO SALMON LIFE HISTORY

A. Adult Coho Salmon Freshwater Entry to Spawning 

In larger river systems like the Klamath River, coho salmon have a broad period of freshwater 

entry (Leidy and Leidy 1984). Overall, earlier migrating fish spawn farther upstream within a 

basin than later migrating fish, which enter rivers in a more advanced state of sexual maturity 

(Sandercock 1991). Adult coho salmon migrate at water temperatures of 45 to 59oF, a minimum 

water depth of approximately 7 inches, and streamflow velocities less than 8 ft/s (Bjornn and 

Reiser 1991). Coho salmon are known to stage at the confluences of tributaries, holding until 

flows and temperatures are suitable for migration into upper tributary spawning habitat. 

Adult coho salmon return to the lowermost Klamath River as early as the first week of 

September, and the peak of migration passes through the Klamath estuary in early October (U.S. 

Bureau of Reclamation (Reclamation) 2007). Further upstream, adult immigration into the 

Klamath River basin and its tributaries begins in mid-October through mid-December, with peak 

immigration in mid-November through early December (Weitkamp et al. 1995). While coho 

salmon are primarily tributary spawners, they do occasionally spawn in the mainstem Klamath 

River. Spawning coho salmon were observed using side channels of the Klamath River near 

Seiad Valley in November and December of 1993 (U.S. Fish and Wildlife Service (USFWS) 

1998). 

B. Coho Salmon Eggs to Emergence 

The length of time required for eggs to incubate in the gravel is largely dependent on water 

temperature. The favorable range for coho salmon egg incubation is 10-13.5oC (Bell 1991). 

Eggs typically hatch at approximately 35 to 50 days, and start emerging from the gravel 2 to 3 

weeks after hatching (Hassler 1987, Nickelson et al. 1992). 

C. Coho Salmon Young-of-Year to Smolts 

Coho salmon fry emerge from the gravel and congregate in shallow, low velocity portions of the 

stream margin. Juvenile coho salmon (i.e., fish post-emergence and prior to ocean arrival) are 

often futher differentiated as either young-of-year (YOY), that is, fish less than one year old, parr 

(stage between emergence and smolt, exhibiting dark “parr” marks on its sides), and smolt 

(seaward migrant stage), depending on age and body characteristics during their typical 1.5 year 

freshwater residency. As their swimming capabilities improve, coho salmon YOY seek out 

portions of the stream channel that provide cover elements and suitable hydraulic parameters that 

allow them to feed and rear efficiently. Flooded riparian vegetation and oxbow channels 

associated with beaver ponds are critical to both winter and summer survival of juvenile coho 

salmon (CDFG 2004, Weitkamp et al. 1995). As coho salmon YOY grow larger, they disperse 

4
upstream and downstream, establishing and defending their territory from other salmonids 

(Hassler 1987). 

Although the Klamath River mainstem lacks much of the classic rearing habitat described above, 

YOY coho salmon are frequently found in the mainstem Klamath River from March through 

June. As irrigation depletions within tributaries begin to limit available habitat, especially in 

dryer years, coho salmon YOY rearing habitat in the mainstem Klamath River may become 

increasingly important. Small numbers of YOY coho salmon were captured in the mainstem 

Klamath River at Big Bar (1992-1995), below the Scott River (1994), and at Presido Bar (1994) 

beginning in early April, peaking in May, and diminishing in late July (USFWS 1998). Recent 

thermal refugial studies on the mainstem Klamath River have documented the persistence of 

small numbers of coho salmon YOY near select tributary confluence habitat throughout the 

summer period (Sutton et al. 2004; Soto 2007). The National Research Council Committee on 

Endangered and Threatened Fishes in the Kamath Basin (NRC) addressed the importance of 

mainstem Klamath River habitat to listed coho salmon in its review of NMFS’ 2002 Biological 

Opinion regarding the effects of Klamath Project Operations on listed coho salmon (NRC 2002). 

The NRC did not find evidence that the mainstem Klamath River is a significant rearing area for 

coho salmon and concluded it seemed unlikely “that the coho is saturating its available mainstem habitat.” Although the importance of tributary rearing habitats to coho salmon YOY 

survival is widely recognized and restoring degraded tributary habitat within the Klamath River 

Basin will likely be paramount to recovering the species (NRC 2002), mainstem habitat may 

nevertheless play a critical role in YOY coho salmon survival in rivers such as the Klamath 

where tributary conditions are particularly inhospitable. 

To survive periods of elevated water temperature, YOY and parr coho salmon likely cope via 

refugial habitats and behavioral adaptations. When water temperatures exceed the preferred 

range, juvenile salmonids likely seek out mainstem areas of cold groundwater seepage or 

tributary inflow that provide small areas of thermal refugia (NRC 2002). Furthermore, NRC 

(2002) concluded that where diurnal fluctuations in water temperature are large, fish may 

experience adequate foraging opportunities while opportunistically exploiting favorable nighttime water temperatures. 

During summer months, YOY coho salmon prefer habitat characteristics observed in small 

streams (i.e., pools and riffles featuring adequate cover, such as large woody debris (LWD), 

undercut banks, and overhanging vegetation), as opposed to habitat features generally found in 

the mainstem Klamath River. Water velocity and the presence of other fish can be important 

constraints on habitat usage, since young coho salmon often must remain in shallow fringe 

habitat within larger pools until they become large enough to secure more favorable habitat in 

deeper, faster water (Meehan and Bjornn 1991). Young coho salmon feed mainly on aquatic and 

terrestrial insects (Mundie 1969 op. cit. Meehan and Bjornn 1991). 

At the onset of fall, parr coho salmon may move considerable distances in response to fall 

freshets (Scarlett and Cederholm 1984). Parr coho salmon will seek out winter habitat that 

contains refuge from high water velocities, utilizing off channel habitats and habitats containing 

cover complexity (Narver 1978, Cederholm and Scarlett 1981). Juvenile coho salmon may 

continue to move throughout the fall/winter period, utilizing a diversity of complex habitat 

5
characteristics to protect them from potential survival risks (e.g., high steam flows, predators). 

As juvenile coho salmon approach the migratory smolt stage, the parr marks become less evident 

and the overall color of the fish lightens and becomes more silvery. 

D. Coho Salmon Smolts 

Coho salmon smolts typically migrate to the sea between March and June (Weitkamp et al. 

1995), but some level of emigration may occur throughout the year. Taking advantage of cooler 

ambient temperatures and the afforded protection from predators, the bulk of seaward migration 

occurs at night. Peak outmigration generally occurs in May, about a year after the fry emerge 

from the gravel. Little is known about residence time or habitat use in estuaries during seaward 

migration. Nickelson et al. (1992) assumed that coho salmon spend only a short time in the 

estuary before entering the ocean. Growth is very rapid once the smolts reach the estuary (Fisher 

et al. 1984). 

Fish that have spent a year or more in streams and are about to undergo the physiological 

changes associated with smoltification begin by defending their territories less vigorously and 

forming aggregations. Once groups have formed, coho salmon of similar size begin to emigrate 

from tributaries, migrating toward the ocean (Hoar 1951, Shapovalov and Taft 1954). In the 

mainstem Klamath River, coho salmon smolts have been captured from mid-March through 

early August (USFWS 1998).

IV. KLAMATH RIVER BASIN COHO SALMON ABUNDANCE 

This section first provides a general overview on the abundance of coho salmon in the Klamath 

River Basin, and ends with a discussion investigating the impact of changing ocean conditions 

on coho salmon abundance. Little information exists to provide insight on the historical 

abundance of coho salmon. Historic records for coho salmon abundance are scarce prior to 

1910, due in part to the inability of people to accurately identify salmon, non-specific 

nomenclature to refer to different species or run-timing, and the subsequent inclusion of all 

salmon into one category of commercial Chinook salmon catch (CDFG 2002, Hamilton et al.

2005, Snyder 1931). Snyder (1931) reported the first commercial gill net catch of 11,162 coho 

salmon in the lower reaches of the Klamath River, in 1919. He was also the first author to report 

a concern for declining salmon populations in California, due to commercial fishing, forestry and 

agricultural practices. Long-term monitoring data (e.g., Shasta River racks) suggest a marked 

decrease in abundance of adult coho salmon by the 1950s, resulting from over-harvest and 

habitat loss (CDFG 2004, Weitkamp et al. 1995, Klamath River Basin Fisheries Task Force 

1991). By 1983, the annual escapement abundance of Klamath River Basin adult coho salmon 

was estimated to range from 15,000 to 20,000 fish (Leidy and Leidy 1984). These estimates, 

which include hatchery stocks, could be less than six percent of their abundance in the 1940s 

(CDFG 2004, Weitkamp et al. 1995). In 1995, leading up to the listing of SONCC coho salmon 

as threatened under the ESA, NMFS concluded that the Klamath populations of coho salmon 

were diminished from historical abundances and were comprised mostly of hatchery fish 

(Weitkamp et al. 1995), suggesting that available habitat is not sustaining wild populations 

necessary for healthy salmon stocks. 

6
Monitoring studies have employed a number of techniques to collect abundance, distribution and 

run timing data on juvenile and adult salmonids. In general, Klamath River Basin salmon 

monitoring studies have primarily been funded to collect abundance information on fall run 

Chinook salmon because of their role in managing the ocean fishery. While these studies 

provide us with some information specific to coho salmon, data are largely incomplete, leading 

the NRC (NAS 2004) to recommend the development of a comprehensive coho salmon 

monitoring plan. NMFS’ Southwest Region and Southwest Fisheries Science Center (SWFSC) 

are currently working with CDFG in developing a California coastal anadromous salmonid 

monitoring plan. The plan will describe the monitoring necessary for gathering data and 

information concerning coho salmon population abundance, diversity, productivity, and spatial 

structure within the Klamath River Basin and its tributaries. 

A. Adult Coho Salmon Abundance 

Monitoring efforts providing information on the abundance of Klamath River adult coho salmon 

indicate that their abundance is depressed, but stable. In the Shasta and Scott Rivers, where 

population-specific data are most detailed and runs are primarily composed of wild stocks, data 

suggest the 2004 adult returning brood year class appears to be the strongest in recent years, 

while the 2005 and 2006 brood year class abundances are extremely depressed (Table 1). 

Table 1. Klamath River Basin adult coho salmon abundance information, 2002-2006. 

Year Yurok 

Tribal 

Harvesta

Trinity 

River 

Weirb

Scott 

River 

Live Fish 

or Redd 

Countsa

Shasta 

River 

Video 

Weira

Bogus 

Creek 

Fish 

Counting 

Facilitya

Iron Gate 

Hatchery 

Returns 

2002 486 14,307 17c 86 n/a 1,193 

2003 343 25,651 8c 187 n/a 1,317 

2004 1,540 35,209 1,577c 373 414 1,495 

2005 n/a 28,267 23d 69 114 1,384 

2006 20,162 7d 45 35 332 

a Annual effort not consistent between years (Yurok Tribal Fisheries Department). 

b Estimated escapement abundance extrapolated from weir observations (CDFG). 

c Live fish counts 

d Redd counts. 

From 2003 through 2005, USFWS extended its mainstem Klamath River adult salmon surveys 

into December, as conditions allowed, to better observe the abundance and distribution of coho 

salmon spawners. There are logistical problems, however, that confound the ability to identify 

coho salmon redds (nests dug in the gravel for egg deposition) in both mainstem and tributary 

reaches. For example, turbid high-flow conditions during November and December can impede 

the ability to observe redds, affecting the results of monitoring studies. In addition, for the crew 

to be sure that observed redds were constructed by coho salmon and not some other species of 

salmon, a positive identification of adult coho salmon on or near the redd site is required. These 

7
logistical challenges, combined with the sparse number of coho salmon spawning in the 

mainstem, have resulted in low numbers of adult coho salmon redds observed in the Iron Gate 

Dam to Indian Creek reach of the mainstem Klamath River (Table 2). These documented cases 

of mainstem coho salmon spawning indicate that the proportion of mainstem spawners may be a 

relatively small percentage of the annual adult coho salmon spawning population. For example, 

attempts at conducting Scott River redd surveys have experienced similar logistical problems, 

resulting in varying levels of annual effort. Data collected since 2001, however, indicate that 

coho salmon spawning is relatively more abundant in the Scott River drainage than in the 

mainstem Klamath River. 

Table 2. Mainstem Klamath River coho salmon redds observed during fall/winter surveys 

(USFWS 2007) from Iron Gate Dam to Indian Creek. 

Year Number of Redds 

2001 21 

2002 6 

2003 7 

2004 6 

2005 6 

Since 1978, CDFG has operated sampling weirs for adult salmon within the mainstem Trinity 

River near Willow Creek and Douglas City, California. Between 1978 and 1995, in-river 

escapement of Trinity River coho salmon (jacks and adults) above Willow Creek has averaged 

10,192 fish, ranging from 58 to 32,373 (USFWS/HVT 1999). Data from 1997 through 2005 

indicate coho salmon runs have generally been higher than average during recent years, although 

wild fish continue to represent a very small portion of the overall run (Figure 2). On average, 

over 90 percent of coho salmon spawning between Willow Creek and Lewiston Dam are of 

hatchery origin (USFWS/Hoopa Valley Tribe (HVT) 1999). 

8
Figure 2: Estimated Coho Run-size Upstream of Willow Creek Weir, Trinity River (1997 – 

2005). Figure from Sinnen et al. (2007). 

0

5,000

10,000

15,000

20,000

25,000

30,000

35,000

40,000

45,000

1997 1998 1999 2000 2001 2002 2003 2004 2005

Year

Number Estimate

TRH

Natural

 

B. Juvenile Coho Salmon Abundance 

Annual monitoring data on juvenile coho salmon (i.e., YOY through smolt life history phases), 

are collected at numerous sites throughout the Klamath River Basin. Key locations include the 

Shasta and Scott Rivers, and the mainstem Klamath River rotary screw trap located near Orleans 

(Big Bar rotary screw trap). Similar to the paucity of information on adult coho salmon in the 

Klamath River Basin, juvenile coho salmon data are limited. Generally, juvenile data are more 

useful as an indicator of general trends in abundance and run timing, rather than as an estimator 

of population size. Methods employed to monitor juvenile coho salmon include the use of rotary 

screw traps and frame nets. USFWS (2007) found frame nets were a more efficient method of 

capturing YOY coho salmon and provide some insight on habitat use and life history strategies. 

For example, Stutzer et al. (2006) concluded from their spring trapping study that YOY coho 

salmon were not consistently migrating through the mainstem Klamath River, but instead were 

holding and rearing for undetermined periods of time as well as moving downstream. 

Reports on Klamath River juvenile coho salmon outmigration indicate the abundance of 

outmigrating YOY and smolt coho salmon is correlated to the abundance of their parent brood 

year class (e.g., CDFG 2007). 

As a result of its annual Shasta River downstream migrant trapping study, CDFG observed a 

relationship between reduced base flows, increasing water temperatures, and early outmigration 

of YOY coho salmon (CDFG 2003). In years when spring base flows were reduced early as a 

result of drought conditions and the onset of agricultural water deliveries, young-of-year coho 

salmon outmigration to the mainstem Klamath River occurred earlier than in years when Shasta 

River base flows were sustained at a higher level through the spring (CDFG 2003). 

9
Similar to the mainstem Klamath River drainage, data on juvenile coho salmon abundance in the 

Trinity basin are lacking. However, juvenile coho salmon are incidentally caught during 

Chinook salmon outmigration trapping performed by the HVT and USFWS (HVT 2006). 

During the 2006 spring trapping season, a total of 1,444 juvenile SONCC coho salmon were 

captured at the Pear Tree rotary screw trap, of which 1,037 (approximately 72 percent of the 

total-season take) were wild fish (i.e., hatched and reared in a natural stream environment, versus 

produced within a hatchery setting). The majority of these fish were captured between early 

May and late June, although small numbers of fish were sporadically captured throughout the 

summer. 

C. Summary of Coho Salmon Abundance Information 

Although information on coho salmon population trends in the Klamath River Basin remains 

incomplete, the information presented above suggests that coho salmon abundance remains 

depressed. One coho salmon brood year class (i.e., 2004 returning adults) is considerably 

stronger than the other two brood year classes. Using an adult-to-smolt relationship, CDFG 

(2007) projects very low abundances of adult coho salmon returning to the Shasta River Basin in 

2007 (54 adults) and 2008 (37 adults). The data also indicate that juvenile coho salmon have a 

strong tendency to redistribute within the basin due to seasonal changes in conditions. 

D. Influence of Ocean Conditions on Coho Salmon Abundance 

Ocean conditions unfavorable for coho salmon survival are believed to be partly responsible for 

the depressed status of naturally produced coho salmon stocks in California. Peterson et al.

(2006) provide evidence that growth and survival rates of salmon in the California current off the 

Pacific Northwest can be linked to fluctuations in ocean conditions. An evaluation of conditions 

in the California Current since the late 1970s reveals a generally warm, unproductive regime that 

persisted until the late 1990s. This regime has been followed by a period of high variability that 

began with colder, more productive conditions lasting from 1999 to 2002. This brief cold cycle 

was immediately succeeded by a 4-year period of predominantly warm ocean conditions 

beginning in late 2002 (Peterson et al. 2006). When marine survival rates for coho salmon are 

plotted against these ocean regime shifts, there is an obvious pattern with higher adult hatchery 

coho returns being associated with cold water conditions and poor returns occurring during warm 

water phases. Predictably, the recent warm phase that began in 2002 has corresponded with low 

numbers of returning adult coho salmon1

. Evidence suggests these regime shifts follow a more 

or less linear pattern beginning with the amount and timing of nutrients provided by upwelling 

and passing “up” the food chain from plankton to forage fish, and eventually, salmon. 

Moreover, the report indicates these same regime shifts affect the migration patterns of larger 

animals that prey on salmon (e.g., Pacific hake, sea birds) resulting in a “top-down” effect as 

well (Peterson et al. 2006). On a more local scale, data from the Rogue River show a general 

correlation between the number of naturally spawning coho salmon and the survival rates for 

 

1

 Although the Peterson et al. (2006) study relates primarily to coho salmon off the coasts of Oregon and Washington, 

it is reasonable to expect the general conclusions relating survival rates and changes in ocean regimes to apply to 

coho salmon in the Klamath River Basin as well since they are also distributed in the CA Current. 

10
hatchery coho salmon2

, indicating ocean conditions influence trends in coho populations (Good 

et al. 2005). Furthermore, when discussing the potential extinctions of salmon populations, 

including California stocks, Francis and Mantua (2003) point out that climate patterns would not 

likely be the sole cause but could certainly increase the risk of extinction when combined with 

other factors. They further conclude that long-term fluctuations in the marine environment, such 

as those associated with the Pacific Decadal Oscillation (PDO), as opposed to annual variability, 

appear to have a greater impact on coho salmon. However, effects from alterations in the marine 

environment can be highly variable and specific to different life stages. Therefore, although 

ocean conditions do impact coho salmon productivity, it is difficult to determine the extent of 

that impact. 

V. ONGOING KLAMATH RIVER BASIN CONSERVATION AND 

MANAGEMENT EFFORTS 

This section highlights several of the broad, overarching conservation efforts and management 

actions currently in place to restore coho salmon and their habitat within the Klamath River 

Basin. Discussions that focus on smaller, more spatially focused efforts that occur at the 

hydrologic sub-area (HSA) scale are referred to specifically in section VI. 

A. Conservation Efforts 

1. Klamath River Basin Conservation Area Restoration Program

Congress authorized $1.0 M annually from 1986 through 2006 to implement the Klamath River 

Basin Conservation Area Restoration Program. The Klamath River Basin Fisheries Task Force 

(Task Force) was established by the Klamath River Basin Fishery Resources Restoration Act of 

1986 (Klamath Act) to provide recommendations to the Secretary of the Interior on the 

formulation, establishment, and implementation of a 20-year program to restore anadromous fish 

populations in the Klamath River Basin to optimal levels. The 16-member Task Force included 

representatives from the fishing community, county, state and federal agencies, and tribes. A 

Technical Work Group of the Task Force provided technical and scientific input. In 1991, the 

Task Force developed the Long Range Plan for the Klamath River Basin Conservation Area 

Fishery Restoration Program to help direct fishery restoration programs and projects throughout 

the Klamath River. 

In addition to creating a fishery restoration plan for the river basin restoration program, the Task 

Force also encouraged local watershed groups to develop restoration plans for each of the five 

sub-basins of the lower Klamath River. These groups included the Shasta River Coordinated 

Resource Management Planning Group (Shasta sub-basin), Scott River Watershed Council 

(Scott sub-basin), Salmon River Restoration Council (Salmon sub-basin), Karuk Tribe and MidKlamath Watershed Council (mid-Klamath sub-basin), and the Yurok Tribe (lower-Klamath subbasin). A short detail of each sub-basin plan follows below. Since 1991, over $1.3 M has been 

 

2

 Rogue River hatchery fish are used in combination with Klamath hatchery stocks as an indicator to estimate 

exploitation rates on wild SONCC coho salmon. 

11
given to these groups to develop the sub-basin plans and conduct restoration activities. Funds 

from the Klamath Act are often leveraged to develop broader restoration programs and projects 

in conjunction with other funding sources, including CDFG restoration grants. As an example, 

nearly $1.9 M of CDFG restoration funding was spent on a variety of Klamath River Basin 

restoration projects during the 2002-2006 period alone. While the Klamath River Basin 

Conservation Area Restoration Program ended in 2006, funds were authorized for fiscal year 

2007, and the USFWS continues to administer funds in the near term consistent with the goals of 

the program. 

Shasta Sub-basin 

A group of Shasta Valley landowners, in coordination with representatives of CDFG, the Natural 

Resources Conservation Service, the BLM and the Task Force, developed the Shasta Watershed 

Restoration Plan (Shasta Valley Coordinated Resources Management and Planning (CRMP) 

(Shasta CRMP 1997)). The CRMP focuses on areas that contain accessible salmonid habitat 

within the Shasta River basin (i.e., below Dwinnell Dam, Parks Creek, Yreka Creek, and the 

Little Shasta River), and includes a description of the conditions desirable for salmon and 

steelhead (Biological Needs Assessment) along with a summary of current conditions in the 

Shasta River. A CRMP Action Plan then identifies and implements restoration work (including 

augmented flow levels) necessary to achieve properly functioning anadromous salmonid habitat. 

Scott Sub-basin 

The Scott River Watershed Council (SRWC) has developed a Scott River Watershed Strategic 

Action Plan (SAP) that will form the basis for setting priorities for future projects and practices 

supported by the SRWC, the communities within the watershed, and the many funding sources. 

