Cle Elum Bull Trout Population

Overview

The upper Cle Elum River originates in the Alpine Lakes Wilderness and is the primary tributary to the reservoir, entering at its extreme northern end. As mentioned above, the river flows for about 19 miles from the outlet of Hyas Lake (Figure X - MAP), with less than a mile of potential habitat in the headwater reach above the lake. About a mile below Hyas Lake, the upper Cle Elum River leaves the wilderness and enters lands owned and managed by the Forest Service. Approximately one mile further downstream, it enters