The primary role of the plan is to inform the community about resource issues, aid in resource 

management, and recommend to the Siskiyou Resource Conservation District (RCD) prioritized 

restoration opportunities in the Scott River Watershed for funding and implementation (SRWC 

2005). Ninety-three strategic actions identified in the SAP by topic and priority indicators are 

specified as high, medium, or low in terms of completion timeframes. Many restoration actions 

have been implemented within the Scott River basin since the SRWC was formed in 1992, 

including water conservation/irrigation efficiency projects that have saved approximately 15 

cubic feet per second (cfs) of Scott River flow, approximately 18,000 feet of stream 

enhancement projects, and 51 diversion screens to prevent juvenile coho salmon entrainment. 

Salmon sub-basin 

The Salmon River Restoration Council (SRRC) was formed in 1992 to assess, protect, restore 

and maintain the Salmon River ecosystems with the active participation of the local community. 

The focus of the SRRC is restoring anadromous fisheries resources within the basin while 

developing a sustainable economy, a goal that can be accomplished by facilitating 

communication and cooperation between the local communities, managing agencies, Native 

American Tribes and other stakeholders. Since its inception in 1992, the SRRC has organized 

and guided over 8,100 volunteer days to educate the public in watershed assessement and 

planning, address numerous fish passage barriers, rehabilitate instream and upslope habitat, and 

12
coordinate fire management and fuel reduction efforts. To guide upslope restoration efforts, the 

SRRC, in cooperation with the Klamath National Forest, recently developed the Salmon River 

Restoration Strategy (Elder et al. 2002) that outlines recommended actions to address upslope 

erosion hazards within high-priority tributary watersheds. 

Mid-Klamath Sub-basin 

The Middle Klamath River sub-basin includes the portion of the Klamath River watershed 

encompassing mainstem Klamath River and tributaries between the Trinity River river-mile (rm) 

43 and Iron Gate Dam (rm 190). The Karuk Tribe has developed a draft Mid-Klamath Sub-basin 

Fisheries Resource Plan (Soto and Hentz 2003) to identify the set of core variables pertaining to 

ecological function in the sub-basin, and to provide management priorities and objectives to 

guide land managers and stakeholders in their efforts to improve conditions within the sub-basin. 

The tribe will administer the long-range plan, in cooperation with federal and state managing 

agencies, private landowners, and local communities. 

The resource plan addresses the primary physical and biological processes in the sub-basin that 

contribute to the Klamath River’s unique ecological and evolutionary attributes (most 

importantly, its anadromous fish runs), focusing active restoration on those processes most 

degraded by historic and current land uses and passive restoration for protection of currently 

functioning sub-basin processes. 

Lower-Klamath Sub-basin 

The Lower Klamath River Sub-basin Watershed Restoration Plan (Gale and Randolph 2000) was 

developed by the Yurok Tribe to “restore aquatic habitat conditions within the lower Klamath 

River tributaries to a level that supports viable, self-sustaining populations of native salmonids.” 

The plan prioritizes restoration actions needed to accomplish this general goal, including 

treatement of upslope sediment sources, improvement of instream and riparian habitat function, 

and working closely with other land managers within the lower basin to implement best 

management practices for land management activities. Sound scientific methods and principles 

will guide the tribe’s implementation of the restoration plan, including necessary monitoring to 

detect geomorphic and fish population response to completed restoration actions. 

2. Trinity River Restoration Program (TRRP)

Restoration in the Trinity River drainage is dominated by the TRRP (USFWS 2000), which 

resulted from the 1984 Trinity River Basin Fish and Wildlife Management Act authorizing the 

Secretary of the Interior to develop and implement a management program to restore fish and 

wildlife populations in the Trinity River Basin to levels which existed prior to construction of the 

Trinity and Lewiston Dams. The current phase of the TRRP is based on the Trinity River 

Mainstem Fishery Restoration Environmental Impact Statement, completed in October 2000, and 

the Record of Decision (ROD) signed on December 19, 2000. The underlying scientific 

foundation of the TRRP was established through the Trinity River Flow Evaluation Final Report 

(USFWS/HVT 1999; hereafter referred to as flow study), an 18-year investigation authored by 

13
the HVT and the U.S. Department of the Interior that recommended riverflow and fluvial habitat 

manipulations necessary to restore anadromous fish populations within the Trinity River. 

Historically, the upper Trinity River functioned as a dynamic, alluvial river reach that effectively 

created and maintained quality spawning and rearing habitat for anadromous fish. However, the 

minimal static flow levels released since the completion of Lewiston Dam in 1964 were 

insufficient to maintain the alluvial nature of the upper river and, as a consequence, much of the 

river channel between Lewiston and the North Fork Trinity River confluence became confined 

within a narrow channel bordered by a dense riparian corridor. To “unchain” the Trinity River 

channel and restore river-floodplain connectivity, the program has begun mechanically removing 

entrenched riparian corridors and gently sloping back the streambank. To maximize the 

effectiveness of these physical restoration projects, the program will incorporate an annual spring 

peak-flow hydrograph that will restore the natural hydrologic and fluvial processes, enabling the 

river to once again naturally create and maintain fish habitat. The TRRP incorporates a strong 

scientific evaluation and modeling program to investigate fish population response to the altered 

flow regime and physical habitat manipulations called for within the flow study. 

Several of the 47 physical restoration sites originally identified within the flow study have been 

implemented as of May 2007, including spawning gravel augmentation below the Lewiston Fish 

Hatchery and at the cableway site near the town of Lewiston, and floodplain/riparian restoration 

at the Hocker Flat site and Canyon Creek complex of sites. Restoration work near the Indian 

Creek confluence will begin in summer 2007. Higher spring flows emanating from Lewiston 

Dam, as called for under the flow study and ROD, have occurred on an annual basis since 2001. 

3. State Recovery Strategy for California Coho Salmon

In August, 2004, the California State Fish and Game Commission listed coho salmon north of 

San Francisco Bay under the CESA. Coho salmon inhabiting coastal watershed between San 

Francisco Bay and Punta Gorda were listed as endangered under CESA, whereas coho salmon 

between Punta Gorda and the Oregon border were listed as threatened. The delineation of the 

two populations at Punta Gorda closely follows that used by NMFS when identifying the two 

distinct coho salmon ESUs within California (i.e., the Cental California Coast and SONCC 

ESUs). Prior to the final listing of coho salmon under CESA, the California Fish and Game 

Commission directed CDFG to develop a recovery strategy for restoring native California coho 

salmon (Recovery Strategy). CDFG created both a multi-stakeholder Coho Recovery Team to 

address rangewide recovery issues, and a sub-working group (Shasta –Scott Recovery Team 

(SSRT)) to develop coho salmon recovery strategies associated specifically with agricultural 

management within the Scott and Shasta Rivers. The teams are comprised of membership from 

a broad range of state, federal, and local interests, including NMFS. The primary objective of 

the Recovery Strategy is to “return coho salmon to a level of sustained viability, while protecting 

the integrity of both ESUs, so they can be delisted and regulations or other protections under the 

CESA will not be necessary” (CDFG 2004). Appendix II of this MSRA Recovery Plan presents 

prioritized coho recovery actions for the Klamath River as found in the CDFG recovery strategy 

(CDFG 2004). 

14
4. CDFG 1600 Incidental Take Permit for Scott and Shasta Valley Agricultural Lands

The SSRT continues to work cooperatively with CDFG on the Shasta and Scott River 

Watershed-wide Permitting Program (Permitting Program) being developed by CDFG in 

consultation with the Siskiyou RCD, Shasta Valley RCD, and agricultural operators within the 

Scott and Shasta River watersheds. By establishing a streamlined process for the issuance of 

Incidental Take Permits and Streambed Alteration Agreements, the Permitting Program would 

implement key coho salmon recovery tasks while facilitating compliance with CESA and Fish 

and Game Code section 1602, respectively. Compliance with these laws is necessary because 

both agricultural water diversions and agricultural land practices may adversely affect coho 

salmon and its habitat. 

5. ESA Recovery Planning for the SONCC Coho Salmon ESU

NMFS is required by the ESA to develop recovery plans for the conservation and survival of 

federally-listed species. Recovery under the ESA is defined as the use of all methods and 

procedures which are necessary to bring any endangered or threatened species to the point at 

which measures provided pursuant to the ESA are no longer necessary. In 2002, NMFS began 

ESA recovery planning for the SONCC and Oregon Coast coho salmon ESUs through a 

scientific technical team created and chaired by the Northwest and Southwest Regional Fishery 

Science Centers, referred to as the Oregon and Northern California Coast coho salmon technical 

recovery team (TRT). As a part of the larger TRT, a SONCC working group is focusing on coho 

salmon populations within the SONCC coho salmon ESU, which includes all populations within 

the Klamath River basin. The final phase of recovery planning for the SONCC coho salmon 

ESU is underway (September 11, 2006, 71 FR 53421) and will consist of: (1) a description of 

management actions to achieve the plan’s goals for the conservation and survival of the species; 

(2) objective, measurable criteria which, when met, would result in the species being de-listed; 

and (3) estimates of time and costs required to achieve the plan’s goal and the intermediate steps 

towards that goal. Currently, a TRT, consisting of researchers, biologists and academics familiar 

with the ESU, is developing key technical information to support recovery plan development. 

The initial TRT product is a description of the historic population structure of the SONCC coho 

salmon ESU and is presented in Williams et al. (2006). Williams et al. (2006) describe 45 

individual populations across the SONCC ESU based upon their viability and independence. 

Populations determined to have minimal demographic influence from adjacent populations and 

were “viable-in-isolation” were classified as Functionally Independent populations. Populations 

that appeared to have been viable-in-isolation, yet demographically influenced by adjacent 

populations, were classified as Potentially Independent populations. Small populations of coho 

salmon that do not have a high likelihood of sustaining themselves over a 100-year time period 

in isolation and receive sufficient immigration to alter their dynamics and extinction risk were 

classified as Dependent populations. Ephemeral populations do not have a high likelihood of 

sustaining themselves over a 100-year time period in isolation, and do not receive sufficient 

immigration to affect this likelihood. Williams et al. (2006) suggest that the Klamath River 

Basin was comprised of nine historic populations of coho salmon (Table 3), and these population 

classifications will inform much of the organization of the SONCC coho salmon ESA recovery 

strategy. Population viability criteria defining the characteristics of sustainable populations 

15
Table 3. Coho salmon population classification within the Klamath River Basin (from Williams 

et al. 2006). 

Historic Population Population Type Location 

Lower Klamath River Independent Mouth of Klamath upstream to 

confluence with Trinity River 

Middle Klamath River Potentially Independent Confluence of Trinity River 

upstream to Portuguese Creek 

(inclusive in Middle Klamath); 

Seiad and Grider Creeks in Upper 

Klamath River Basin 

Upper Klamath River Independent Portuguese Creek (non-inclusive) 

upstream to Spencer Creek 

(inclusive) 

Salmon River Potentially Independent 

Scott River Independent 

Shasta River Independent 

Lower Trinity River Potentially Independent Confluence of Klamath River 

upstream to confluence with North 

Fork Trinity River (non-inclusive) 

Upper Trinity River Independent Confluence of North Fork Trinity 

River (inclusive) upstream to 

Ramshorn Creek (inclusive) 

South Fork Trinity River Independent 

within the ESU are expected to be released in summer 2007. Finally, the TRT will develop a list 

of research and monitoring needs specific to the SONCC coho salmon ESU to identify 

information gaps and address uncertainties. Taken together, these TRT products will provide the 

scientific “building blocks” of the SONCC coho salmon recovery plan. 

Fundamental to the SONCC coho salmon recovery plan will be a comprehensive threats 

assessment for the individual populations identified in Williams et al. (2006). The threats 

assessment will be an extensive compilation and synthesis of existing data, as well as input and 

technical review from an array of individuals that have knowledge of the species and conditions 

it faces. This threats assessment will identify key limiting factors for the various life history 

stages of coho salmon across the ESU, including populations within the Klamath River Basin. 

The threats assessment, in conjunction with the population viability criteria, will facilitate the 

development of focused and prioritized recovery actions. NMFS is currently working with 

various co-managers in both Oregon and California to develop a draft recovery plan. 

As detailed above, the TRT will describe the criteria for restoring to a viable status those historic 

populations deemed essential for recovery. The concept of Viable Salmonid Populations (VSP) 

is described in McElhaney et al. (2000) and consists of four population viability parameters: 

abundance, population growth rate (productivity), spatial structure and population diversity. 

Thus, for populations to be considered viable, they must not only possess a minimum level of 

abundance and productivity, but must also be well distributed across their current range and 

encompass a range of genetic and biological diversity that is capable of withstanding 

environmental variation over long time periods. The criteria under development by the TRT will 

apply these VSP concepts to the SONCC coho salmon ESU. Guided by these VSP concepts and 

the TRT information, the federal ESA recovery plan will provide the road map for achieving 

viable coho salmon populations. Finally, these viable populations will be aggregated across 

16
major population groups to exemplify a sustainable coho salmon ESU that no longer warrants 

listing under the ESA. 

6. NMFS and CDFG Restoration Grant Programs

NOAA administers several grant programs to further restoration efforts in the Klamath River 

Basin. Since 2000, NMFS has issued grants to the States of California and Oregon, and Klamath 

River Basin tribes (Yurok, Karuk, Hoopa Valley and Klamath) through the Pacific Coast Salmon 

Restoration Fund (PCSRF) for the purposes of restoring coastal salmonid habitat. From 2000 

through 2005 (2006 data are not yet available), NMFS issued grants of nearly $13.9 M to 

California and $6.2 M to Klamath River Basin tribes that funded restoration projects within the 

Klamath River basin. California integrates the PCSRF funds with their salmon restoration funds 

and issues grants for habitat restoration, watershed planning, salmon enhancement, research and 

monitoring, and outreach and education. These projects include a wide range of activities, 

including establishing conservation easements; conducting road inventories and restoration; 

improving fish passage; fostering public outreach and watershed planning; riparian fencing; and 

species and habitat monitoring. Through the use of federal, state, tribal and local funds, over 360 

projects have been funded in the Klamath River Basin. The NOAA Restoration Center 

administers several types of grants programs that have provided funding to support Klamath 

River restoration efforts. 

In 2006, the State of California dedicated an additional $10 M toward restoration actions 

specifically identified within the Klamath River Basin. The program funded 26 restoration 

projects within Humboldt and Siskiyou Counties that remove permanent or seasonal barriers to 

otherwise functioning historical salmonid habitats; prevent entrapment of juvenile salmonids; 

improve streamflows that benefit spawning access or rearing areas for salmonids; and install 

instream habitat improvement structures that recruit and sort spawning gravel and create summer 

rearing and over-wintering habitat for juveniles. Critical limiting factors addressed through the 

program include improving fish passage and summer water quality by removing several 

flashboard dams on the mainstem Shasta River. 

B. Management Efforts 

1. Federal Energy Regulatory Commission (FERC) Re-licensing of the Klamath Hydroelectric 

Project

PacifiCorp’s FERC license for the Klamath Hydroelectric Project (Project), which includes four 

dams on the mainstem Klamath River, expired on March 1, 2006. Until a new license is issued, 

PacifiCorp will operate the Project under an annual license with the same terms and conditions 

of the existing license. The existing license contains no provision for passage of anadromous 

salmon, steelhead and lamprey. Under the Federal Power Act, the Secretary of Commerce and 

the Secretary of the Interior have the discretionary authority to prescribe that fish passage be 

included as a mandatory condition in new hydropower licenses. 

In March 2006, the Department of Commerce and the Department of the Interior filed with 

FERC joint preliminary fishway prescriptions for the relicensing of the Project. The 

17
Departments filed their joint modified (final) fishway prescriptions in January 2007. Among 

other things, the modified prescriptions take into account the following: findings of fact issued 

by an Administrative Law Judge in September 2006 after a hearing on disputed issues of 

material fact regarding the Departments’ joint preliminary fishway prescriptions; FERC's draft 

environmental impact statement, which was also issued in September 2006; an alternative to the 

Departments’ joint preliminary fishway prescriptions proposed by PacifiCorp; and public 

comments. These are among the first fishway prescriptions issued in the nation to have gone 

through the hearing and alternative procedures created by Congress in the Energy Policy Act of 

2005. In his ruling, the Administrative Law Judge found that providing fish passage into the 

Project reach would benefit coho salmon (Administrative Law Judge Decision 2006). 

Like the USFWS/NMFS March 2006 preliminary prescriptions for the Klamath Dams, the 

modified prescriptions include fish passage, both upstream and downstream, for the Project’s 

Iron Gate, Copco I and II and J.C. Boyle dams. However, the January modified prescriptions 

were changed to provide a lower cost alternative for down stream passage at Copco Dam, a less 

prescriptive approach for tailrace barriers and spillway modifications, and to clarify the 

description of attraction flows. The Departments of Commerce and the Interior did not adopt the 

long-term adaptive trap and haul alternative proposed by PacifiCorp. After conducting a full 

analysis, the Departments concluded that PacifiCorp’s alternative was less protective than the 

Departments’ joint prescriptions for volitional fish passage for the Project. 

In the project area, the fishway prescriptions would restore access to approximately 58 miles of 

habitat for Chinook salmon and steelhead, provide access to this habitat for Pacific lamprey, and 

improve habitat connectivity for resident redband trout. This includes approximately 46 miles of 

habitat (mainstem and tributary) for threatened coho salmon. Fish passage could also result in 

the reintroduction (return) of Chinook salmon, steelhead and lamprey to more than 350 miles of 

habitat from which they were excluded by construction of the first dam in 1918. 

2. Reclamation’s Klamath Project Operations

NMFS issued a biological opinion on the effects of Reclamation’s Klamath Project Operations 

on SONCC coho salmon on May 31, 2002, concluding that Reclamation’s proposed 10-year 

operation would jeopardize the continued existence of SONCC coho salmon (NMFS 2002). For 

this reason, NMFS developed, with Reclamation, a reasonable and prudent alternative (RPA) 

consisting of the following elements: (1) water management measures over the next 10 years 

structured in three phases; (2) a water bank program to provide flows to the Klamath River to 

improve coho salmon habitat; (3) an agreed upon long-term flow target to be achieved by 2012; 

(4) an inter-governmental task force to develop, procure, and manage water resources in the 

Klamath River Basin (Conservation Implementation Program); and (5) an inter-governmental 

science panel to develop and implement a research program to identify and fill gaps in existing 

knowledge regarding coho salmon and their habitat requirements during various life history 

stages and water-year types. 

On March 27, 2006, U.S. District Judge Saundra Armstrong issued an order granting a motion 

for injunctive relief following remand of NMFS’s 2002 biological opinion on Reclamation’s 10-

year Klamath Project (Pacific Coast Federation of Fisherman’s Association vs. U.S. Bureau of 

18
Reclamation and NMFS, No. C02-2006 SBA). Specifically, Judge Armstrong ordered: (1) 

NMFS and Reclamation to reinitiate consultation on the Klamath Project and (2) Reclamation to 

limit Klamath Project irrigation deliveries if they would cause water flows in the Klamath River 

at and below Iron Gate Dam to fall below 100 percent of the long-term flows specified in 

NMFS’ 2002 biological opinion, until a new consultation is completed. 

NMFS and Reclamation have begun exploring approaches to the next section 7 consultation on 

the Klamath Project. NMFS will be considering a suite of new information in its next 

consultation with Reclamation, including the Evaluation of Instream Flow Needs in the Lower 

Klamath River Final Report (INSE 2006, also known as “Hardy Phase 2 report”), Reclamation’s 

Undepleted Natural Flow Study (Reclamation 2005), as well as TRT documents related to 

SONCC coho salmon population structure (e.g., Williams et al. 2006). NMFS will also consider 

the results from the NRC review of the Hardy Phase 2 report and the undepleted natural flow 

study, which are expected in October 2007. 

3. Hatchery and Genetics Management Plan (HGMP) development

For much of the last century, fish hatcheries have been viewed as a substitute for addressing 

declining salmonid abundance caused by lost or degraded habitat, blocked migration, and 

overharvest. While “mitigation” hatcheries have been largely successful in replacing lost natural 

production, genetic and ecological impacts can result as hatchery fish interact with natural 

populations (Waples 1991; CDFG and NMFS 2001). 

On June 28, 2005 (70 FR 37160), NMFS adopted a rule under section 4(d) of the ESA 

prohibiting the take of 20 groups of threatened salmon and steelhead. In addition to prohibiting 

take of threatened salmon and steelhead, the rule also included a set of 13 limits on the 

application of the ESA take prohibitions for specific categories of activities that contribute to the 

conservation of the listed salmon and steelhead or adequately limit their adverse impacts. With 

regard to fish hatchery impacts, the section 4(d) rule does not prohibit take of listed fish for a 

variety of hatchery purposes if a state or federal management agency develops an HGMP and 

NMFS approves it. An HGMP is currently being drafted for the Trinity River Hatchery by a 

multi-agency/tribal technical team in order to limit adverse impacts on SONCC coho salmon and 

achieve compliance under the ESA. CDFG submitted a draft HGMP for Iron Gate Hatchery to 

NMFS in June 2006, but both agencies decided to suspend action on the plan in light of the 

impending FERC relicensing of the Klamath Hydroelectric Project. 

4. Five Counties Road Maintenance Program

Limit Number 10 of the ESA section 4(d) rule pertains to take of threatened salmon and 

steelhead arising from routine road maintenance. Specifically, the limit does not prohibit take 

resulting from routine road maintenance conducted by the employees or agents of a state, county, 

city, or port under a program that complies substantially with the “Transportation Maintenance 

Management System Water Quality and Habitat Guide (Oregon Department of Transportation 

(ODOT) 1999). To qualify their road programs under Limit 10, Humboldt, Del Norte, Trinity, 

Siskiyou and Mendocino Counties (Five Counties) collaboratively developed the “Water Quality 

and Stream Habitat Protection Manual for County Road Maintenance in Northwestern California 

19
Watersheds” (Five Counties Salmon Conservation Program 2002; hereafter referred to as 

“Manual”), which is based largely on ODOT (1999). The Manual includes design and 

construction guidelines and best management practices that minimize erosion and rectify fish 

passage problems. Since 1998, the Five Counties have repaired or replaced 48 faulty road 

culverts, increased available fish habitat by 119 miles, and completed Road Erosion Inventories 

on over 2,000 miles of road (Five Counties Salmonid Conservation Program 2006). NMFS is in 

the process of reviewing the County’s Routine Road Maintenance Plan and expects to make a 

determination under Limit Number 10 in summer 2007. 

5. Green Diamond Habitat Conservation Plan (HCP)

Along the lower Klamath River, Green Diamond Resource Company (Green Diamond) owns 

and manages approximately 265 square miles of lands below the Trinity River confluence for 

timber production. The company has completed an HCP (Green Diamond 2006) for aquatic 

species, including SONCC coho salmon, and NMFS issued an ESA section 10(a)(1)(B) 

Incidental Take Permit on June 12, 2007. A key element of the HCP is prioritization and 

treatment of high- and moderate-priority road erosion sites. As part of the HCP, Green Diamond 

has prioritized road work for 30 sub-basins across its lower Klamath River holdings. The HCP 

commits Green Diamond to repairing approximately half of its high- and moderate-priority sites, 

property-wide, over the first 15 years of implementation. Within the lower Klamath watershed, 

the work will be accomplished through the joint efforts of Green Diamond and the Yurok Tribe. 

6. Northwest Forest Plan (NFP)

The NFP is an integrated, comprehensive design for ecosystem management, intergovernmental 

and public collaboration, and rural community economic assistance for federal forests in western 

Oregon, Washington, and northern California. The essential component of the NFP is an 

Aquatic Conservation Strategy that conserves and protects aquatic and riparian dependent 

species, specifically anadromous salmonids and their critical habitats. Since adoption of the NFP 

in 1994, timber harvest and road building have decreased dramatically on federal lands within 

the range of the Northern spotted owl, including federal lands within the Klamath River Basin 

(i.e., Six Rivers, Klamath, and Shasta-Trinity National Forests (NF)). The reduction in timber 

harvest will likely increase LWD levels, decrease stream temperatures, and decrease sediment 

delivery to the aquatic environment, all of which will ultimately aid SONCC coho salmon 

recovery. Adoption and implementation of the NFP has also reduced road construction on 

federal lands within the Klamath River Basin. This reduction in new road construction will 

result in less road-related impacts on SONCC coho salmon habitat. Also, since implementation 

of the NFP began in 1994, there have been at least 450 miles of roads decommissioned on the 

Klamath, Six Rivers, Mendocino, and Shasta-Trinity NF. Road decommissioning reduces 

chronic erosion delivery to streams and decreases the potential for catastrophic delivery of roadrelated sediment, especially sediment associated with stream crossing failure. In addition to the 

restoration and conservation principles resulting from NFP implementation, the three Klamath 

River Basin River NFs (Klamath NF, Six Rivers NF, and Shasta-Trinity NF) have accomplished 

signficant restoration results through their individual land and resource management plans. For 

instance, the Klamath NF recently reconstructed 20 existing USFS-administered road crossings 

20
by installing open-bottomed crossings to reestablish natural stream bottom configuration and 

achieve fish passage objectives. 

7. California Forest Practice Rules

 

Timber harvest on private land is regulated and enforced through Forest Practice Rules (Rules) 

by the California Department of Forestry (CDF). During the listing process for Northern 

California Steelhead (O. mykiss) in 2000, NMFS reviewed the Rules and concluded they do not 

adequately protect anadromous salmonids or provide for properly functioning habitat conditions. 

As a result of the listing of Northern California steelhead under the ESA, CDF imposed stricter 

guidelines to protect and restore watersheds with threatened or impaired values (T&I Rules) 

beginning on July 1, 2000. The T&I Rules minimize impacts to salmonid habitat resulting from 

timber harvest by requiring special management actions in planning watersheds where 

populations of anadromous salmonids listed as threatened, endangered, or candidate under the 

state or federal ESA currently preside or are restorable. Examples of the special management 

actions required include constructing watercourse crossings that allow for unrestricted fish 

passage, increasing large woody debris recruitment, increasing soil stabilization measures, and 

requiring coordination between CDF and the State and Regional Water Quality Control Boards 

to minimize sediment discharge. The T&I Rules have not been permanantly adopted, but instead 

have been reauthorized by CDF several times since their inception in 2000. 

8. Total Maximum Daily Load (TMDL) development

Under section 303(d) of the Clean Water Act of 1972, the State Water Resources Control Board 

and the United States Environmental Protection Agency (USEPA) are authorized to establish 

water quality standards through development of TMDLs that ensure the protection of identified 

beneficial uses. To begin the TMDL process, waterbodies are first evaluated as to whether they 

are meeting water quality standards and designated beneficial uses. If not, waterbodies are 

placed on the section 303(d) list of impaired waterbodies (USEPA 2003), which triggers the 

development of a water pollution control plan (i.e., a TMDL). A TMDL provides a quantitative 

assessment of water quality problems, contributing sources of pollution, and the pollutant load 

reductions or control actions needed to restore and protect the beneficial uses of an individual 

waterbody impaired from loading of a particular pollutant. 

The entire mainstem Klamath River below Iron Gate Dam is impaired by high nutrient levels, 

low dissolved oxygen levels, and elevated water temperatures. A TMDL addressing this reach is 

expected to be finalized sometime in 2009. Major Klamath River tributaries (i.e., Trinity, South 

Fork Trinity, Salmon, Scott and Shasta Rivers) are also listed as water quality impaired for 

various pollutants, and each has a completed TMDL in place. 

9. Natural Resource Conservation Service (NRCS) Programs

The NRCS continues to provide assistance to farmers and ranchers in the Klamath River Basin 

for planning and application of conservation practices that include reducing agricultural demand 

for water, improving hydrologic conditions, and restoring habitat and water quality for fish and 

wildlife. Through the NRCS Farm Bill programs, conservation systems are being implemented 

21
on private lands using the best applied science. Future efforts will be increasingly effective as 

the NRCS, conservation districts, and landowners gain experience from the practices currently 

applied. 

10. Fish Passage Forum

In November 1999, the California Resources Agency convened a group of interested state, local 

and federal agencies, fisheries conservation groups, researchers, restoration contractors, and 

others to discuss ways to restore and recover anadromous salmonid populations by improving 

fish passage at fabricated barriers. Now recognized as the Fish Passage Forum, this diverse 

group meets on a quarterly basis to promote the protection and restoration of listed anadromous 

salmonid species in California, primarily by encouraging collaboration among public and private 

sectors for fish passage improvement projects and programs. The Fish Passage Forum’s work 

not only includes identifying and inventorying known barriers, but also entails assisting fish 

passage restoration through streamlined permitting and providing fish passage education to the 

public. Although the Forum addresses fish passage issues throughout all anadromous state 

waters, a large number of projects have resolved passage issues within the Klamath River Basin. 

11. Harvest Management

Coho salmon have been harvested in the past in both coho- and Chinook-directed ocean fisheries 

off the coasts of California and Oregon. More stringent management measures that began to be 

introduced in the late 1980s have reduced coho salmon harvest substantially. Initial restrictions 

in ocean harvest were due to changes in the allocation of Klamath River fall-run Chinook salmon 

(KRFC) between tribal and non-tribal fisheries. These restrictions focused on the Klamath 

Management Zone where the highest KRFC impacts were observed (Good et al. 2005). 

Subsequent regulations designed specifically to protect coho salmon were implemented 

beginning in 1993 when the retention of coho salmon in ocean commercial fisheries was 

prohibited from Cape Falcon, Oregon south to the U.S./Mexico border. The following year, 

coho salmon retention was prohibited in ocean recreational fisheries from Cape Falcon, Oregon 

to Horse Mountain, California, and expanded to include all California waters in 1995. With the 

exception of some mark-selective recreational coho salmon fisheries that have taken place in 

recent years in Oregon waters that only allow hatchery coho salmon marked with a healed 

adipose fin clip to be retained, these prohibitions have remained in effect south of Humbug 

Mountain, Oregon (where the Pacific Fisheries Management Council (PFMC) estimates the 

majority of SONCC coho salmon harvest occurs) since their original implementation (PFMC 

2007, Good et al. 2005). 

Each year during the ocean salmon fishery preseason planning process, NMFS provides 

guidance to the PFMC on actions necessary to protect species listed under the ESA. For 

federally listed coho salmon stocks in California, this guidance is supplied by the RPA of the 

NMFS 1999 Supplemental Biological Opinion and Incidental Take Statement for SONCC and 

CCC coho salmon (NMFS 1999). Insufficient data on the natural escapement of coho salmon in 

the Klamath River (and California rivers in general) make the status of parent spawner 

recruitment difficult to assess. Because there are also no data available on exploitation rates on 

wild SONCC coho salmon, Rogue and Klamath River hatchery stocks are used as an indicator to 

22
estimate those exploitation rates. The conservation objectives established in the RPA require 

that no directed coho salmon fisheries or retention of coho salmon in Chinook salmon-directed 

fisheries be allowed off California and that management measures developed under the Fishery 

Management Plan (FMP) be designed to achieve an ocean exploitation rate on Rogue/Klamath 

hatchery coho salmon stocks of no more than 13 percent to protect CCC and SONCC coho 

salmon, respectively. As previously mentioned, coho salmon retention has been prohibited off 

the coast of California and the southern portion of Oregon for over a decade. With the exception 

of some authorized harvest by the Yurok, Hoopa Valley and Karuk tribes for subsistence, 

ceremonial and commercial purposes3

, the retention of coho salmon is also prohibited in 

California river fisheries. In order to comply with the SONCC coho salmon conservation 

objective, projected exploitation rates on Rogue/Klamath River hatchery coho salmon stocks are 

calculated during the preseason planning process using the coho salmon Fishery Regulation 

Assessment Model (FRAM, Kope 2005). Season options are then crafted that satisfy the 13 

percent maximum ocean exploitation rate. In recent years, these rates have been well below 13 

percent with five of the last eight years at or below 6 percent and no year exceeding 9.6 percent. 

Post-season estimates are not performed due to a lack of information necessary to generate 

accurate expansions of inriver coded wire tag (CWT) recoveries (Kope 2005). 

Although the conservation objectives discussed above are designed to protect a broad range of 

coho salmon populations in California, they also provide adequate protection for Klamath River 

coho salmon with respect to harvest related mortality until monitoring programs can be 

developed that will allow a better assessment of population trends. Therefore, with harvest 

restrictions in place through state and federal regulations that prohibit fishing for or retaining 

coho salmon in California, NMFS is confident that any existing harvest impacts to Klamath 

River coho salmon play a minor role in their viability and that habitat needs must now be 

addressed. 

VI. THREATS TO COHO SALMON HABITAT AND RECOMMENDED 

RESTORATION ACTIVITIES 

Fishing for coho salmon in the Klamath River and in the ocean has likely effected the viablity of 

coho salmon populations in the past and was one of the factors that led to SONCC coho salmon’s 

threatened status under the ESA. These direct impacts have been addressed in both State and 

Federal regulations that prohibit fishing for and retaining coho salmon. With those protections in 

place, the habitat needs of coho salmon now must be met, as well as addressing potential impacts 

associated with hatcheries. Since coho salmon do not, for the most part, spawn and rear within 

mainstem river habitat, restoration efforts should focus on addressing habitat limitations within 

critical tributary watersheds (NAS 2004). For example, chronic erosion from roads, timberharvest areas and recently burned forestland simplifies instream habitat, raises turbidity levels, 

and indirectly elevates water temperatures. Federal, state and local restoration efforts continue to 

address the many factors limiting salmon production within the basin by addressing upslope 

 

3

 Good et al. (2005) reported that coho salmon harvest by the Yurok tribe, which were the only tribal harvest data available, 

ranged from 42 to 135 fish between 1997 and 2000 and increased to 895 fish in 2001. The majority of this catch (63-86 percent)

was comprised of hatchery fish. 

23
sediment sources, improving instream flow levels, replacing legacy road crossings that impede 

fish passage, and removing dangerous understory fuels that precipitate catastrophic forest fires. 

However, much restoration work remains before instream habitat conditions within the Klamath 

River, as a whole, is of the quality and quantity necessary to support viable and robust coho 

salmon populations. 

This section provides a synopsis of specific threats and recommended restoration actions at the 

hydrologic unit (HU), hydrologic area (HA), and hydrologic sub-area (HSA) levels (Figure 3). 

Each task has been identified as a high priority in restoring anadromous fish populations and 

habitat within the Klamath River Basin. Much of the information presented below is synthesized 

from the CDFG coho salmon recovery strategy (CDFG 2004), along with USFS watershed 

analyses and various individual sub-watershed management plans where noted. Appendix I 

summarizes threats to coho salmon and their habitat at the HSA level across the Klamath River 

Basin. 

A. Klamath River HU 

The Klamath River HU covers approximately 1,531 square miles of the mainstem Klamath River 

and associated tributaries (excluding the Trinity, Salmon, Scott and Shasta sub-basins) from the 

estuary to above Copco Reservoir. Although anadromous fish passage is currently blocked at 

Iron Gate Dam (rm 190), coho salmon were once common and widely distributed within the 

Klamath River watershed, likely inhabiting mainstem and suitable tributary habitat up to and 

including Spencer Creek (rm 228). Today, coho salmon occupy a small fraction of that historical 

area, primarily restricted to small pockets of tributary habitat where suitable conditions persist 

(NAS 2004). 

The Klamath River drainage suffers from many natural and anthropogenic impairments that limit 

coho salmon production. Foremost is the over-allocated nature of water resources throughout the 

mainstem Klamath River and major sub-basins, which is generally acknowledged as the primary 

mechanism responsible for the poor water quality, elevated disease incidence, and impaired 

passage conditions common to much of the Klamath River Basin. Intensive studies aimed at 

identifying flow levels necessary to protect salmon and maximize instream habitat levels are 

ongoing or undergoing review at this time (e.g., Hardy Phase 2), and federal, state and local 

water managers will need to consider study recommendations as part of the overall goal of 

managing both anadromous fish production and local economies dependent on Klamath River 

water allocation. Restoration funds can restore impaired water quality conditions by 

rehabilitating degraded tributary habitat, such as addressing upslope sediment sources that can 

lower pool volumes and decrease stream depth, or by restoring riparian function to increase 

streamside shading. 

Dams and improperly designed road crossings are obvious impediments to coho salmon passage 

within the Klamath River Basin, but other less obvious mechanisms can negatively influence fish 

migration. Research has demonstrated that upstream migration of Klamath River Chinook 

salmon is suppressed at mean daily water temperatures above 23.5°C if temperatures are falling, 

24
Figure 3: Map of the Klamath and Trinity River basins showing the Hydrologic Areas used in the the 

CDFG Recovery Strategy for California Coho Salmon (CDFG 2004). 

25
below 21.0°C if temperature are rising, and above 22.0°C if temperatures are stable (Strange 

2007). Insufficient flushing flows can lead to the formation of gravel/sediment berms at 

tributary confluences, likely impairing adult migration into natal tributary spawning habitat. 

Preserving cold tributary streamflows and implementing higher mainstem “channel 

maintenance” flows could alleviate these issues and increase fish passage opportunities within 

the Klamath HU. Furthermore, removing or modifying the Pacificorp hydropower project with 

fish ladders could allow coho salmon passage into 30 miles of historic mainstem habitat located 

above the dams (Hamilton et al. 2005). A group representing federal, state, and local 

governments, as well as other non-governmental groups, is currently discussing passage and dam 

decommissioning options as part of FERC’s proposed relicensing of Pacificorp’s project. The 

outcome of these proceedings has the potential to substantially benefit salmon populations within 

the basin. 

Fish disease mechanisms are poorly understood within the Klamath River Basin, but researchers 

suspect low flows and modification of the historic hydrologic regime, combined with poor water 

quality, have created instream conditions that favor disease proliferation and fish infection. High 

water temperatures stress adult fish and slow upstream migration rates, facilitating parasite 

transmission between healthy and sick fish as they congregate in the few cold water refugial 

areas of the lower Klamath River (USFWS 2003). Similarly, juvenile infection rates have 

increased in the past several years as instream habitat conditions suited to the parasites 

(Ceratomyxa shasta and Parvicapsula minibicornis) and their intermediate hosts have expanded 

spacially and temporally as drought and water diversions alter the natural hydrology of the basin. 

Disease monitoring and investigation of the dynamics relating to each parasite’s life-cycle and 

the factors influencing infection rates are critical to implementing restoration measures necessary 

to bring parasite/host populations to more natural levels. 

1. Klamath Glen HSA

This lowest section of the Klamath River extends from the river mouth to its confluence with the 

Trinity River. Yurok Tribal lands extend upslope for 1 mile from each river bank in this reach; 

beyond tribal land, much of the tributary habitat extends into timber production land owned by 

Green Diamond. Although the Klamath River estuary is, for the most part, largely intact and 

unaffected by urban encroachment, several factors limit its ability to support properly 

functioning habitat for anadromous salmonids. As part of their ongoing coho salmon 

overwintering study, the Yurok Tribe has documented substantial use of off-channel habitat by 

juvenile coho salmon within non-natal tributaries of the Klamath River estuary (Voight 2007). 

Preliminary results from the study suggest displaced fish exhibit high fidelity with regard to this 

non-natal habitat, as well as a greater fitness level at the smolt stage as compared to fish that 

overwintered solely within their natal tributary. The lower reaches of estuarine tributaries such 

as Salt Creek, Hunter Creek and Terwer Creek often suffer from poor water quality and 

compromised riparian function, primarily due to unregulated cattle grazing adjacent to the stream 

channel. Riparian fencing projects implemented in cooperation with willing landowners would 

immediately improve habitat conditions within these critical watersheds by minimizing 

streambank erosion and rehabilitating riparian habitat, but further study will ultimately be 

necessary to fully understand how the lower Klamath River estuary and associated off-channel 

habitat function to provide for the different life stages of anadromous salmonids. 

26
Several large tributaries in the Klamath Glen HSA historically supported healthy coho salmon 

populations, but timber harvesting and construction of the associated road network has impaired 

instream habitat conditions throughout much of the HSA. For example, McGarvey, Tarup, 

Tectah, and Ah Pah Creeks all suffer from excessive sediment input that has simplified instream 

habitat, limited food production, and lowered spawning and rearing success. In some tributaries, 

large sediment loads have accumulated at their confluence with the Klamath River, potentially 

interrupting tributary dispersal of coho salmon during winter months (Voight and Gale 1998). 

Moreover, many road crossings still exist that impede or prevent fish passage. Much effort and 

resources have been expended to upgrade failing road crossings and control upslope sediment 

sources through road decommissioning and upgrading. However, continued work along these 

lines will be necessary to fully restore the functioning of these critical watersheds. 

Blue Creek is one of the few lower Klamath River tributaries that is relatively intact with regard 

to habitat function. The confluence of Blue Creek with the Klamath River regularly provides an 

area of cool, high quality water that functions as refugial habitat for adult salmon migrating 

through the lower Klamath River during late summer/early fall. Thus, protection and 

maintenance of the Blue Creek watershed is of utmost importance to the health of the lower 

Klamath River, and several key restoration actions are needed in this regard. Grazing by feral 

cattle has severely degraded riparian function within the lower Blue Creek watershed, 

simplifying the composition of riparian species and weakening streambank structure. Removing 

the cattle will help improve streambank stability and minimize erosion. To increase riparian 

species diversity and promote recruitment of functional LWD into the stream environment, 

revegetation efforts emphasizing conifer recruitment should be a part of riparian restoration 

projects. Even though the upper half of the Blue Creek watershed is publicly owned (Siskiyou 

Wilderness Area), the watershed is still hampered by elevated instream sediment conditions 

resulting from anthropogenic upslope erosion (mainly from poorly-built road networks) and in 

need of upslope restoration. 

2. Mid-Klamath HSAs

For the most part, the mid-Klamath HSAs (Orleans, Ukonom, Happy Camp, Seiad Valley, 

Beaver Creek, and Hornbrook) suffer similar limiting factors with regard to coho salmon habitat 

and production. Therefore, to avoid redundancy, this section speaks generally of the restoration 

needs common to the entire mid-Klamath reach. Recommendations specific to a given HSA will 

follow. 

Many mid-Klamath tributaries provide summer cold water accretion to the mainstem Klamath 

River when water quality conditions in the basin are often compromised. Therefore, the 

overriding restoration priority should be the restoration and maintenance of cool, high quality 

tributary streamflow. A review of current water allocations and the use of a watermaster to 

ensure water right compliance could significantly improve instream flows during periods deemed 

critical to juvenile coho salmon survival. Also, purchasing water-rights from willing landowners 

represents an effective means to dedicate high-quality surface flows to instream beneficial use. 

Where water rights cannot be purchased, efforts should be made to encourage landowners to 

incorporate innovative water-saving measures to foster efficient use of water resources. 

27
Riparian restoration is another tool that can significantly improve water quality in adjacent 

stream channels. Many tributaries of the mid-Klamath region are lacking large, functional LWD 

input, specifically coniferous species. Forestry practices that improve existing riparian zones by 

emphasizing native species and conifer recruitment during riparian planting projects and removal 

of alders and himalayan blackberry should be encouraged. Once riparian corridors have been 

restored, riparian fencing should be utilized to prevent future degradation in areas where cattle 

grazing occurs adjacent to the stream channel. 

Implementing measures to reduce sediment input from upslope sources is critically necessary 

within the mid-Klamath River HSA, where vast road networks continue to degrade and 

contribute fine sediment into the stream environment. Little-used road segments and skid trails 

should be decommissioned when possible; those not decommissioned should be upgraded and 

maintained to reduce hydrologic connectivity between upslope road surfaces and the aquatic 

environment. Large, severe wildland fires can also precipitate chronic sediment routing between 

upslope sources and stream channels, particularly when coupled with salvage logging. 

Landscapes scorched by intense fire lose soil integrity as plant and tree roots degrade, triggering 

landslides that introduce large quantities of sediment into creeks and rivers. Re-establishing a 

more natural fire regime of smaller, more frequent controlled burns can help prevent the buildup 

of understory vegetation that fuel large, hot, catastrophic fires. 

Finally, in light of the heavy road development within much of the HSA, impaired fish passage 

at road crossings is commonly a bottleneck to migrating coho salmon. Many roads administered 

by the California Department of Transportation have faulty or poorly designed culverts that 

block upstream and downstream migration. Problem culverts should first be inventoried and 

ranked in order to optimize use of limited funding resources. Another less obvious fish passage 

impairment can occur at stream diversion structures, where improperly screened intake pipes and 

canals can entrain juvenile coho salmon. These losses can be minimized by working with local 

agricultural and municipal diverters to ensure diversion structures are properly equipped with 

fish screens consistent with NMFS guidelines (NMFS 1997). 

a. Orleans HSA 

The Orleans HSA is the portion of Klamath River watershed beginning at the Trinity River 

confluence and extending upstream to the Salmon River. Many tributaries within this reach 

support coho salmon populations, and several require special management consideration. Bluff 

and Red Cap Creeks contain quality coho salmon habitat and have been designated by the USFS 

as key watersheds under the NFP (Forest Ecosystem Management and Assessment Team 1993). 

Key watersheds serve as biological refugia for maintaining and recovering habitat for stocks of 

anadromous fish at risk, such as coho salmon. Likewise, Boise and Camp Creeks have been 

identified as high priority tributaries for coho salmon spawning and rearing. Restoration actions 

should focus on maintaining these areas of high-quality coho salmon habitat. 

28
b. Ukonom HSA 

The Ukonom HSA extends from the Salmon River confluence upstream to Indian Creek and 

contains several tributaries that historically supported coho salmon. Juvenile coho salmon 

migration between mainstem and tributary habitat is often compromised in this reach by faulty 

stream crossings along Highway 96. Low tributary flow can also curtail passage at tributary 

confluences where high sediment loads aggrade and force streamflow subsurface. Stanshaw, 

Sandy Bar and Coon Creeks have been identified as needing fish passage remediation. 

c. Happy Camp HSA 

The Happy Camp HSA is located between the confluence of Indian Creek and Grider Creek. 

Upstream fish passage concerns have been documented along Highway 96 at Cade, Portugese 

and Fort Goff Creeks. Restoration work should focus on replacing/retrofitting these crossings to 

ensure they meet NMFS fish passage requirements (NMFS 2001). 

d. Seiad Valley HSA 

The Seiad Valley HSA extends from Grider Creek upstream to and including the Horse Creek 

drainage. Fish passage and riparian problems exist in Seiad Creek, where road crossings impede 

fish passage and degrade riparian functions (USDA 1999a). A private water diversion on Middle 

Creek (tributary of Horse Creek) may impede coho salmon passage and should be investigated. 

e. Beaver Creek HSA 

The Beaver Creek HSA encompasses the portion of the Klamath River between Horse Creek and 

the Shasta River confluence. Many of the larger tributaries within the Beaver Creek and Seiad 

Valley HSAs suffer from low pool frequency, elevated fine sediment, low LWD levels, low 

streamflow and high water temperatures (USDA 1993). A specific problem area within the 

Beaver Creek HSA is West Fork Beaver Creek, where Beaver Creek Road continues to supply 

high levels of sediment to the waterway. To correct this problem, the road should either be 

upgraded or decommissioned, depending on the level of anticipated future use. Fish passage 

barriers in lower Horse and Collins Creeks should be fixed. Over half of the Beaver Creek HSA 

is made up of private land inholdings within the national forest system; therefore, a coordinated 

effort toward fish passage restoration must be developed with support from private land owners 

within the HSA. 

f. Hornbrook HSA 

The Hornbrook HSA, which extends from the confluence of the Shasta River upstream to Little 

Bogus Creek, is plagued by low recruitment of mainstem spawning gravel and diminished 

flushing flows caused largely by the presence of Iron Gate Dam immediately upstream. The 

HSA has two large tributaries, Willow Creek and Cottonwood Creek, which historically 

provided productive coho salmon spawning and rearing habitat. Today, both subwatersheds 

have experienced anthropogenic degradation largely resulting from agricultural/livestock 

encroachment close to the stream channel and excessive water diversions, and, as a result, 

29
sightings of coho salmon are now rare. Restoration funding should first focus on improving fish 

passage within the HSA (there currently exists a large, impassable impoundment on mainstem 

Cottonwood Creek). Additionally, cooperatively working with farmers and landowners to 

preserve cold instream flows during summer months should greatly improve over-summer 

rearing habitat for juvenile fish. 

B. Salmon River HU 

The Salmon River watershed drains an area of 751 square miles predominantly comprised of 

federal land (approximately 90 percent). Because of the large area of public land, the Salmon 

River Basin is sparsely populated and, therefore, does not suffer water quality and quantity issues 

to the same degree as the rest of the Klamath River Basin, although the river is currently listed 

by the state as impaired due to high nutrient levels and water temperature. Sediment emanating 

from the basin’s road network is the predominate factor affecting instream habitat quality within 

the basin. For the most part, the Salmon River Basin is ill-suited for high coho salmon 

production, with much of the watershed dominated by bedrock-confined tributaries of moderate 

to steep gradients instead of the low-gradient, alluvial channels generally preferred by coho 

salmon for spawning and rearing. Despite this shortfall in suitable habitat, the Salmon River 

likely supported a small population of coho salmon in past years, perhaps a few thousand fish 

(California Department of Water Resources 1965 op. cit. CDFG 2004), although that number has 

likely dropped precipitously in the last two decades (Brown et al. 1994). 

Some of the critical problems facing coho salmon within the Salmon River HU include barriers 

to fish passage, high sediment loads, limited riparian function, and unstable spawning gravel. To 

address sediment emanating from road surfaces, the USFS should work closely with federal, 

state, tribal and local cooperators to complete road sediment source inventories. Fish passage at 

each stream crossing should be analyzed as part of this process. These inventories should be 

used to prioritize future restoration funding throughout the basin. Large, catastrophic wildland 

fires have scarred large portions of the Salmon River landscape in past years and are responsible 

for areas of chronic hillslope failure and soil erosion that often feeds sediment directly into 

downslope stream channels (Elder et al. 2002). Since the extent of fire-related erosion is often 

positively correlated with fire severity (Robichaud 2000), Federal and private forest managers 

should work cooperatively to reduce understory fuel sources through controlled burns and brush 

clearing. Smaller, more frequent controlled burns closely mimic the historic fire regime of the 

basin, and will help prevent future catastrophic fires. 

1. Lower Salmon River HSA

Fish passage into and out of Nordheimer Creek can be restricted during summer months by low 

flow and sediment aggradation at its confluence with the Salmon River. Restoration actions 

should focus on addressing the underlying causes of this phenomena, whether they are upslope 

sediment reduction or improving instream flow levels. 

30
2. Wooley Creek HSA

Much of the Wooley Creek watershed lies within the Marble Mountain Wilderness Area, and 

salmonid habitat conditions remain largely unaffected by human influence. 

3. Sawyers Bar HSA

The North Russian, South Russian, and Specimen Creek drainages suffer from increased soil 

erosion via the extensive road network within each drainage. Problem roads in these drainages 

should be upgraded or decommissioned where appropriate, and unstable slopes associated with 

these roads should be stabilized to prevent future mass-wasting and landslides. Sections of the 

North Fork Salmon River contain poorly functioning riparian corridors and are in need of 

restoration actions aimed at restoring native tree species (predominantly conifers and other 

deciduous types) that will help address low LWD levels in the future. 

4. Cecilville HSA

The Cecilville HSA encompasses the South Fork Salmon River drainage, the largest of the four 

Salmon River HSAs. The South Fork Salmon River experienced intensive hydraulic mining 

during the late nineteenth and early twentieth centuries, and large tailing piles still exist adjacent 

to the mainstem river channel as a remnant byproduct of these activities. The tailing piles inhibit 

the establishment of functional riparian habitat throughout this reach, and combined with the 

east/west alignment of the South Fork channel, serve to increase solar input and ultimately 

instream water temperatures. In light of these factors, protecting and maintaining tributary water 

quality is critical within the upper Salmon River Basin. 

C. Scott River and Shasta Valley HUs 

The Shasta River watershed covers approximately 795 square miles, originating in the higher 

elevations of the Eddy Mountains, southwest of the town of Weed, in Siskiyou County, 

California (CDFG 2004). The river flows approximately 50 miles in a northerly direction, 

passing first through the Shasta Valley and then a steep-sided canyon before emptying into the 

Klamath River at rm 177. Seventy-two percent of the watershed is in private ownership. Access 

to the Shasta River and its tributaries is limited to a few miles of the lower Shasta River still in 

federal ownership, at public road crossings, and at locations where landowners provide access. 

The portion (approximately 3 rm) of the Shasta River that passes through Shasta Canyon is in 

BLM ownership. The BLM portion of the Shasta River is afforded protected status as an Area of 

Critical Environmental Concern. 

The Scott River enters the Klamath River at rm 143 at an elevation of 1,580 feet (CDFG 2004). 

The watershed drains approximately 814 square miles and covers a large area with substantial 

variation in geology, geomorphology, and climate. Major tributaries to the 58-mile-long Scott 

River are Shackelford/Mill, Kidder, Etna, French, and Moffett Creeks, and the South and East 

Fork of the Scott River. The Klamath National Forest manages approximately 35 percent of the 

total Scott River watershed area, with the remaining 65 percent under other public management 

or private ownership. The mainstem river through Scott Valley is predominantly surrounded by 

31
irrigated farmland (50 square miles) and range land (80 square miles) comprising 16 percent of 

the watershed. 

The mainstem Scott and Shasta Rivers, and their low gradient tributaries favored by coho 

salmon, suffer many of the ailments common to drainages supporting extensive agricultural 

development. High summer diversion rates throughout both valleys limit mainstem and tributary 

flow levels, raise water temperatures, and lower water quality, making the mainstem Scott and 

Shasta Rivers unsuitable for rearing juvenile coho salmon. Particularly in the Scott drainage, 

groundwater pumping in areas where groudwater is hydrologically connected with a stream 

channel can further lower instream flows levels and limit riparian function and survival. 

Furthermore, earthen “push up” dams are still employed in some areas of the Scott Valley to 

divert streamflow for agriculture. These seasonal dams often block fish migration, and 

downstream reaches can go dry when diverters fail to release minimum bypass flows. To 

address these issues, restoration efforts should focus on working cooperatively with local 

ranchers to increase irrigation efficiency and water conservation through the implementation of 

“fish friendly” diversion structures and mandatory bypass flows. Incentives for local landowners 

with adjudicated water rights to forgo diverting during critical periods remains an important, yet 

currently not sufficiently funded, mechanism to establish coordinated water strategies in the 

Scott River and Shasta River. 

Furthermore, high sediment loads resulting from upslope timber harvesting and road building in 

the Scott River watershed have simplified tributary rearing habitat, while sediment flushed from 

those tributaries often accumulates at tributary confluences, impairing mainstem-tributary 

connectivity. Implementation of the Scott River TMDL should provide guidance for 

restoration/management actions intended to limit sediment impacts within the basin. Finally, 

large, catastrophic fires have become more common throughout the Klamath River Basin due to 

past fire-management actions and the unchecked buildup of understory fuel. Since higher 

erosion and hillslope failure rates often result from catastrophic fires due to the intense heat and 

scorching of the forest floor, restoring a more natural fire regime within the basin through 

controlled burns and understory fuel removal projects is an important step in controlling post-fire 

erosion rates. It should be noted that both the Scott and Shasta Rivers have coho salmon 

populations that are dominated by one strong brood-year. The depressed nature of the two 

remaining brood-years compromises the long-term viability of the species within these two 

basins (CDFG 2004, Williams et al. 2006). 

1. Scott Bar HSA

The Scott Bar HSA encompasses the lower canyon reach of the Scott River. Spawning and 

rearing habitat for coho salmon is limited in this reach, since many triburaries are high gradient, 

bedrock dominated systems ill suited for coho salmon spawning and rearing. Although the 

canyon reach is sparsely populated and does not suffer as much from the water quality/quantity 

impacts common to the upper Scott Valley, the surrounding hillsides do contain a large network 

of logging roads that can accelerate sediment routing into the lower Scott River. Restoration 

work should therefore focus on inventorying, prioritizing and ultimately fixing problem roads 

and culverts that exist within the HSA. Fish passage is also an issue within some of the larger 

tributaries that contain anadromous salmonid habitat, such as Tompkins Creek, Middle Creek 

32
and Mill Creek (USDA 2000b). Creeks such as these that support anadromous salmonid 

production should have priority for limited restoration funding. 

2. Scott Valley HSA

Agricultural water diversions (i.e., surface diversions and groudwater pumping) and upslope road 

building are the primary mechanisms responsible for the degraded aquatic conditions within the 

Scott Valley HSA. As noted above, water quality throughout much of the mainstem Scott River 

and lower tributary habitat becomes unsuitable for coho salmon rearing following the beginning 

of irrigation season in late spring. Higher flows are needed to restore this habitat, and efforts to 

engage local ranchers in water conservation and other innovative solutions to dedicate more 

water to instream use are crucial to restoring coho salmon habitat. Although PCSRF has helped 

screen many diversion canals within the basin in the past several years, a few unscreened 

diversions remain. Similarly, riparian fencing projects have been popular within the Scott River 

watershed during past restoration funding cycles, but several unfenced tributary reaches still 

exist. Lower tributary habitat on the valley floor has been severely degraded through destruction 

of the riparian corridor and past channel re-alignment projects meant to ease water delivery to 

farms. Specifically, Big Mill Creek should be rerouted into its original channel to alleviate fish 

passage concerns that block coho salmon access to 1.25 miles of spawning and rearing habitat 

(USDA 1997). Tailings piles from past dredge mining in the Callahan area have altered the 

hydrologic and riparian function of the upper mainstem Scott River. The river flows subsurface 

during summer months through much of this reach. 

3. Shasta Valley HSA

Poor water quality throughout the middle and lower Shasta River watershed severely limits 

juvenile coho salmon rearing success. Irrigation dams can back up river flow and create 

impoundments that increase solar input to the river and create habitat supporting non-native fish 

that prey on juvenile salmonids. Improperly-laddered dams can also impair upstream and 

downstream dispersal of juvenile coho salmon. To address this issue, restoration funding from 

CDFG is currently being utilized to remove several irrigation dams (e.g., Aruja and Shasta 

Valley Water Users Association) along the mainstem Shasta River. Removing these dams 

should improve water quality conditions while restoring a more natural hydrologic regime. 

Incentive-based alternatives with willing participants should be investigated as a means of 

preserving water quality, quantity and coho salmon habitat in the Big Springs area of the upper 

Shasta River. Riparian habitat throughout much of the Shasta Valley has been degraded by 

uncontrolled cattle grazing adjacent to the mainstem Shasta River and tributaries, though recent 

riparian remediation through fencing projects and off-channel watering systems has improved 

conditions along key river reaches. Resources and incentives should be provided to landowners 

to protect all high-value stream reaches and restore riparian corridors where cattle grazing occurs 

adjacent to the river. Dwinnel Dam currently prevents coho salmon from utilizing high quality 

headwater habitat above the impounded reservoir, and also stores cool water that could benefit 

coho salmon residing in the mainstem Shasta River below the project (NAS 2004). The NRC 

suggested that removing Dwinnel Dam be considered as a potential action to help recover coho 

salmon populations in the Shasta River (NAS 2004). 

33
D. Trinity River HU 

The Trinity River is the largest tributary to the Klamath River, draining approximately 2,038 

square miles in Humboldt and Trinity Counties (CDFG 2004). The headwater streams originate 

in the pristine wilderness of the Trinity Alps and Trinity Mountains located in eastern Trinity 

County. From its headwaters, the Trinity River flows 172 miles south and west through Trinity 

County, then north through Humboldt County and the Hoopa Valley and Yurok Indian 

Reservations until joining the Klamath River at Weitchpec, about 40 rm from the Pacific Ocean. 

Anadromous fish passage is blocked by Lewiston Dam, approximately 112 rm upstream from the 

mouth of the Trinity River. The construction of Lewiston and Trinity Dams blocked access to 

approximately 109 miles of salmon and steelhead habitat (USFWS/HVT 1999). 

Most of the mainstem Trinity River watershed is in public ownership (predominantly USFSmanaged land); only 24 percent of the watershed is in private ownership. Two Indian tribes, the 

Hoopa and Yurok, occupy reservation land within the Trinity River Basin. Both of theses tribes 

continue to rely on anadromous fish runs as they have since time immemorial, and much of their 

cultures are derived from resources found within the basin. 

Large portions of the South Fork Trinity River watershed is publicly owned and managed by the 

Shasta-Trinity NF. Much of the basin is still recovering from impacts resulting from the large 

flood of 1964 that introduced massive volumes of sediment into the South Fork Trinity River and 

most tributary reaches. Due to the substantial sediment influx, much of the mainstem South Fork 

Trinity River and Hayfork Creek still lack deep pool holding habitat for adult salmon (USDA 

1996, 2000c). Although sparsely populated in general, the basin does support some agriculture 

and grazing operations (primarily within the Hayfork Valley) that likely degrade water quality 

and riparian function (USDA 1998). 

1. Lower Trinity HA

The lower Trinity HA spans the section of river between the North Fork Trinity River and the 

confluence with the Klamath River at Weitchpec and includes the following HSAs: Hoopa, 

Willow Creek, Burnt Ranch, New River and Helena. The lower Trinity River watershed is 

mostly federally-owned and managed by the USFS (Six Rivers and Shasta-Trinity NFs), except 

for sections below Tish Tang Creek (Hoopa Reservation) and small residential communities 

spread out along the river (e.g., Willow Creek, Denny, etc.). Large wildland fires have impacted 

the watershed in the past several years, precipitating high hillslope erosion rates within affected 

tributary subwatersheds. Current fish population and habitat monitoring is carried out by CDFG, 

USFS and Hoopa Tribe scientists. 

a. Hoopa HSA 

The Hoopa HSA extends from the confluence of the Trinity and Klamath Rivers upstream to 

Willow Creek. The lower third of the HSA winds through a deep bedrock canyon which offers 

little spawning and rearing opportunity for coho salmon. Just upstream of the canyon reach lies 

the Hoopa Valley, which contains several productive coho salmon tributaries, such as Mill 

Creek, Tish Tang Creek, and Supply Creek. Horse Linto Creek, perhaps the most productive 

34
anadromous salmonid stream in the HSA, enters the mainstem Trinity River just south of the 

Hoopa reservation boundary. Intensive road development has increased erosion rates and 

sediment delivery into streams within the Hoopa Reservation, whereas the Horse Linto Creek 

watershed lies entirely within USFS boudaries and comparably has a lower road density. 

Restoration actions within the Hoopa HSA should be primarily focused on containing erosion 

and hillslides resulting from the Megram Fire, which occurred in 1999 and burned large portions 

of the Mill, Tish Tang, and Horse Linto watersheds (~125,000 acres total, USDA 2000a). The 

greatest erosion threats exist in the Horse Linto Watershed, since more acres of high and 

moderate burn severity are located on steep, erodible slopes in that watershed. Restoration 

funding should first focus on stabilizing exposed slopes within the three drainages that have the 

highest potential for hillslope failure. Rehabilitating damaged riparian habitat will also help 

minimize hydrologic connectivity between upslope sediment sources and the stream 

environment. LWD loading rates will also likely be impacted by the fire, and should be 

evaluated as a potential management concern. 

b. Willow Creek HSA

Highway 299 parallels much of mainstem Willow Creek as the highway climbs from the town of 

Willow Creek over Berry Summit and into the Redwood Creek watershed. Many of the 

restoration needs within the HSA derive from impacts attributed to Highway 299 and other roads 

within the watershed, such as decreased riparian function, low LWD recruitment, and increased 

upslope erosion (USDA 2003a). LWD and instream habitat surveys should be conducted to 

identify appropriate, high-value restoration projects. Upslope sediment sources and fish passage 

impediment occurring on private land within the watershed should be inventoried and treated. 

c. Burnt Ranch HSA

The Burnt Ranch HSA covers a large portion of the middle Trinity River Basin, extending from 

the confluence of the South Fork Trinity River upstream to the North Fork Trinity River 

confluence (excluding the New River, the largest tributary of the reach). Much of the mainstem 

river within this HSA is deeply incised and confined by bedrock banks, with many of the smaller 

tributaries exhibiting steep gradients that preclude coho salmon usage. Thus, coho salmon 

spawning and rearing habitat is generally lacking in the Burnt Ranch HSA except for portions of 

Big French and Manzanita Creeks (Everest 2007). Road densities are typically low within the 

two creeks, except for steep headwater areas that occur outside accessible anadromous reaches. 

Instream sediment levels are highest within Sailor Bar and Big Bar Creeks. Where excessive 

sediment aggradation has occurred at tributary confluences, low flows can limit mainstemtributary connectivity during the summer and fall periods. Restoration efforts should focus on 

addressing instream sediment levels through road remediation and hillslope stabilization where 

necessary. 

d. New River HSA 

The 123,000-acre New River watershed is almost entirely under public ownership, with 

approximately 78,000 acres of designated wilderness area. Anthropogenic impacts are few 

within the basin due to the wilderness designation, so robust instream habitat conditions support 

35
healthy anadromous salmonid populations, mainly Chinook salmon and steelhead. 

Unfortunately, low-gradient tributary habitat is scarce, so coho salmon are uncommon within the 

basin. The 1999 Big Bar Complex fire affected a large portion of the upper watershed; 

landslides and hillslope erosion from fire-scarred hillsides will be the predominant source of 

sediment entering the system in the future (USDA 2000d). However, the increased sediment 

influx is not expected to appreciably change instream flow timing, turbidity, or temperature 

regimes. Management actions should continue to focus on rehabilitating riparian habitat and 

unstable upslope areas damaged by the Big Bar Complex fire. 

e. Helena HSA 

North Fork Trinity River and Canyon Creek are the two dominant watersheds within the Helena 

HSA, and also contain much of the available anadromous salmonid habitat. Because these 

stream drainages flow out of the steep Trinity Alps Wilderness Area, existing stream gradients 

are often too steep to support high quality spawning and rearing conditions for coho salmon. 

Only the East Fork of the North Fork Trinity River likely supports a moderate level of coho 

salmon production (USDA 2003b). Management recommendations should focus on restoring 

channel degradation in Canyon Creek caused by past mining activities in order to re-establish 

riparian function and bank stability. 

2. Middle Trinity HA

The Douglas City and Weaver Creek HSAs encompass the upper anadromous reaches of the 

Trinity River watershed, spanning from Lewiston Dam downstream to Browns Creek. Several 

watersheds within these two HSAs support moderate populations of coho salmon, including 

Weaver Creek, Rush Creek, Browns Creek, Little Browns Creek, and Indian Creek. Most of 

these subwatersheds are privately owned except for the headwater reaches of Weaver Creek and 

Indian Creek, which lie within USFS boundaries. In general, water quality is often good within 

the Middle Trinity River reach since most creeks are fed from high elevation snow melt from the 

Trinity Alps and surrounding mountains. However, water diversions from Weaver, Rush, 

Reading, Indian and Browns Creeks diminish instream flows and water quality during summer 

months (USDA 2004). The effect of these water diversions on coho salmon habitat should be 

investigated and, where necessary, diversion screens meeting CDFG/NMFS juvenile and adult 

screening guidelines should be installed. Riparian function is compromised in many tributary 

within the Middle Trinity River watershed. Incentives and resources should be provided to 

willing landowners to reduce riparian impacts from agricultural and grazing practices. Erosion 

and sediment delivery mechanisms should also be addressed, since many tributaries suffer from 

simplified instream habitat conditions due to high sediment levels. 

3. South Fork Trinity HA

The South Fork Trinity River watershed spans 932 square miles within Humboldt and Trinity 

Counties. Hayfork Creek is the largest subwatershed in the South Fork Trinity River drainage. 

As stated in an earlier section, much of the South Fork Trinity River is impaired by high instream 

sediment loads related to both high road densities and chronic mass-wasting initiated by the 

catastrophic 1964 flood. Excessive water diversion has been documented within the Hayfork 

36
Creek watershed and should be investigated. Where legal water rights are being exercised, 

cooperative agreements with landowners should be explored to dedicate more water to instream 

use. 

a. Grouse Creek HSA and Forest Glen HSA

Intensive logging and road building have occurred within the Grouse Creek watershed since the 

1940s, and approximately 40 percent of the watershed had been harvested by 1970 (U. S. 

Environmental Protection Agency (EPA) 1998). Since the western portion of the South Fork 

Trinity River watershed is underlain by highly erosive geology, erosion rates are 

disproportionally large within the Grouse Creek watershed compared to other sub-watersheds. 

Opportunities exist within the Grouse Creek watershed to stabilize unstable upslope areas, 

enhance existing riparian habitat, and storm proof or decommission problem road segments. The 

Forest Glen HSA spans the upper South Fork Trinity River watershed upstream of Hayfork 

Creek, and suffers from many of the same stressors as the lower watershed (USDA 1999b). 

Chronic sediment introduction from roads in the Rattlesnake Creek and Plummer Creek 

watersheds should be addressed through hillslope stabilization projects and road 

decommissioning work. Riparian restoration projects are needed to improve riparian function 

and help lower instream water temperatures during summer months. 

b. Hyampom HSA

The Hyampom HSA includes the South Fork of the Trinity River and its tributaries from 

Eltapom Creek upstream to Hayfork Creek. Historical data show that the South Fork Trinity 

River and its larger tributaries were once important spawning grounds for coho salmon. The 

frequency and size of coho salmon runs in the South Fork Trinity River are not well documented, 

though they have been reported to migrate as far upstream as Hyampom (CDFG 2004). Since it 

represents one of the few alluvial reaches throughout the mainstem South Fork Trinity River, the 

Hyampom Valley is a natural spot for sediment aggradation from upstream sources and has been 

slow to recover from the effects of the 1964 flood. To address the high erosion rates in the area, 

the USFS should develop a management plan for the Big Slide to reduce sediment mobilization 

and investigate moving the county road that crosses the Big Slide. Fuel reduction projects will 

help minimize the future occurrence of large, catastrophic wildland fires. 

c. Hayfork Valley HSA and Corral Creek HSA

The Hayfork Creek watershed suffers from low flows, high instream sediment concentrations, 

and poor instream habitat complexity (USDA 1998, 2000c). Farming within the low gradient 

Hayfork Valley diverts large volumes of water from mainstem Hayfork Creek and the valley 

portion of some tributaries, severely restricting instream flow levels and compromising water 

quality. Innovative solutions stressing water conservation and the purchase of available water 

rights should be explored with willing landowners. Similarly, Trinity County should amend its 

Critical Water Resources Overlay Zone to address new water right developments that are arising 

from the subdivision of existing land parcels. Restoration and protection projects are necessary 

to improve dysfunctional riparian habitat. Finally, fuel reduction projects will minimize the 

chance of future high intensity, catastrophic fires and help facilitate a more natural fire regime to 

37
the area. Research has demonstrated that erosion and hillslope wasting processes are much less 

severe following small, low intensity wildland fires (Robichaud 2000). 

VII. CONCLUSIONS 

Built on the foundation of the extensive work already accomplished, NMFS has relied heavily on 

the existing recovery strategies developed by CDFG (2004) for coho salmon using substantial 

local stakeholder participation to develop this MSRA Recovery Plan. Our overview of coho 

salmon life history information available for the Klamath River Basin in Section III found that 

typical of large river systems, adult coho salmon have a broad period of freshwater entry in the 

Klamath River and juvenile coho salmon have a strong tendency to redistribute within the 

Klamath River Basin due to seasonal changes in conditions. Although information on coho 

salmon population trends in the Klamath River Basin remains incomplete, the available data 

suggest that coho salmon stock abundance remains at low levels and depressed, with one coho 

salmon brood year class considerably stronger than the other two brood year classes. 

As described in Section V, a variety of important conservation programs and management 

actions are underway to improve water quality and quantity and restore habitat in the Klamath 

River Basin. Many actions have been completed, others are in the process of implementation, 

and still others are in the developmental stage. Native American tribes have worked for many 

years to improve land-use practices and fisheries practices, and have implemented salmon 

monitoring, research and habitat restoration programs while striving to maintain their native 

cultural, economic, and spiritual values associated with Klamath River aquatic resources. The 

RCDs are currently working at the local level to develop programs to improve irrigation 

practices and irrigation water use to reduce effects to aquatic habitat in important coho salmon 

spawning and rearing tributaries in the Klamath River Basin while maintaining sustainable 

agricultural practices. Commercial and recreational fishing for coho salmon in California ocean 

waters and rivers ceased a decade ago when abundance plummeted. Past and future wetland and 

habitat restoration programs in the upper Klamath River Basin will improve water quality and 

provide more flexibility for water management. 

Still, more needs to be accomplished to recover coho salmon in the Klamath River Basin. 

Section VI’s synopsis of specific threats and recommended restoration actions highlight high 

priority areas and actions. Progress to provide necessary resources and incentives both to 

improve forestry practices, agricultural practices, remove artificial barriers, and curb potential 

habitat threats from urbanization in the Klamath River Basin is necessary to improve the viablity 

of coho salmon populations in the Klamath River Basin. Moreover, fish disease mechanisms are 

poorly understood in the Klamath River Basin. Although researchers suspect that low flows and 

modifications of the historic hydrologic regime, combined with poor water quality conditions, 

have created instream conditions that favor disease proliferation and fish infection, to what 

extent disease impacts coho salmon population viablity is unknown. Despite the economic and 

cultural value of robust and healthy Klamath salmon populations, few sources of reliable funding 

for fish health studies are available. Funding for multi-year disease studies in the Klamath River 

Basin remains a critical resource need to allow more scientifically-supportable management 

decisions and enable effective habitat restoration actions. 

38
For decades, a wide variety of public and private entities have been active in the Klamath River 

Basin collaborating and coordinating on a wide-array of important and useful research, 

monitoring and restoration actions. Despite the need for a Basin-wide centralizing tool or 

instrument to guide and collaboratively coordinate and prioritize monitoring, restoration and 

research efforts, no such tool exists. Such a tool could optimize benefits from existing efforts 

and resources, identifying gaps in current programs, prioritize activities that fill those gaps, 

identify funding opportunities and partners, and illustrate how monitoring, research and 

restoration efforts fit together in the Basin as a whole. 

This MSRA Recovery Plan should serve as a valuable tool for NMFS development of its 

SONCC coho salmon recovery plan under the ESA. For instance, the MSRA Recovery Plan 

summarizes ongoing threats affecting Klamath River coho salmon and current conservation 

efforts throughout the Klamath River Basin, as well as provides up-to-date scientific information 

on coho salmon status and trends. The list of “top priority” actions below should help prioritize 

implementation of critical coho recovery actions in the Klamath River Basin. 

Recovery plans developed under the ESA serve as a “road map to recovery,” and, therefore, are 

an important tool for promoting sound scientific and logical decision-making throughout the 

recovery process. While no agency or entity is required by the ESA to implement specific 

actions in a recovery plan, the ESA clearly envisions recovery plans as the central organizing 

tool for guiding each species recovery process. Recovery plans also provide context and a 

framework for implementation of section 7(a)(1) and (2), section 10, and section 4(d) of the ESA 

and serve as outreach tools by helping interested parties understand the rationale behind the 

recovery actions identified and how they can facilitate species recovery. 

As described in more detail in Section VI, efforts have been underway for several years to 

develop the ESA SONCC coho salmon recovery plan. NMFS recognizes that California has 

recently undertaken extensive conservation and recovery planning efforts for coho salmon in 

collaboration with a variety of stakeholders, including NMFS. Similarly, Oregon has also 

developed coho salmon conservation planning strategies. NMFS’ development of the SONCC 

coho salmon federal ESA recovery plan will recognize, consider and utilize, to the maximum 

extent possible, California and Oregon’s coho salmon conservation plans. NMFS is in the 

process of developing additional analyses to supplement information developed by the states. 

For instance, fundamental to the SONCC coho salmon recovery plan developed under the ESA is 

a comprehensive “threats assessment”. The SONCC coho salmon threats assessment will be an 

extensive compilation and synthesis of existing data, and will include input and technical review 

from an array of individuals that have knowledge of the species and conditions it faces. This 

threats assessment will identify key limiting factors to the various life history phases of coho 

salmon across the range of SONCC coho salmon, including populations within the Klamath 

River Basin. The threats assessment, in conjunction with the population viability criteria and 

integrated with conservation and management actions underway, will facilitate the development 

of focused and prioritized recovery actions for SONCC coho salmon. NMFS will also develop 

specific delisting criteria and recovery goals for integration into the federal ESA SONCC coho 

salmon recovery plan. Although the estimated cost of recovering Klamath River coho salmon is 

approximately $1.785 billion according to CDFG’s Coho Salmon Recovery Strategy (CDFG 

2004), the actual cost will likely be higher since anticipated water purchases outside of the 

39
Shasta/Scott basins were not included in the CDFG estimate. A cost estimate from the ESA 

recovery planning effort has not yet been derived. 

NMFS is working with tribes, local governments and other entities, and will conduct substantial 

public outreach as we prepare the draft and final ESA recovery plan for SONCC coho salmon. 

NMFS is currently working with various co-managers in both Oregon and California and will 

hold public meetings to solicit review and comment on its limiting factors analysis in August 

2007. NMFS expects to make the draft SONCC coho salmon recovery plan developed under the 

ESA available to the public for comment by spring 2008. 

A. High Priority Recovery Actions 

Appendix II presents the recommended restoration actions and rankings from CDFG’s recovery 

strategey (CDFG 2004) for coho populations within the Klamath River Basin. In addition, based 

on the review of information presented in this MSRA Recovery Plan, NMFS has identified 

below the high priority strategic actions that are necessary for coho salmon recovery in the 

Klamath River Basin. The order of presentation in this list provides a preliminary indication of 

the significance of each action in its potential contribution to coho salmon recovery. The order 

in which these actions are taken and the methods that will be applied will be refined in the ESA 

SONCC coho salmon recovery plan that will address the broader ESU of which coho salmon 

populations in the Klamath River Basin are a part. 

A. Complete and implement the NMFS recovery plan for the SONCC coho salmon under 

the ESA. 

B. Restore access for coho salmon to the upper Klamath River Basin by providing passage 

beyond existing mainstem dams. 

C. Implement fully the Trinity River Restoration Program. 

D. Provide incentives for private landowners and water users to cooperate in: (1) restoring 

access to tributary streams that are important for coho spawning and rearing; and (2) 

enhancing mainstem and tributary flows to improve instream habitat conditions. 

E. Continue to improve the protective measures already in place to address forestry practices 

and road building/maintenance activities that compromise the quality of coho salmon 

habitat. 

F. Implement restorative measures identified through fish disease research results to 

improve the health of Klamath River coho salmon populations. 

40
VIII. LITERATURE CITED 

Administrative Law Judge Decision. 2006. Decision and Attachment D: Rulings on Proposed 

Findings of Fact in the Matter of Klamath Hydroelectric Project, Docket Number 2006-

NMFS-0001, FERC Project No. 2082. Department of Commerce, September 27, 2006. 

Bell, M. C. 1991. Fisheries handbook of engineering requirements and biological criteria. 

Third edition. U.S. Army Corps of Engineers, Office of the Chief of Engineers, Fish Passage 

Development and Evaluation Program, North Pacific Division, Portland, OR. 

Bjornn, T. C. and D. W. Reiser. 1991. Habitat requirements of salmonids in streams. In: W. R. 

Meehan (ed.). Influences of forest and rangeland management on salmonid fishes and their 

habitats, pp. 83-138. Am. Fish. Soc. Spec. Pub. 19. Bethesda, MD. 751 pp. 

Brown, L. B., P. B. Moyle, and R. M. Yoshiyama. 1994. Historical Decline and Current Status 

of Coho Salmon in California. North Americal Journal of Fisheries Management 14:237-

261. 

California Department of Fish and Game (CDFG) and National Marine Fisheries Service 

(NMFS). 2001. Joint Hatchery Review Committee: Final Report on Anadromous Salmonid 

Fish Hatcheries in California. Review Draft June 27, 2001. California Department of Fish 

and Game, Sacramento, California. 36 pp. 

California Department of Fish and Game. 2002. Status Review of California Coho Salmon 

North of San Francisco: Report to the California Fish and Game Commission, April 2002. 

232 pp. 

California Department of Fish and Game. 2003. Department of Fish and Game Annual Report: 

Shasta and Scott River Juvenile Salmonid Outmigration Study, 2003. Northern California, 

North Coast Region. 

California Department of Fish and Game. 2004. Recovery strategy for California coho salmon. 

Report to the California Fish and Game Commission. 594pp. Copies/CD available upon 

request from California Department of Fish and Game, Native Anadromous Fish and 

Watershed Branch, 1419 9th Street, Sacramento, CA 95814, or on-line: 

http://www.dfg.ca.gov/nafwb.cohorecovery. 

California Department of Fish and Game. 2007. Annual Report: Shasta and Scott River 

Juvenile Salmonid Outmigrant Study, 2006. Anadromous Fisheries Resource Assessment 

and Monitoring Program, March 2007. 68 pp. 

Cederholm, C. J., and W. J. Scarlett. 1981. Seasonal immigrations of juvenile salmonids into 

four small tributaries of the Clearwater River, Washington. Pages 98-110 in E. L. Brannon 

and E. O. Salo, editors. Proceedings of the first international symposium for salmon and 

trout migratory behavior. University of Washington, School of Fisheries, Seattle. 

41
Elder, D., B. Olsen, A. Olsen, J. Villeponteaux, and P. Brucker. 2002. Salmon River Sub-basin 

Restoration Strategy: Steps to Recovery and Conservation of Aquatic Resources. Report 

prepared for The Klamath River Basin Fisheries Task Force (Interagency Agreement 14-48-

11333-98-H019). Copy available at http://www.fs.fed.us/r5/klamath/publications/. 

Everest, L. 2007. Personal communication. Fishery Biologist. U.S. Department of AgricultureForest Service, Shasta-Trinity National Forest. Redding, California. 

Forest Ecosystem Management Assessment Team (FEMAT). 1993. Forest ecosystem 

management: an ecological, economic, and social assessment. Washington, D.C. U.S. 

Forest Service and collaborating agencies. July, 1993. 

Fisher, J. P., W. G. Pearcy, and A. W. Chung. 1984. Studies of juvenile salmonids off the 

Oregon and Washington coast, 1983. Oceanographic Cruise Report 84-2. Oregon State 

University, Corvallis. 

Five Counties Salmon Conservation Program. 2002. A water quality and stream protection 

manual for county road maintenance in northwestern California watersheds. Adminstrative 

draft. September 2002. 324 pp. Copies available at 

http://www.5counties.org/PDF_Files/Roads percent20Manual/5C percent20Roads

percent20Manual.pdf

Five Counties Salmonid Conservation Program. 2006. October 1, 2006, letter to Rod McInnis 

transmitting the Submittal of Five Counties Salmonid Conservation Program’s Road 

Maintenance Manual under Limit No. 10, section 4(d) of the Endangered Species Act (ESA). 

Also available at: http://www.5counties.org/PDF_Files/Roads percent20Manual/4d

percent20Inclusion/5C percent20Submittal percent20package-Final.pdf

Francis, R.C., and N.J. Mantua. 2003. Climatic influences on salmon populations in the 

Northeast Pacific. pp. 37-67. In A.D. MacCall and T.C. Wainwright (eds.). Assessing 

Extinction Risk for West Coast Salmon. U.S. Department of Commerce, NOAA Technical 

Memo, NMFS-NWFSC-56, 198 pp. 

Gale, D. B. and D. B. Randolph. 2000. Lower Klamath River sub-basin watershed restoration 

plan (draft). Yurok Fisheries Program, Klamath, California. 77 pp. plus appendices. 

Good, T.P., R.S. Waples, and P. Adams (editors). 2005. Updated status of federally listed ESUs 

of West Coast salmon and steelhead. U.S. Dept. Commer., NOAA Tech. Memo. NMFSNWFSC-66, 598 pp. 

Green Diamond Resource Company. 2006. Aquatic Habitat Conservation Plan and Candidate 

Conservation Agreement with Assurances. Korbel, California. October. 2 volumes plus 

appendices. 

42
Hamilton, J. B., G. L. Curtis, S. M. Snedaker and D. K. White. 2005. Distribution of 

anadromous fishes in the Uper Klamath River watershed prior to hydroelectric dams – a 

synthesis of historical evidence. Fisheries 30(4):10-20. 

Hassler, T. J. 1987. Species profiles: Life histories and environmental requirements of coastal 

fishes and invertebrates (Pacific Southwest)--coho salmon. U.S. Fish and Wildl. Serv. Biol. 

Rep. 82(11.70). 19 pp. 

Hoar, W.S. 1951. The behaviour of chum, pink and coho salmon in relation to their seaward 

migration. Journal of the Fisheries Research Board of Canada 8: 241–263. 

Hoopa Valley Tribe. 2006. Emigrant Surveys and Rotary Screw Trap Poerations in the Upper 

Trinity River, 2006. Prepared for the U.S. Bureau of Reclamation under Trinity River 

Restoration Program permit 1072. December 31, 2006. 5 p. 

Institute for Natural Systems Engineering (INSE). 2006. Evaluation of instream flow needs in 

the lower Klamath River – Phase II: Final Report. Prepared for the U.S. Department of the 

Interior. July 31, 2006. 229 pp. 

Klamath River Basin Fisheries Task Force. 1991. The Long Range Plan for the Klamath River 

Basin Conservation Area Fishery Restoration Program. U.S. Fish and Wildlife Service, 

Klamath River Fishery Resource Office, Yreka, California. 

Kope, R. 2005. Performance of Ocean Salmon Fisheries Management relative to National 

Marine Fisheries Service Endangered Species Act Consultation Standards. National Marine 

Fisheries Service, Northwest Fisheries Science Center. November 17, 2005. 28 pp. 

Leidy, R.A., and G. R. Leidy. 1984. Life stage periodicies of anadromous salmonids in the 

Klamath River basin, northwestern California. U.S. Fish and Wildlife Service, Sacramento, 

California. 21 pages, plus tables and appendices. 

McElhany, P., M. H. Ruckelshaus, M. J. Ford, T. C. Wainwright, and E. P. Bjorkstedt. 2000. 

Viable salmonid populations and the recovery of evolutionarily significant units. U.S. Dept. 

Commer., NOAA Tech. Memo NMFS-NWFSC-42. 

Meehan, W. R. and T. C. Bjornn. 1991. Salmonid distributions and life histories. In: W.R. 

Meehan (ed.), Influences of forest and rangeland management on salmonid fishes and their 

habitats, pp. 47-82. Am. Fish. Soc. Spec. Pub. 19. Bethesda, MD. 751 pp. 

Narver, D. W. 1978. Ecology of juvenile coho salmon. Pages 38-43 in B. G. Shepards and R. 

M. J. Ginetz, editors. Proceedings of the Northeast Pacific Chinook and Coho Salmon 

Workshop. Fisheries Minstry Service. (Canadian) Technical Report 769, Winnipeg, 

Manitoba. 

National Academy of Science (NAS). 2004. Endangered and Threatened Fishes in the Klamath 

River Basin: Causes of decline and strategies for recovery. Prepared for the NAS by the 

43
National Research Council, Division on Earth and Life Studies, Board on Environmental 

Studies and Toxicology, Committee on Endangered and Threatened Fishes in the Klamath 

River Basin. Washington, D.C. 358 pp. 

National Research Council (NRC). 2002. Scientific Evaluation of Biological Opinions on 

Endangered and Threatened Fishes in the Klamath River Basin – Interim Report. Committee 

on Endangered and Threatened Fishes in the Klamath River Basin. National Academy Press. 

Washington, D.C. 26 pp. 

Nickelson, T. E., J. W. Nicholas, A. M. McGie, R. B. Lindsay, D. L. Bottom, R. J. Kaiser, and S. 

E. Jacobs. 1992. Status of anadromous salmonids in Oregon coastal basins. Unpublished 

manuscript. Oregon Dept. Fish Wildl., Research and Development Section, Corvallis, and 

Ocean Salmon Management, Newport. 83 pp. 

NMFS. 1997. Fish Screening Criteria for Anadromous Salmonids. Southwest Region. Long 

Beach, California. 10 pp. 

NMFS. 1999. Endangered Species Act – Section 7 Consultation; Supplemental Biological 

Opinion and Incidental Take Statement. Pacific Coast Salmon Plan and Amendment 13 to 

the Plan. National Marine Fisheries Service, Protected Resources Division. April 28, 1999. 

40 pp. 

National Marine Fisheries Service (NOAA Fisheries). 2001. Guidelines for salmonid passage at 

stream crossings. NOAA Fisheries, Southwest Region, Long Beach, CA. 

NMFS. 2002. Biological Opinion: Klamath Project Operations. National Marine Fisheries 

Service, Southwest Region, Long Beach, California. May 31, 2002. 

Oregon Department of Fish and Wildlife (ODFW). 2005. Native Fish Conservation Policy. 

Oregon Department of Fish and Wildlife, 3406 Cherry Avenue N.E., Salem, OR 97303. 

November 8, 2002; revised September 12, 2003. 11 pp. 

Oregon Department of Transportation (ODOT). 1999. Routine Road Maintenance: Water 

Quality and Habitat Guide Best Management Practices, July 1999. Available at 

http://www.odot.state.or.us/eshtm/images/4dman.pdf

Pacific Fishery Management Council. 2007. Preseason Report III: Analysis of Council Adopted 

Management Measures for 2007 Ocean Salmon Fisheries. (Document prepared for the 

Council and its advisory entities). Pacific Fishery Management Council, 7700 NE 

Ambassador Place, Suite 101, Portland, Oregon 97220-1384. 

Peterson, W., R. Hooff, C. Morgan, K. Hunter, E. Casillas, and J. Ferguson. 2006. Ocean 

Conditions and Salmon Survival in the Northern California Current. National Marine 

Fisheries Service, Northwest Fisheries Science Center. November, 2006. 44 pp. 

44
Robichaud, P. R. 2000. Forest Fire Effects on Hillslope Erosion: What We Know. USDA – 

Forest Service, Rocky Mountain Research Station, Moscow, Idaho. Copy available at 

http://watershed.org/news/win_00/2_hillslope_fire.htm. 

Sandercock, F. K. 1991. Life history of coho salmon. In: C. Groot and L. Margolis (eds.), 

Pacific salmon life histories, pages 397-445. Univ. British Columbia Press, Vancouver. 564 

pp. 

Scarlett, W.J. and C.J. Cederholm. 1984. Juvenile coho salmon fall-winter utilization of two 

small tributaries of the Clearwater River, Jefferson County, Washington. Pages 227- 242 in 

J.M. Walton and D.B. Houston, eds. Proceedings of the Olympic Wild Fish Conference, Port 

Angeles, Washington. March 23- 25, 1983. 

Scott River Watershed Council. 2005. Initial Phase of the Scott River Watershed council 

Strategic Action Plan: October 2005 Update. Available at: http://www.scottriver.org/PlanOct2005-Update.pdf

Shapovalov, L., and A. C. Taft. 1954. The life histories of the steelhead rainbow trout (Salmo 

gairdneri gairdneri) and silver salmon (Oncorhynchus kisutch) with special reference to 

Waddell Creek, California, and recommendations regarding their management. Calif. Dept. 

Fish Game Bull. 98. 

Shasta Valley Coordinated Resource Management and Planning Committee (Shasta CRMP). 

1997. Shasta Watershed Restoration Plan. Available at: 

http://www.snowcrest.net/shastacrmp/biblio/shasta/crmp/crmpln.pdf.

Sinnen, W, M. Knechtle, P. Garrison, S. Borok. 2007. Annual Report Trinity River Basin 

Salmon and Steelhead Monitoring Project, 2005-2006 Season. California Department of 

Fish and Game. Trinity River Restoration Project. 

Snyder, J.O. 1931. Salmon of the Klamath River, California. Calif. Fish Game Fish. Bull. 

34:130. 

Soto, T. 2007. Personal communication. Fishery Biologist. Karuk Tribe Fisheries Program, 

Orleans, California 

Soto, T. L. and M. M. Hentz. 2003. Mid-Klamath Subbasin Fisheries Resource Recovery Plan: 

Working Draft. Prepared for the Karuk Tribe of California. Funded by the Klamath River 

Basin Fisheries Task Force. August 25, 2003. 42 pp. Available at: 

http://www.mkwc.org/publications/subbasinplanning/Mid percent20Klamath

percent20Subbasin percent20Fisheries percent20Resource percent20Recovery

percent20Plan.pdf

Strange, J. 2007. Adult Chinook Salmon Migration in the Klamath River Basin: 2005 Sonic 

Telemetry Study Final Report. Yurok Tribal Fisheries Program and School of Aquatic and 

45
Fishery Sciences – University of Washington, in collaboration with Hoopah Valley Tribal 

Fisheries. 96 pp. 

Stutzer, G. M., J. Ogawa, N. J. Hetrick, and T. Shaw. 2006. An initial assessment of radio 

telemetry for estimating juvenile coho salmon survival, migration behavior, and habitat use 

in response to Iron Gate Dam discharge on the Klamath River, California. U. S. Fish and 

Wildlife Service, Arcata Fish and Wildlife Office, Arcata Fisheries Technical Report 

Number TR2006-05, Arcata, California. 

Sutton, R., M. Deas, R. Faux, R. A. Corum, T. Soto, M. Belchik, J. E. Holt, B. W. McCovey Jr., 

and F. J. Myers. 2004. Klamath River Thermal Refugia Study, Summer 2003. Prepared for 

the Klamath Area Office, Bureau of Reclamation, Klamath Fall, OR. 147 pp. 

U.S. Bureau of Reclamation. 2005. Natural flow of the upper Klamath River-Phase 1. Bureau 

of Reclamation Technical Service Center, Denver, Colorado. 77 p. plus attachments. 

U.S. Bureau of Reclamation. 2007. Estimation of Returns of Naturally Produced Coho to the 

Klamath River – Review Draft. Tech Memorandum #1 of 8. Klamath Coho Integrated 

Modeling Framework Technical Memorandum Series. Prepared by Cramer Fish Sciences for 

U.S. Bureau of Reclamation. November 2, 2006. 26 pp. 

U.S. Department of Agriculture - Forest Service. 1993. Beaver Creek Watershed Analysis. 

Klamath National Forest. Copy available at 

http://www.fs.fed.us/r5/klamath/publications/pdfs/watershed/beavercreek/index.shtml. 

U.S. Department of Agriculture - Forest Service. 1996. Lower Hayfork Creek Watershed 

Analysis. Shasta-Trinity National Forest. Copy available at 

http://www.fs.fed.us/r5/shastatrinity/publications/st-main/watershed-analysis/lowerhayfork.shtml. 

U.S. Department of Agriculture - Forest Service. 1997. Callahan Watershed Ecosystem 

Analysis. Klamath National Forest. Copy available at 

http://www.fs.fed.us/r5/klamath/publications/pdfs/watershed/callahan/index.shtml. 

U.S. Department of Agriculture - Forest Service. 1998. Upper Hayfork Creek Watershed 

Analysis. Shasta-Trinity National Forest. Copy available at 

http://www.fs.fed.us/r5/shastatrinity/publications/st-main/watershed-analysis/u-hayforkck.shtml. 

U.S. Department of Agriculture - Forest Service. 1999a. Thompson/Seiad/Grider Ecosystem 

Analysis. Klamath National Forest, Happy Camp Ranger District. Copy available at 

http://www.fs.fed.us/r5/klamath/publications/pdfs/watershed/tsg/index.shtml. 

U.S. Department of Agriculture - Forest Service. 1999b. Upper South Fork Trinity River – 

Happy Camp Creek Watershed Analysis. Hayfork Ranger District, Shasta-Trinity National 

Forest. 62 pp. 

46
U.S. Department of Agriculture - Forest Service. 2000a. Horse Linto, Mill and Tish Tang Creek 

Watershed Analysis, version 1.0. Six Rivers National Forest. Copy available at 

http://www.fs.fed.us/r5/sixrivers/publications/. 

U.S. Department of Agriculture - Forest Service. 2000b. Lower Scott Ecosystem Analysis. 

Klamath National Forest, Scott River Ranger District. Copy available at 

http://www.fs.fed.us/r5/klamath/publications/pdfs/watershed/lowerscott/index.shtml. 

U.S. Department of Agriculture - Forest Service. 2000c. Middle Hayfork-Salt Creek Watershed 

Analysis. Shasta-Trinity National Forest. 107 pp. 

U.S. Department of Agriculture - Forest Service. 2000d. New River Watershed Analysis. 

Shasta-Trinity National Forest. 97 pp. 

U.S. Department of Agriculture – Forest Service. 2003a. Mainstem Trinity Watershed Analysis. 

Prepared by Natural Resources Management Corporation for Pacific Southwest Region, Six 

River National Forest, Lower Trinity Ranger District, Eureka, California. 444 pp. 

U.S. Department of Agriculture - Forest Service. 2003b. North Fork Trinity River, East Fork 

North Fork Trinity River, and Canyon Creek Watershed Analysis. Shasta-Trinity National 

Forest, Trinity River Management Unit. 12 pp. 

U.S. Department of Agriculture - Forest Service. 2004. Weaverville Watershed Analysis. 

Shasta-Trinity National Forest, Trinity River Management Unit. 107 pp. 

U.S. Environmental Protection Agency (EPA). 1998. South Fork Trinity River and Hayfork 

Creek Sediment Total Maximum Daily Loads. U.S. EPA Region 9. 75 pp. Available at: 

http://www.epa.gov/region09/water/tmdl/trinityso/fsftmdl.pdf

U.S. Environmental Protection Agency. 2003. 2002 CWA Section 303(d) List of Water Quality 

Limited Segment. North Coast Regional Water Quality Control Board. Copy available at 

http://www.swrcb.ca.gov/tmdl/docs/2002reg1303dlist.pdf. 

USFWS. 1998. Klamath River (Iron Gate Dam to Seiad Creek) Life History Periodicities for 

Chinook, Coho and Steelhead. U.S. Fish and Wildlife Service, Coastal California Fish and 

Wildlife Office, Arcata, California. 51 pp. 

USFWS. 2000. Record of Decision, Trinity River Mainstem Fishery Restoration, Final 

Environmental Impact Statement/Environmental Impact Report, U.S. Department of the 

Interior, Washington, DC. 

USFWS. 2003. Klamath River Fish Die-Off September 2002: Causative Factors of Mortality. 

Report number AFWO-01-03. Arcata Fish and Wildlife Office, Arcata, CA. 29 pp. 

47
48

USFWS. 2007. Mainstem Klamath River Coho Salmon Redd Surveys, 2001 to 2005. U.S. Fish 

and Wildlife Service, Arcata Fish and Wildlife Office, Arcata, California. 21 pp. 

USFWS/HVT. 1999. Trinity River Flow Evaluation. Final Report. U.S. Fish and Wildlife 

Service, Arcata Fish and Wildlife Office, and Hoopa Valley Tribe, U.S. Department of the 

Interior, Washington, DC. 

Voight, H.N., and D.B. Gale. 1998. Distribution of fish species in tributaries of the lower 

Klamath River: an interim report, FY 1996. Yurok Tribal Fisheries Program, Habitat 

Assessment and Biological Monitoring Division Technical Report No. 3, Klamath, 

California. 

Voight, H. 2007. Personal communication. Fishery Biologist. Yurok Tribe Fisheries 

Department, Klamath, California. 

Waples, R. S. 1991. Genetic interactions between hatchery and wild salmonids: lessons from 

the Pacific Northwest. Canadian Journal of Fisheries and Aquatic Sciences 48:124-133. 

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. 

U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-24. 

Williams, T. H., E. P. Bjorkstedt, W. G. Duffy, D. Hillemeier, G. Kautsky, T. E. Lisle, M. 

McCain, M. Rode, R. G. Szerlong, R. S. Schick, M. N. Goslin, and A. Agrawal. 2006. 

Historical Population Structure of Coho Salmon in the Southern Oregon/Northern California 

Coasts Evolutionarily Significant Unit. U.S. Dept. Commer., NOAA Tech. Memo. NOAATM-NMFS-SWFSC-390. 

Federal Register Notices

71 FR 53421. National Marine Fisheries Service. Endangered and Threatened Species: 

Recovery Plan Preparation for 5 Evolutionarily Significant Units (ESUs) of Pacific Salmon and 

5 Distinct Population Segments (DPSs) of Steelhead Trout. September 11, 2006. 

71 FR 37160. National Marine Fisheries Service. Endangered and Threatened Species: Final 

Listing Determinations for 16 ESU’s of West Coast Salmon, and Final 4(d) Protective 

Regulations for Threatened Salmonid ESUs. June 28, 2005. 
IX. APPENDIX I: THREATS TABLE ORGANIZED AT THE HSA LEVEL. 

Hydrologic Area 

Lower 

Klamath 

River Middle Klamath River Salmon River 

Scott 

River 

Shasta 

Valley Lower Trinity River 

Middle 

Trinity 

River 

Hydrologic SubArea 

Klamath Glen 

Orleans 

Ukonom 

Happy Camp 

Seiad Valley 

Beaver Creek 

Hornbrook 

Iron Gate 

Lower Salmon 

Wooley Creek 

Sawyers Bar 

Cecilville 

Scott Bar 

Scott Valley 

Shasta Valley 

Hoopa 

Willow Creek 

Burnt Ranch 

New River 

Helena 

Douglass City 

Weaver Creek 

Degraded HabitatEstuarine and Nearshore 

Marine 

x

Degraded HabitatFloodplain Connectivity 

and Function 

x 0

Degraded HabitatChannel Structure and 

Complexity 

x x 0 0 x x x 0 x 0 0 

Degraded HabitatRiparian Areas and LWD 

Recruitment 

x x x x x x x x 0 x 0 0 x 0 

Degraded HabitatStream Substrate x x x 0 x x x x x x x x 0 x ‡ 0 x 0 Degraded HabitatStream Flow x 0 x x 0 x x 

Degraded Habitat - 

Water Quality x x x x 0 0 0 x 0 x x 0 

Degraded Habitat - Fish 

Passage x x x x x x 0 0 x x x 

Hatchery-related 

Adverse Effects ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆ ∆

Harvest-related Adverse 

Effects x x

Predation/Competition/ 

Disease † † † † † † † † 

Symbol Code: x = CDFG Coho Recovery Strategy (CDFG 2004); 0 = various USFS watershed analyses; ∆ = Joint CDFG/NMFS H

and NMFS 2001) and SONCC coho salmon status review (Good et al. 2005); † = NAS Report (NAS 2004); ‡ = Everett 2007.

49
X. APPENDIX II: CDFG’S IMPLEMENTATION SCHEDULE FOR KLAMATH WATE

RECOMMENDATIONS. CDFG’s Implementation Schedule for Klamath Watershed Recommendations (as appears in CDFG 2004), organpriority, task level, action entities, and estimated duration. Watershed priority ranges from 1 (lowest priority) to represents the watershed’s restoration and management potential. Task levels denote the relative importance or pimplementation, and range from C (lowest) to E (highest). Task level E symbolizes recommendations critical to 

recovery that must be implemented rapidly, while level C tasks contribute to stated recovery goals or criteria (or delayed recovery if not implemented).

IMPLEMENTATION SCHEDULE FOR KLAMATH RIVER BASIN

HSA

PRIORITY

TASK 

LEVEL

TASK

NUMBER TASK DESCRIPTION IDENTIFIED ACTION ENTI

KLAMATH RIVER HU 

E KR-HU-01 Facilitate development of a cooperative adaptive management plan in 

preparation for low-flow emergencies. 

POTENTIAL LEAD: CDFG, PacOTHERS: USBR, NOAA FisheUSFWS, DOI, Tribes, SWQCstakeholders 

E KR-HU-02 Develop a plan to restore and maintain tributary and mainstem habitat 

connectivity where low flow or sediment aggradation is restricting coho salmon 

passage. 

POTENTIAL LEAD: CDFG 

OTHERS: RWQCB, NOAA Fi

USFS, Yurok Tribe, CDF, CaLandowners 

C KR-HU-03 Develop a plan (including a feasibility analysis) for coho salmon passage over 

and above Iron Gate and Copco dams to restore access to historic habitat. 

POTENTIAL LEAD: FERC, PacOTHERS: USFWS, USBR, NOFisheries, CDFG 

C KR-HU-04 Analyze the feasibility and appropriateness of site-specific FGC §2084 permits 

for sport fishing for hatchery coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries 

E KR-HU-05 Complete comprehensive flow study activities (e.g. Hardy Phase II) and use 

them to educate water managers on how to reduce impacts to coho salmon. 

POTENTIAL LEAD: BIA, USFWOTHERS: NOAA Fisheries, CD

50
D KR-HU-06 Implement the comprehensive flow study in a manner that will restore natural 

stream processes 

POTENTIAL LEAD: USBR 

OTHERS: USFWS, NOAA Fis

E KR-HU-07 Apply protective down-ramp rates at Iron Gate Dam to minimize stranding of 

coho salmon fry. 

POTENTIAL LEAD: CDFG, USPacifiCorp OTHERS: USFWS 

E KR-HU-08 Improve water quality coming into the Klamath River mainstem from the Upper 

Klamath River Basin through ongoing efforts. 

POTENTIAL LEAD: CDFG 

OTHERS: USBR, USFWS, NO

D KR-HU-09 Perform cost/benefit analysis of full or partial Hydroelectric Project removal for 

the purposes of improving water quality, fish passage, and sediment transport. 

POTENTIAL LEAD: PacifiCorp, OTHERS: USBR, USFWS, NOFisheries, CDFG 

D KR-HU-10 Manage the streams and uplands in key cold-water tributaries, to preserve their 

cold-water thermal regime. 

POTENTIAL LEAD: USFS 

OTHERS: Tribes, NOAA Fishe

USFWS, CDFG, LandownersWatershed Groups 

D KR-HU-11 Investigate coho salmon non-natal rearing and refugia use in lower reaches of 

tributaries and mainstem confluences. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, US

D KR-HU-12 Protect and enhance tributary reaches identified as providing refugia to juvenile 

coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries, US

E KR-HU-13 Develop a plan to address water quality and quantity in Klamath River 

tributaries that exacerbate mainstem water quality problems. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Private Landow

D KR-HU-14 Implement the plan that addresses water quality and quantity in the Klamath 

River tributaries that exacerbate mainstem water quality problems. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Private Landow

E KR-HU-15 Assess hatchery operations in terms of coho salmon recovery in accordance with 

the policies and guidelines included in this document. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, US

E KR-HU-16 Continue disease monitoring of juvenile salmon emigration in the Klamath 

River mainstem so that major disease outbreaks can be identified and their causes evaluated. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries, US

51
E KR-HU-17 Conduct disease monitoring of migrating adult Chinook and coho salmon during 

fall migration. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, US

D KR-HU-18 Conduct studies in and around the Klamath River Hydroelectric Project to see if 

the Project is contributing to habitat for the Ceratomyxosis intermediate host. 

POTENTIAL LEAD: PacifiCorp 

OTHERS: USBR, CDFG, NOA

USFWS 

C KR-HU-19 Restore appropriate coarse sediment supply and transport near Iron Gate Dam. 

Means to achieve this could include full or partial removal of the Klamath Project, or gravel introduction such as is done below other major dams (e.g., Trinity Dam). 

POTENTIAL LEAD: FERC, PacOTHERS: USFWS, NOAA Fis

E KR-HU-20 Acquire additional water through conservation easements and purchases of 

water and water rights from willing sellers, where lack of flows is a limiting factors and dedicate these flows to instream coho salmon needs 

POTENTIAL LEAD: CDFG 

OTHERS: USBR, NOAA Fishe

E KR-HU-21 Acquire interim, emergency water through transfers of water and water rights 

from willing sellers, when necessary to meet critical instream coho salmon needs. 

POTENTIAL LEAD: CDFG OTHERS: USBR, NOAA Fishe

D KR-HU-22 Provide watermaster service for all diversions with partial funding provided by 

the state or federal governments. 

POTENTIAL LEAD: DWR 

OTHERS: SWRCB, CDFG, US

C KR-HU-23 Promote public interest in the Klamath River Basin’s coho salmon, their 

beneficial use and habitat requirements. 

POTENTIAL LEAD: CDFG OTHERS: USFWS, RCDs, WaGroups 

KLAMATH GLEN HSA 5 E KR-KG-01 Resume estuary investigations to better understand the estuary’s role in the 

survival of Klamath River Basin River coho salmon. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, YuCoastal Commission, NPS 

52
5 D KR-KG-02 Develop a plan to restore off-channel estuarine, wetland, and slough habitat in 

the Klamath River estuary and adjoining lower tributary reaches that includes: 

a. Determining if key properties, conservation easements, or development 

rights need to be purchased and the work with wiling landowners; and 

b. Determining the need and installation of livestock exclusion fencing to 

protect restored areas. 

POTENTIAL LEAD: CDFG 

OTHERS: Yurok Tribe, Private 

5 D KR-KG-03 Implement the plan to restore off-channel estuarine, wetland, and slough habitat 

in the Klamath River estuary and adjoining lower tributary reaches 

POTENTIAL LEAD: CDFG OTHERS: Yurok Tribe, Private 

5 D KR-KG-04 Develop a plan to maintain Blue Creek watershed tributaries as key thermal 

refugia for their cool water contributions to the mainstem Klamath River. The plan should emphasize that: 

a. Sediments from upslope activities do not impact the refugia; b. Upslope stabilization and restoration activities continue, including road 

assessment and treatment; 

c. In-channel and riparian restoration efforts (target riparian retention efforts) 

continue; and 

d. Feral cattle are removed. 

POTENTIAL LEAD: Yurok Trib

OTHERS: Simpson, USFS, NO

Fisheries, CDFG, USFWS 

5 D KR-KG-05 Implement the plan to maintain Blue creek watershed tributaries as key thermal 

refugia for their cool water contributions to the mainstem Klamath River. 

POTENTIAL LEAD: Yurok TribOTHERS: USFS, CDFG, CCC

5 D KR-KG-06 Develop a plan to protect and restore Klamath River mainstem tributaries, even 

those that do not support populations of coho salmon but that provide cool water and which improve mainstem Klamath water quality, particularly during warm summer months. Plan should emphasize the: 

a. Protection and/or restoration of riparian habitat; b. Stabilization of upslope areas to prevent sedimentation and aggradation of 

tributaries at their mouths; and 

c. Improvement of federal land management activities to reduce impacts to 

riparian corridors and decrease sediment loads. 

d. Finalize and/or refine the Lower Klamath Sub-Basin Watershed Restoration 

Plan (Gale and Randolph 2000) that focuses on the tributaries to the Lower Klamath within the Klamath Glen HSA. 

POTENTIAL LEAD: Yurok Trib

OTHERS: Simpson, USFS, NO

Fisheries, RWQCB, Yurok TrValley Tribe, USFWS

5 D KR-KG-07 Finalize and Implement the Lower Klamath Sub-Basin Watershed Restoration 

Plan (Gale and Randolph 2000) to protect and restore Klamath River mainstem tributaries. 

POTENTIAL LEAD: Yurok TribOTHERS: USFS, CDFG, CCC

53
5 D KR-KG-08 Reduce sediment input from upslope sources, including activities such as: 

a. Decommissioning skidtrails and unmaintained roads, where possible; b. Upgrading roads and maintenance practices; c. Stabilizing slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams, and 

d. Minimizing alteration of natural hillslope drainage patterns. 

POTENTIAL LEAD: Yurok Trib

OTHERS: USFS, CDFG, CCC

5 E KR-KG-09 Review existing inventory and assessment of barriers (Gale 2003) and prioritize 

barriers impeding migration of adult and juvenile coho salmon throughout the Lower Klamath River tributaries. 

POTENTIAL LEAD: Yurok TribOTHERS: Simpson, Del NorteCaltrans, CDFG, CCC, SCC 

5 D KR-KG-10 Treat prioritized barriers impeding migration of adult and juvenile coho salmon 

throughout the Lower Klamath River tributaries. 

POTENTIAL LEAD: CDFG 

OTHERS: County, Tribes, NOA

USFWS, Landowners, Caltran

5 D KR-KG-11 Investigate temporal and spatial magnitude of tributary deltas and seasonal 

subsurface flow reaches to determine impacts to juvenile and adult coho migration and to quantify seasonal loss of lower tributary habitat. Investigation should include assessment of long-term delta size trends, annual variation in coho salmon access periodicity by tributary, quantification of seasonal habitat loss and fish stranding, and the relation of delta and subsurface flow formation to upslope erosion, river and tributary flow, mainstem bedload deposition and other causative factors. 

POTENTIAL LEAD: Yurok TribOTHERS: Simpson, CDFG, CC

5 D KR-KG-12 Conduct feasibility study to reestablish adult coho salmon passage above major 

barriers in lower Roaches and Tully creeks and the Middle and North Forks of Ah Pah Creek. 

POTENTIAL LEAD: CDFG, Yur

OTHERS: Simpson, CCC, NOA

5 D KR-KG-13 Treat sediment sources and improve riparian and instream habitat conditions to 

provide adequate and stable spawning and rearing areas for coho salmon. 

POTENTIAL LEAD: Yurok TribCCC OTHERS: USFS, CDFG, SCC 

5 D KR-KG-14 Develop a plan to restore in-channel and riparian habitat in tributaries to 

address: 

a. Revegetating riparian zones with native species (e.g., conifers) to stabilize 

stream banks and promote a long-term supply of LWD; 

b. Providing adequate protection from development, grazing, etc; and c. Relocating roads out of riparian areas when feasible. 

POTENTIAL LEAD: Yurok Trib

OTHERS: Landowners, CCC, C

NOAA Fisheries 

54
5 D KR-KG-15 Implement the plan to restore in-channel and riparian habitat in tributaries. POTENTIAL LEAD: Yurok Trib

CCC OTHERS: NOAA Fisheries, CDSCC, Landowners 

5 D KR-KG-16 Develop a plan to provide suitable accumulations of woody cover in slowvelocity habitats for coho salmon winter rearing on a short-term basis by placing 

wood in needed areas until natural supplies become available. 

POTENTIAL LEAD: CDFG 

OTHERS: Tribes, Landowners, 

5 D KR-KG-17 Implement the plan to provide suitable accumulations of woody cover in slowvelocity habitats for coho salmon winter rearing on a short-term basis by placing 

wood in needed areas until natural supplies become available. 

POTENTIAL LEAD: CDFG OTHERS: Tribes, Landowners, 

5 C KR-KG-18 Construct livestock exclusionary fencing and corresponding riparian restoration 

as necessary in Salt, lower High Prairie, lower Hunter and lower Terwer creeks. Provide funding and incentives to landowners and/or restoration groups where necessary to achieve this goal. 

POTENTIAL LEAD: CCC, Yuro

OTHERS: Landowners, CDFG 

5 C KR-KG-19 Develop a plan to remove feral cattle from lower Blue and Bear Creeks. POTENTIAL LEAD: Yurok Trib

OTHERS: Simpson 

5 C KR-KG-20 Implement the plan to remove feral cattle from lower Blue and Bear creeks. POTENTIAL LEAD: Landowner5 D KR-KG-21 Work with Humboldt County, NOAA Fisheries and existing and future gravelmining operators to restrict gravel-mining operations to appropriate mainstem 

Klamath locations. Gravel mining should not be conducted within Lower Klamath tributary watersheds until a scientifically valid and peer-reviewed geomorphic analysis is conducted to determine existing channel stability, causes of excess aggradation, and identifies gravel mining as an appropriate restorative measure, as outlined in task RW-XXXV-A-1. 

POTENTIAL LEAD: CDFG OTHERS: County, NOAA Fishexisting and future gravel min

5 C KR-KG-22 Encourage cooperation between industrial timber land managers and tribes to 

restore coho salmon habitat Use the successful Tribal/Simpson Resource Company program as an example. 

POTENTIAL LEAD: CDFG 

OTHERS: Tribes, Simpson Tim

55
5 D KR-KG-23 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; b. Management to promote conifer recruitment; c. Improvement of existing riparian zones through planting and release of 

conifers, and control of alders, blackberries, and other competitors; and 

d. Provide technical support as an incentive for landowners. 

POTENTIAL LEAD: CDFG OTHERS: USFS, NOAA FisheTribe, CDF, Landowners 

5 D KR-KG-24 Provide technical and financial support to implement riparian restoration 

throughout alluvial reaches in lower Blue, Terwer, Hunter and Salt creeks. 

POTENTIAL LEAD: CDFG 

OTHERS: Landowners, CCC, Y

5 C KR-KG-25 Investigate straying and impacts of exotic fish (bass and bullhead) populations 

in an abandoned mill pond in lower Richardson Creek to coho salmon in the adjoining Klamath River estuary. 

POTENTIAL LEAD: CDFG OTHERS: Yurok Tribe, RNSP, Fisheries 

5 C KR-KG-26 Continue funding and technical support for the California Conservation Corps to 

continue their collaborative participation with the Yurok Tribe and Simpson Resource Company to implement watershed restoration throughout the lower Klamath River subbasin. 

POTENTIAL LEAD: CDFG 

OTHERS: Yurok Tribe, Simpso

Company 

5 E KR-KG-27 Support continued implementation of the Coho Salmon Regional Abundance 

Inventory throughout the lower Klamath River subbasin. 

POTENTIAL LEAD: CDFG OTHERS: 

5 C KR-KG-28 Develop a plan to restore the historic flood plain on Hoppaw Creek, in 

cooperation with landowners and Caltrans. 

POTENTIAL LEAD: CDFG 

OTHERS: Simpson, Yurok Trib

5 C KR-KG-29 Implement the plan to restore the historic flood plain on Hoppaw Creek. POTENTIAL LEAD: CDFG 

OTHERS: Landowners, Caltran

56
ORLEANS HSA 

3 D KR-OR-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon that provide cool water and which improve mainstem Klamath River water quality and which provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Include improved land management to reduce impacts to riparian corridors, 

reduce sediment loads, and protect water resources; 

b. Request SWRCB to review existing water appropriations for compliance; c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners 

3 D KR-OR-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, but which provide cool water and which improve mainstem Klamath River water quality and/or provide thermal refugia 

for coho salmon, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Landowners 

3 D KR-OR-03 Continue activities that maintain connectivity (flow) between mainstem habitat 

and tributary habitat in Slate and Red Cap creeks. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CD

3 C KR-OR-04 Develop a plan to protect and enhance spawning and rearing habitats in Boise 

and Camp creeks. 

POTENTIAL LEAD: USFS 

3 C KR-OR-05 Implement the plan to protect and enhance spawning and rearing habitats in 

Boise and Camp creeks. 

POTENTIAL LEAD: USFS 

3 E KR-OR-06 Develop a plan to protect and enhance Bluff and Red Cap creek watersheds, 

which are classified as Key Watersheds in the Northwest Forest Plan, and are refugia for coho salmon. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, 

LEAD: CDFG 

3 D KR-OR-07 Implement the plan to protect and enhance Bluff and Red Cap creek watersheds POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CDFG 

3 C KR-OR-08 Reestablish natural fire regimes consistent with the Northwest Forest Plan to 

reduce the risk and impact of large, severe fire on coho salmon. 

POTENTIAL LEAD: USFS, BLM 

OTHERS: CDF, Landowners 

57
3 C KR-OR-09 Support efforts to provide livestock exclusion fencing where feasible and 

appropriate, while providing off-site watering. 

POTENTIAL LEAD: USFS OTHERS: Landowners 

3 D KR-OR-10 Reduce sediment input from upslope sources, including measures to: 

a. Decommission skid trails and unmaintained roads where possible; b. Upgrade roads and maintenance practices, c. Stabilize slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams, and 

d. Minimize alteration of natural hillslope drainage patterns. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CD

Landowners 

UKONOM HSA 3 D KR-UK-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, but which provide cool water, improve mainstem Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Include improved land management to reduce impacts to riparian corridors, 

reduce sediment loads, and protect water resources; 

b. Request that SWRCB review existing water appropriations for compliance; c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

Potential Lead: USFS Others: NOAA Fisheries, RWCDFG, CDF, Landowners 

3 D KR-UK-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, but which provide cool water, improve mainstem Klamath water River quality, and provide thermal refugia for coho salmon, particularly during warm summer months. 

Potential Lead: USFS Others: NOAA Fisheries, RWCDFG, CDF, Landowners 

58
3 D KR-UK-03 Reduce sediment input from upslope sources, including measures to: 

a. Decommission skid trails and unmaintained roads where possible; b. Upgrade roads and maintenance practices; c. Stabilize slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams; and 

d. Minimize alteration of natural hillslope drainage patterns. 

Potential Lead: USFS Others: NOAA Fisheries, CDLandowners 

3 D KR-UK-04 Develop a plan to restore and maintain tributary and mainstem habitat 

connectivity where low flow or sediment aggradation is restricting coho salmon 

passage. 

POTENTIAL LEAD: CDFG 

OTHERS: Caltrans, USFS, Kar

USFS 

3 D KR-UK-05 Implement the plan to restore and maintain tributary and mainstem habitat 

connectivity where low flow or sediment aggradation is restricting coho salmon passage. 

POTENTIAL LEAD: CDFG OTHERS: Caltrans, USFS, KarUSFS 

3 D KR-UK-06 Implement highest priority barrier repairs as identified in the Caltrans, USFS, 

and the Karuk Tribe inventories, specifically the identified culverts on Highway 96 at Stanshaw, Sandy Bar, and Coon. 

POTENTIAL LEAD: CDFG 

OTHERS: Caltrans, USFS, Kar

USFS 

3 D KR-UK-07 Develop a plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems, including measures to: a. Conduct riparian revegetation and stream bank restoration; b. Where feasible, relocate roads out of riparian areas and off of unstable land 

features (e.g., active landslides, granitic terrain, toe zones, wet-seepy areas); 

c. Increase the number of conifers and deciduous trees, where appropriate, for 

more stable stream banks, stream shading, and eventual recruitment of LWD; and 

d. Revegetate floodplain areas using native species. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners 

3 D KR-UK-08 Implement the plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Landowners 

59
3 D KR-UK-09 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; b. Management to promote conifer recruitment; c. Planting conifers in riparian zones; and d. Release of conifers by controlling alders, blackberries, and other 

competitors. 

POTENTIAL LEAD: USFS OTHERS: Fisheries, CDFG, CDLandowners 

3 D KR-UK-10 Provide technical support as an incentive to landowners for ongoing efforts of 

restoring LWD and shade to the watershed. 

POTENTIAL LEAD: USFS 

OTHERS: Fisheries, CDFG, CD

Landowners 

3 C KR-UK-11 Reestablish natural fire regimes consistent with the Northwest Forest Plan to 

reduce the risk and impact of large, severe fire on coho salmon. 

POTENTIAL LEAD: USFS, BLM OTHERS: CDF, Landowners 

3 C KR-UK-12 Where necessary, provide riparian protection from livestock through exclusion 

fencing, while establishing off-site watering. 

POTENTIAL LEAD: RCDs 

OTHERS: Landowners 

3 E KR-UK-13 Install screens on diversions to Department-NOAA Fisheries standards and 

provide funding, or other incentives to landowners where necessary to achieve this goal. 

POTENTIAL LEAD: CDFG OTHERS: DWR, NOAA Fishe

3 E KR-UK-14 Increase efficiency of water diversions and delivery systems. POTENTIAL LEAD: SWRCB 

OTHERS: CDFG, DWR 

3 D KR-UK-15 Continue restoration and monitoring of Siskon Mine to prevent further 

degradation of the riparian resource. 

POTENTIAL LEAD: CGS OTHERS: RWQCB, EPA 

3 D KR-UK-16 Request SWRCB to investigate the legality of diversions and use of water on 

Stanshaw Creek. 

POTENTIAL LEAD: CDFG 

OTHERS: SWRCB, Landowne

60
HAPPY CAMP HSA 

4 D KR-HC-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, that provide cool water, improve mainstem Klamath water River quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Improve land management to reduce impacts to riparian corridors, reduce 

sediment loads, and protect water resources; 

b. Request that SWRCB review existing water appropriations for compliance; c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners 

4 D KR-HC-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, that provide cool water, improve mainstem 

Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Landowners 

4 D KR-HC-03 Reduce sediment input from upslope sources, including measures to: 

a. Decommission skid trails and unmaintained roads where possible; b. Upgrade roads and maintenance practices, c. Stabilize slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams, and 

d. Minimize alteration of natural hillslope drainage patterns. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CDLandowners 

4 E KR-HC-04 Develop a plan to improve coho salmon passage at stream and road crossings, 

including measures to: 

a. Replace culverts on both USFS and Caltrans roads with structures allowing 

fish passage (USFS and Karuk Tribe have identified culverts under Highway 

96 at Cade, Portuguese, and Fort Goff creeks as needing treatment); 

b. Prioritize crossings for upgrade to accommodate 100-year storm runoff and 

associated bedload and debris; and 

c. Establish an adequate funding source basin-wide for road maintenance and 

upgrades (possible funding sources are USFS, County and state agencies). 

POTENTIAL LEAD: CDFG 

OTHERS: USFS, Caltrans, Kar

Counties 

61
4 D KC-HC-05 Implement the plan to improve coho salmon passage at stream and road 

crossings. 

POTENTIAL LEAD: CDFG OTHERS: USFS, Caltrans, KarCounties 

4 D KR-HC-06 Develop a plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems, including measures to: 

a. Conduct riparian re-vegetation and stream bank restoration; b. If feasible, relocate roads out of riparian areas and off of unstable land 

features (e.g., active landslides, granitic terrain, toe zones, wet-seepy areas); 

c. Increase the number of conifers and deciduous trees, where appropriate, for 

more stable stream banks, stream shading, and eventual recruitment of LWD; and 

d. Revegetate floodplain areas using native species. 

POTENTIAL LEAD: CDFG 

OTHERS: USFS, Tribes, Lando

4 D KR-HC-07 Implement the plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems. 

POTENTIAL LEAD: CDFG OTHERS: USFS, Tribes, Lando

4 D KR-HC-08 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: 

a. LWD placement; b. Management to promote conifer recruitment; c. Planting conifers in riparian zones; and d. Release of conifers by controlling alders, blackberries, and other 

competitors. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CD

Landowners 

4 C KR-HC-09 Reestablish natural fire regimes consistent with the Northwest Forest Plan to 

reduce the risk and impact of large, severe fires on coho salmon. 

POTENTIAL LEAD: USFS, BLM OTHERS: CDF, Landowners 

4 C KR-HC-10 Where necessary, provide riparian protection from livestock through exclusion 

fencing, while establishing off-site watering. 

POTENTIAL LEAD: USFS 

OTHERS: Landowners 

4 E KR-HC-11 Install screens on diversions to Department-NOAA Fisheries standards and 

provide funding, or other incentives to landowners where necessary to achieve this goal. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, La

4 E KR-HC-12 Increase efficiency of water diversions and delivery systems where feasible and 

appropriate. Provide funding and incentives to landowners where necessary to meet this goal. 

POTENTIAL LEAD: SWRCB 

OTHERS: CDFG, DWR 

62
4 D KR-HC-13 Request the NCRWQCB to continue monitoring Grey Eagle Mine and tailings 

as a follow-up to remediation that has already been done. 

POTENTIAL LEAD: CDFG OTHERS: RWQCB 

D KR-HC-14 Request that EPA Region 9 consider coho salmon when dealing with both 

emergency and remedial actions. 

POTENTIAL LEAD: CDFG 

OTHERS: EPA 

SEIAD VALLEY HSA 4 D KR-SV-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, that provide cool water, improve mainstem Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Improve land management to reduce impacts to riparian corridors, reduce 

sediment loads, and protect water resources; 

b. Request that the SWRCB review existing water appropriations for 

compliance; 

c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners

4 D KR-SV-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, that provide cool water, improve mainstem 

Klamath River water quality, and provide thermal refugia for fish, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Landowners

4 D KR-SV-03 Reduce sediment input from upslope sources by: 

a. Decommissioning unmaintained roads (where possible) and skid trails; b. Upgrade roads and maintenance practices; c. Stabilize slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams; and 

d. Minimize alteration of natural hill slope drainage patterns. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CDLandowners 

63
4 E KR-SV-04 Improve fish passage at stream and road crossings, including measures to: 

a. Replace culverts on both USFS and Caltrans roads with structures allowing 

coho salmon passage; 

b. Treat coho salmon passage problems associated with the USFS roads; c. Prioritize crossings for upgrade to accommodate 100-year storm runoff and 

associated bedload and debris; and 

d. Establish an adequate funding source basin-wide for road maintenance and 

upgrades (possible funding sources are USFS, County and state agencies). 

POTENTIAL LEAD: CDFG 

OTHERS: USFS, Caltrans, 

4 D KR-SV-05 Develop a plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems, including measures to: a. Conduct riparian re-vegetation and stream bank restoration; b. Relocate roads out of riparian areas and off of unstable land features (e.g., 

active landslides, granitic terrain, toe zones, seep areas); 

c. Increase the number of conifers and deciduous trees, where appropriate, for 

more stable stream banks, stream shading, and eventual recruitment of LWD; and 

d. Re-vegetate floodplain areas using native species. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners 

4 D KR-SV-06 Implement the plan to ensure continued yields of high quality water by the 

maintenance and ecological function of tributary riparian systems 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, RW

CDFG, CDF, Landowners 

4 D KR-SV-07 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; b. Management to promote conifer recruitment; c. Planting conifers in riparian zones; and d. Release of conifers by controlling alders, blackberries, and other 

competitors. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CDLandowners 

4 D KR-SV-08 Provide technical support as an incentive to landowners for ongoing efforts of 

restoring LWD and shade to the watershed. 

POTENTIAL LEAD: USFS, NOA

CDFG 

OTHERS: CDF, Landowners 

4 C KR-SV-09 Manage roadless areas to be consistent with land use allocations under the 

Northwest Forest Plan to reduce the risk of large, severe fires by re-establishing the natural fire regimes. 

POTENTIAL LEAD: USFS 

64
4 C KR-SV-10 Where necessary, provide riparian protection from livestock through exclusion 

fencing, while establishing off-site watering. 

POTENTIAL LEAD: USFS 

OTHERS: Landowners 

4 E KR-SV-11 Install screens on diversions to Department-NOAA Fisheries standards and 

provide funding, or other incentives to landowners where necessary to achieve this goal. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, La

4 E KR-SV-12 Study the likely benefits to instream flow of increasing the efficiency of water 

diversions and delivery systems where feasible and appropriate. Provide funding 

and incentives to landowners where necessary to meet actions that are given a high priority. 

POTENTIAL LEAD: SWRCB 

OTHERS: CDFG, DWR 

4 E KR-SV-13 Identify illegal water diverters and request that the SWRCB take appropriate 

action. 

POTENTIAL LEAD: CDFG OTHERS: SWRCB, Landowne

4 E KR-SV-14 Request that the SWRCB review and/or modify water use based on the needs of 

coho salmon and authorized diverters. 

POTENTIAL LEAD: CDFG 

OTHERS: SWRCB, Landowne

4 D KR-SV-15 Look for opportunities to acquire water rights for instream flow from willing 

participants who possess valid water rights. 

POTENTIAL LEAD: CDFG OTHERS: Landowners, RCDs 

4 D KR-SV-16 Assess potential coho salmon passage problem associated with private water 

diversion at the mouth of Middle Creek (tributary to Horse Creek). 

POTENTIAL LEAD: CDFG 

OTHERS: Landowners 

4 D KR-SV-17 If necessary, design and implement a remediation project for coho salmon fish 

passage at the mouth of Middle Creek. 

POTENTIAL LEAD: CDFG OTHERS: Landowners 

BEAVER CREEK HSA 4 C KR-BC-01 Reestablish natural fire regimes consistent with the Northwest Forest Plan to 

reduce the risk and impact of a large, severe fire on coho salmon. 

POTENTIAL LEAD: USFS OTHERS: BLM, CDF 

4 C KR-BC-02 Encourage landowners to manage fuels to prevent large, severe fires and to 

evaluate the application of the Watershed Evaluation Mitigation Addendum. 

POTENTIAL LEAD: USFS 

OTHERS: CDF, County, Lando

CDFG 

4 D KR-BC-03 Assess fine sediment production and delivery from the USFS road adjacent to 

the West Fork of Beaver Creek. 

POTENTIAL LEAD: USFS OTHERS: 

4 D KR-BC-04 Implement appropriate remediation for the sediment from the USFS road 

adjacent to the West Fork of Beaver Creek. 

POTENTIAL LEAD: USFS 

65
4 C KR-BC-05 Hydrologically disconnect the USFS Beaver Creek Road north of West Beaver 

Creek. 

POTENTIAL LEAD: USFS OTHERS: 

4 D KR-BC-06 Support actions to reduce sediment from upslope sources such as: 

a. Decommission roads and skid trails; b. Upgrade roads and maintenance practices; c. Ensure adequate coho salmon migration is provided for at stream/road 

crossings; 

d. Stabilize slopes to minimize or prevent erosion and to minimize future risk 

of eroded material entering streams; 

e. Minimize alteration of natural hillslope drainage patterns; and f. Encourage the relocation of roads out of riparian areas and off of unstable 

land features (e.g., active landslides, granitic terrain, toe zones, seep areas). 

POTENTIAL LEAD: USFS, NOA

OTHERS: CDFG, CDF, Lando

4 D KR-BC-07 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, that provide cool water, improve mainstem Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Improve land management to reduce impacts to riparian corridors, reduce 

sediment loads, and protect water resources; 

b. Request that the SWRCB review existing water appropriations for 

compliance; 

c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWCDFG, CDF, Landowners

4 D KR-BC-08 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, that provide cool water, improve mainstem 

Klamath River water quality, and provide thermal refugia for fish, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, 

RWQCB,CDFG, CDF, Lando

66
4 E KR-BC-09 Improve coho salmon passage at stream and road crossings, including measures 

to: a. Replace culverts on both USFS and Caltrans roads with structures allowing 

coho salmon passage; 

b. Treat coho salmon passage problems associated with the USFS roads; c. Prioritize crossings for upgrade to accommodate 100-year storm runoff and 

associated bedload and debris; and 

d. Encourage the USFS and County and state agencies to provide adequate 

budgets basin-wide for road maintenance and upgrades. 

POTENTIAL LEAD: CDFG OTHERS: USFS, Caltrans, 

4 D KR-BC-10 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; b. Management to promote conifer recruitment; and c. Improvement of existing riparian zones through plantings, release of 

conifers, and control of alders, blackberries, and other competitors. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CD

Landowners 

4 D KR-BC-11 Provide technical support as an incentive to landowners for ongoing efforts of 

restoring LWD and shade to the watershed. 

POTENTIAL LEAD: USFS, NOACDFG OTHERS: CDF, Landowners 

4 C KR-BC-12 Where necessary, provide riparian protection from livestock while providing 

off-site watering. 

POTENTIAL LEAD: USFS 

OTHERS: Landowners 

SALMON RIVER HA 

D SA-HA-01 Reduce sediment and provide coho salmon passage for all life history stages 

where roads affect streams inhabited by coho salmon. 

POTENTIAL LEAD: Road ManaFisheries Barrier Work Group USFS OTHERS: Landowners, County

D SA-HA-02 Reduce sediment by accelerating the Northwest Forest Plan road assessment 

schedule. 

POTENTIAL LEAD: USFS 

OTHERS: County, CDFG 

D SA-HA-03 Reduce sediment where roads affect streams inhabited by coho salmon by 

completing the road sediment inventory assessment of County roads. 

POTENTIAL LEAD: County OTHERS: USFS, CDFG 

67
D SA-HA-04 Reduce sediment where roads affect streams inhabited by coho salmon by 

implementing the treatment of the road sediment inventory of county roads. 

POTENTIAL LEAD: County 

OTHERS: USFS, CDFG 

D SA-HA-05 Provide coho salmon passage to all life history stages where roads affect streams 

inhabited by coho salmon implement the recommendations for the completed assessment of barriers. 

POTENTIAL LEAD: County, RoManagement and Fisheries BaGroup Task Force OTHERS: USFS, CDFG, Land

E SA-HA-06 Foster the multi-agency task force to identify and prioritize barriers to fish 

passage, and implement corrective treatments.l. This task force would include at a minimum, representatives from the Salmon River Restoration Council, Karuk Tribe, USFS, NOAA Fisheries, USFWS, and the Department. 

POTENTIAL LEAD: Road Mana

Fisheries Barrier Work Group (Salmon River Restoration CoTribe, USFS., NOAA FisherieCounty, and CDFG) 

D SA-HA-07 Educate landowners, restoration specialist, and watershed groups to reduce the 

impacts of private roads on coho salmon. 

POTENTIAL LEAD: CDFG, RoaManagement and Fisheries BaGroup Task Force OTHERS: Salmon River RestoCouncil, Landowners 

C SA-HA-08 Encourage collaborative efforts among agencies and stakeholders to control or 

remove invasive exotics using integrated pest management techniques, emphasizing manual treatments. 

POTENTIAL LEAD: CDFG, Sal

Noxious Weed Management A

OTHERS : Landowners, acade

plant advocacy 

C SA-HA-09 Reduce the risk of large, severe fires through fuels management around 

residential structures, homes, and fire escape routes. Implement Salmon River Fire Safe Council recommendations promoting the reduction of fuel near residences to reduce human-caused fires spreading into the forest and causing harm to coho salmon habitat. 

POTENTIAL LEAD: Salmon Riv

Council 

OTHERS: County, CDFG, CDF

C SA-HA-10 Reestablish fire regimes consistent with Northwest Forest Plan objectives to 

reduce the risk and impact of large, severe fire on coho salmon. 

POTENTIAL LEAD: CDFG, NOSalmon River Fire Safe CounOTHERS: USFS 

C SA-HA-11 If necessary, integrate coho salmon conservation into the Northwest Forest Plan 

regarding fire suppression and overall fuel management plan. 

POTENTIAL LEAD: USFS 

68
D SA-HA-12 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade, primarily in tributaries and key refugia areas, through: a. LWD placement; b. Management to promote conifer recruitment; c. Improvement of existing riparian zones through plantings, release of 

conifers, and control of alders, blackberries, and other competitors; and 

d. Incentives to landowners, such as technical support. 

POTENTIAL LEAD: USFS, CDFOTHERS: NOAA Fisheries, WGroups, County, USFWS, KaSalmon River Reststoration CLandowners 

C SA-HA-13 Develop a plan to prioritize and remediate mine tailings. POTENTIAL LEAD: CDFG, CG

Coast RWQCB, USFS 

OTHERS: NOAA Fisheries, K

USFWS, Salmon River RestoCouncil, Landowners 

C SA-HA-14 Implement the plan to remediate prioritized mine tailings, focusing on tributaries 

and key area of the Salmon River. 

POTENTIAL LEAD: CGS, USFSCoast RWQCB OTHERS: NOAA Fisheries, CDUSFWS, Karuk Tribe, SalmoRestoration Council 

LOWER SALMON HSA 3 D SR-LS-01 Restore and maintain habitat connectivity between the Salmon River and 

Nordheimer Creek where low flow or sediment aggradation has been known to restrict coho salmon passage. 

POTENTIAL LEAD: USFS, WatOTHERS: Karok 

SR-LS-02 Support ongoing maintenance and operations for the Nordheimer Creek Fish 

Ladder

POTENTIAL LEAD: OTHERS: 

69
SAWYERS BAR HSA 

3 D SR-SB-01 Reduce current and future sediment inputs to Specimen, North Russian, and 

South Russian creeks: a. Do road upgrade/improvement/maintenance/storm proofing (out sloping 

roads, reducing hydrologic connectivity); 

b. Provide slope stabilization where feasible; c. Reduce or avoid alteration of natural hill slope drainage patterns: and d. Upgrade stream/road crossings and ensure coho salmon passage. 

POTENTIAL LEAD: USFS, WatOTHERS: Karok 

3 D SR-SB-02 Conduct riparian re-vegetation and stream bank stabilization along entire North 

Fork: a. Control vegetation removal in the streamside zone; b. Increase the number of conifers and deciduous trees to provide stable stream 

shading and which will eventually become a source for LWD; and 

c. Re-vegetate floodplain areas using native species. 

POTENTIAL LEAD: USFS, Wat

OTHERS: Karok 

SHASTA VALLEY AND SCOTT RIVER HSA (See Chapter 10 for recommendations for agricultural land and water use.) 4 C SS-HA-01 Reduce the risk of large, severe fires (especially in the Scott) by implementing 

the Fire Safe Council’s recommendations promoting the reduction of fuel near residences to reduce human-caused fires spreading into the forest and causing harm to coho salmon habitat. 

POTENTIAL LEAD: CDF, USFS OTHERS: County, Landowner

4 D SS-HA-02 Reduce human-caused sediment input from upslope sources identified through 

public and private inventories. 

POTENTIAL LEAD: USFS, CDF

Landowners 

OTHERS: Caltrans, County, CD

4 D SS-HA-03 Prioritize and implement remediation activities for human-caused sediment, 

which would include slope stabilization, minimizing sediment production, and eliminating coho salmon passage barriers. 

POTENTIAL LEAD: USFS, CDFLandowners OTHERS: Caltrans, County, CD

4 D SS-HA-04 Encourage federal, state, and county agencies and private landowners to reduce 

impacts to coho salmon habitat from public and private road systems. 

POTENTIAL LEAD: CDFG 

OTHERS: USFS, CDF, Caltran

Landowners 

70
4 D SS-HA-05 Continue road and/or watershed assessments to identify and prioritize sources 

and risks of road-related sediment delivery to watercourses. 

POTENTIAL LEAD: Counties, UOTHERS: CDFG, CDF, CaltraLandowners 

4 D SS-HA-06 Reduce road densities where necessary and appropriate. POTENTIAL LEAD: Counties, U

OTHERS: CDFG, CDF, Caltra

Landowners 

4 D SS-HA-07 Decrease potential for stream flow to become diverted at road crossings during 

high flow events, resulting in flow along the road that returns to the channel at undesirable locations. 

POTENTIAL LEAD: Counties, UOTHERS: CDFG, CDF, CaltraLandowners 

4 D SS-HA-08 Stabilize slopes along roadways to minimize or prevent erosion and to minimize 

future risk of eroded material entering streams. 

POTENTIAL LEAD: Counties, U

OTHERS: CDFG, CDF, Caltra

Landowners 

4 D SS-HA-09 Minimize alteration of natural hill slope drainage patterns to decrease erosion 

and sediment input into the streams. 

POTENTIAL LEAD: Counties, UOTHERS: CDFG, CDF, CaltraLandowners 

4 D SS-HA-10 Encourage funding authorities to allocate adequate budgets to federal, state, and 

local agencies and private landowners for road maintenance activities, capital project activities, and dedicated funding to pay for coho salmon passage projects. 

POTENTIAL LEAD: CDFG, Cou

NOAA Fisheries 

OTHERS: CDF, Caltrans, Land

4 E SS-HA-11 Encourage funding authorities to allocate adequate resources to prioritize and 

upgrade crossings to provide coho salmon passage within the range of coho salmon to pass 100-year flows and the expected debris loads (e.g., LWD that might be mobilized). 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, USLandowners 

4 E SS-HA-12 Identify barriers to passage and prioritize them for removal, through 

collaborative efforts with other agencies. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries, US

CDF, County, Landowners 

4 C SS-HA-13 Design a reclamation plan to remediate effects of historical mining (i.e., tailings 

near Callahan) with the goal of enhancing the production and survival of coho salmon. 

POTENTIAL LEAD: CDFG OTHERS: NOAA Fisheries, CoLandowners 

71
4 C SS-HA-14 Implement the reclamation plan that remedies effects of historical mining (i.e., 

tailings near Callahan) with the goal of enhancing the production and survival of coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries, Co

Landowners 

4 C SS-HA-15 Identify locations, costs, and restoration potential of intensively mined areas. POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries, CoLandowners 

4 D SS-HA-16 Improve water quality by reducing or minimizing both domestic and municipal 

sources of nutrient input (i.e., sewage treatment plant discharge and storm drain 

runoff). Support efforts by cities and rural communities to complete system upgrades to achieve CWA compliance. 

POTENTIAL LEAD: RWQCB 

OTHERS: County, Landowner

4 D SS-HA-17 Minimize impacts of cattle grazing on watercourses though exclusion fencing as 

necessary and appropriate (i.e., providing off-site watering, preventing overgrazing, etc.). 

POTENTIAL LEAD: RCDs OTHERS: Landowners, CDFGFisheries 

4 D SS-HA-18 Support cooperative state and local efforts to redirect Big Mill Creek into its 

historic channel under State Route 3, thereby restoring adult and juvenile coho salmon access to approximately 1.25 miles of quality spawning and rearing habitat. 

POTENTIAL LEAD: CDFG 

OTHERS: Caltrans, Landowne

4 E SS-HA-19 Assess the potential benefits and technical feasibility of increasing stream flows 

in the Scott River for fish and wildlife within the Klamath National Forest. 

POTENTIAL LEAD: CDFG OTHERS: SWRCB, DWR, Lan

4 D SS-HA-20 Request the USBR to study the potential benefits of adjusting Iron Gate flows to 

better meet the needs of adult and juvenile life stages to enhance Scott/Shasta coho salmon production, consistent with the flow needs of the Klamath and Trinity rivers. 

POTENTIAL LEAD: CDFG 

OTHERS: USBR 

4 D SS-HA-21 Complete the comprehensive, peer-reviewed watershed restoration plans for the 

Shasta and Scott rivers that include identification and prioritization of all restorative needs in each basin. When restoration funds are limited, implementation should occur on the highest priority issues most likely to effectively address coho salmon needs within each basin. 

POTENTIAL LEAD: RCDs, WatCouncil OTHERS: CDFG, NOAA Fish

4 C SS-HA-22 Financially support ongoing watershed planning. POTENTIAL LEAD: RCDs, Wat

Council 

OTHERS: CDFG, NOAA Fish

72
4 E SS-HA-23 Preserve water quality, quantity and coho salmon habitat in the Big Springs area 

in the Shasta River by possibly using incentive-based alternatives with willing participants. 

POTENTIAL LEAD: CDFG OTHERS: Landowners, RCD 

4 E SS-HA-24 Maintain and re-vegetate, where appropriate, riparian trees in headwaters and 

along creeks that provide shade habitat essential for coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: Landowners, RCD 

4 D SS-HA-25 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; and b. Management to promote conifer recruitment. 

POTENTIAL LEAD: CDFG OTHERS: Landowners, RCD 

HORNBROOK HSA 4 D KR-HB-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, that provide cool water, improve mainstem Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Improve land management to reduce impacts to riparian corridors, reduce 

sediment loads, and protect water resources; 

b. Request that the SWRCB review existing water appropriations for 

compliance; 

c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWQCB,CDFG, CDF, Lando

4 D KR-HB-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, that provide cool water, improve mainstem 

Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, 

RWQCB,CDFG, CDF, Lando

73
4 E KR-HB-03 Improve coho salmon passage at stream and road crossings, including measures 

to: a. Replace culverts on both the USFS and Caltrans roads with structures 

allowing coho salmon passage; 

b. Treat coho salmon passage problems associated with the USFS roads; c. Prioritize crossings for upgrade to accommodate 100-year storm runoff and 

associated bedload and debris; and 

d. Encourage the USFS, County and state agencies to provide adequate budgets 

basin-wide for road maintenance and upgrades. 

POTENTIAL LEAD: CDFG OTHERS: USFS, Caltrans 

4 D KR-HB-04 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: a. LWD placement; b. Management to promote conifer recruitment; c. Improvement of existing riparian zones through plantings, release of 

conifers, and control of alders, blackberries, and other competitors; and 

d. Incentives to landowners, such as technical support. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CD

Landowners 

4 E KR-HB-05 Study the likely benefits to instream flow of increasing the efficiency of water 

diversions and delivery systems where feasible and appropriate. Provide funding and incentives to landowners where necessary to meet actions that are given a high priority. 

POTENTIAL LEAD: SWRCB OTHERS: CDFG, DWR 

4 E KR-HB-06 Identify water diverters; request that the SWRCB review and/or modify water 

use based on the needs of coho salmon and authorized diverters. 

POTENTIAL LEAD: CDFG 

OTHERS: SWRCB, Landowne

4 D KR-HB-07 Look for opportunities to acquire water rights for instream flow from willing 

participants who possess valid water rights. 

POTENTIAL LEAD: CDFG OTHERS: Landowners, RCDs 

74
IRON GATE HSA 

4 D KR-IG-01 Develop a plan to protect and restore tributaries, even those that do not support 

populations of coho salmon, that provide cool water, improve mainstem Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. The plan should: a. Improve land management to reduce impacts to riparian corridors, reduce 

sediment loads, and protect water resources; 

b. Request that the SWRCB review existing water appropriations for 

compliance; 

c. Petition the SWRCB to designate streams with critical summer flows as fully 

appropriated streams during the appropriate period; and 

d. Provide measures that reduce hydrologic connectivity between streams and 

roads where feasible. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, RWQCB,CDFG, CDF, Lando

4 D KR-IG-02 Implement the plan to protect and restore tributaries, even those that do not 

support populations of coho salmon, that provide cool water, improve mainstem 

Klamath River water quality, and provide thermal refugia for coho salmon, particularly during warm summer months. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, 

RWQCB,CDFG, CDF, Lando

4 E KR-IG-03 Improve coho salmon passage at stream and road crossings, including measures 

to: a. Replace culverts on both USFS and Caltrans roads with structures allowing 

coho salmon passage; 

b. Treat coho salmon passage problems associated with the USFS roads; c. Prioritize crossings for upgrade to accommodate 100-year storm runoff and 

associated bedload and debris; and 

d. Encourage the USFS, County and state agencies to provide adequate budgets 

basin-wide for road maintenance and upgrades. 

POTENTIAL LEAD: USFS, CaltOTHERS: CDFG, 

4 D KR-IG-04 Supplement on-going efforts to provide short-term and long-term benefits to 

coho salmon by restoring LWD and shade through: 

a. LWD placement; b. Management to promote conifer recruitment; c. Improvement of existing riparian zones through plantings, release of 

conifers, and control of alders, blackberries, and other competitors; and 

d. Incentives to landowners, such as technical support. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, CD

Landowners 

75
4 E KR-IG-05 Study the likely benefits to instream flow of increasing the efficiency of water 

diversions and delivery systems where feasible and appropriate. Provide funding and incentives to landowners where necessary to meet actions that are given a high priority. 

POTENTIAL LEAD: SWRCB OTHERS: CDFG, DWR 

4 E KR-IG-06 Identify water diverters and request that the SWRCB review and/or modify 

water use based on the needs of coho salmon and authorized diverters. 

POTENTIAL LEAD: CDFG 

OTHERS: SWRCB, Landowne

4 D KR-IG-07 Look for opportunities to acquire water rights for instream flow from willing 

participants who possess valid water rights. 

POTENTIAL LEAD: CDFG OTHERS: Landowners, RCDs 

TRINITY RIVER HU 

E TR-HU-01 Implement the Trinity River Record of Decision (ROD), which would provide: 

a. Variable annual instream flows for the Trinity River from the Trinity River 

Dam (TRD) based on forecasted hydrology for the Trinity River Basin as of April 1st of each year, ranging from 369,000 acre-feet in critically dry years to 815,000 af in extremely wet years; 

b. Physical channel rehabilitation, including the removal of riparian berms and 

the establishment of side-channel habitat; 

c. Sediment management, including the supplementation of spawning gravels 

below the TRD and reduction in fine sediments which degrade coho salmon habitats; 

d. Watershed restoration efforts, addressing negative impacts which have 

resulted from land use practices in the Basin; and 

e. Infrastructure improvements or modifications, including rebuilding or 

fortifying bridges and addressing other structures affected by the peak instream flows provided by the ROD. 

POTENTIAL LEAD: USBR OTHERS: USFS, NOAA FisheCDFG 

C TR-HU-02 Recommend to the NCRWQCB that the TMDL process consider alterations in 

the sediment load allocations and targets due to implementation of the ROD. 

POTENTIAL LEAD: CDFG 

OTHERS: RWQCB 

D TR-HU-03 Implement the Trinity River TMDL instream flushing flows without affecting 

ROD allocations. 

POTENTIAL LEAD: CDFG, USOTHERS:, RWQCB 

D TR-HU-04 Establish TMDL implementation plans for the mainstem and South Fork using 

the upslope indicators and targets established in the Main Stem Load Allocation.

POTENTIAL LEAD: CDFG, RW

OTHERS: USBR 

E TR-HU-05 Develop a County grading ordinance based on exemption, certification, and 

permitting criteria. 

POTENTIAL LEAD: County OTHERS: CDFG 

76
C TR-HU-06 Implement county grading ordinance based on exemption, certification, and 

permitting criteria. 

POTENTIAL LEAD: County 

OTHERS: CDFG 

C TR-HU-07 Implement the Five Counties Water Quality and Stream Habitat Protection 

Manual for County Road Maintenance in Northwestern California Watersheds. 

POTENTIAL LEAD: Trinity CouOTHERS: CDFG 

D TR-HU-08 Support continued state and federal funding for the implementation of sediment 

reduction programs for private lands and the implementation and funding of treatment of sediment source sites on County roads using the prioritization of the Direct Inventory of Roads and Their Treatment (DIRT). 

POTENTIAL LEAD: County 

OTHERS: Landowners, CDFG 

C TR-HU-09 Establish incentives and standards for private riparian and wetland areas 

protection based on flexible subdivision design; road, curb and gutter requirements; minimum lot size and density; clustering and other techniques. 

POTENTIAL LEAD: CDFG OTHERS: County 

C TR-HU-10 Establish riparian setbacks for grading activities on private lands, based on 

Department 1994 recommendations to District I counties. 

POTENTIAL LEAD: CDFG 

OTHERS: County 

D TR-HU-11 Evaluate the impacts of non-native fish species on coho salmon. POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries 

D TR-HU-12 Develop management guidelines to reduce impacts from non-native fish species. POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries 

C TR-HU-13 Develop or amend existing County Conservation, Open Space and Land Use 

Elements and Community Plans to focus development away from riparian habitats, wetland habitats, or steep slopes. Consider all species habitats, wildland-urban fire hazard, and other land uses factors in making allocations. 

POTENTIAL LEAD: CDFG OTHERS: Trinity County 

C TR-HU-14 Analyze the feasibility and appropriateness of site-specific 2084 authorization 

for sport fishing for hatchery coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: NOAA Fisheries 

DOUGLAS CITY HSA 5 E TR-DC-01 Investigate all water diversions on Reading Creek, Indian Creek, and Browns 

Creek. 

POTENTIAL LEAD: CDFG 

OTHERS: SWRCB, NOAA Fis

5 E TR-DC-02 Restore coho salmon passage and instillation of screens to Department-NOAA 

Fisheries standards. Provide incentives to landowners when necessary to reach this goal. 

POTENTIAL LEAD: CDFG OTHERS: SWRCB, NOAA Fis

77
5 D TR-DC-03 Increase riparian function in lower Reading, Indian, Browns creeks with 

conservation easements or landowner incentives that reduce agricultural and grazing impacts. 

POTENTIAL LEAD: CDFG 

OTHERS: RCD, Landowners 

5 D TR-DC-04 Implement sediment reduction plans consistent with County plans and policies. POTENTIAL LEAD: CDFG 

OTHERS: RCD, County, Land

GROUSE CREEK HSA 3 D TR-GC-01 Continue implementation of habitat restoration, including measures to stabilize 

upslope areas, enhance riparian zones, storm proof, stabilize, and/or decommission roads, and replace culverts. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CoCDFG, CDF, Landowners 

HYAPOM HSA 2 D TR-HY-01 Develop a management plan for Big Slide to reduce human contributions to 

mobilization of sediments, including evaluating relocation of the county road that crosses Big Slide. 

POTENTIAL LEAD: USFS OTHERS: CDFG, County 

2 D TR-HY-01 Implement the management plan for Big Slide to reduce human contributions to 

mobilization of sediments, including evaluating relocation of the county road 

that crosses Big Slide. 

POTENTIAL LEAD: USFS, Cou

OTHERS: CDFG 

2 C TR-HY-02 Manage forest stands to reduce their susceptibility to large, severe fires. Where 

appropriate, this should include actions to accelerate the growth of conifers for LWD recruitment, develop mature shade canopy in the riparian zone, and to provide for other multiple use goals. 

POTENTIAL LEAD: CDFG OTHERS: USFS 

2 D TR-HY-03 Continued implementation of habitat restoration, including measures to stabilize 

upslope areas, enhance riparian zones, storm proof, stabilize, and/or decommission roads, and replace culverts. 

POTENTIAL LEAD: USFS 

OTHERS: NOAA Fisheries, Co

CDFG, CDF, Landowners 

HAYFORK HSA 2 E TR-HA-01 Establish agricultural/residential water conservation programs using incentive 

programs if necessary. 

POTENTIAL LEAD: CDFG OTHERS: SWRCB, Landowne

78
2 D TR-HA-02 Amend Trinity County’s Critical Water Resources Overlay zone to address new 

riparian water rights developed as a result from parcel subdivision. The amendment should include expanding the overlay zoning to additional watersheds where summer surface flows are limiting factors for residents and 

coho salmon. 

POTENTIAL LEAD: CDFG 

OTHERS: County 

2 C TR-HA-03 Continue implementation of riparian improvements through restoration 

activities, land use planning, and conservation easements. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CDPrivate Landowners 

2 D TR-HA-04 Support efforts to provide livestock exclusion fencing where feasible and 

appropriate, while providing off-site watering. 

POTENTIAL LEAD: Landowner

OTHERS: NRCS 

2 D TR-HA-05 Continue to implement habitat restoration, including measures to stabilize 

upslope areas, enhance riparian zones, storm proof, stabilize, and/or decommission roads, and replace culverts. 

POTENTIAL LEAD: USFS OTHERS: NOAA Fisheries, CoCDFG, CDF, andowners 

79


U.S. Department of Commerce

National Oceanic and Atmospheric Administration

National Marine Fisheries Service

Southwest Region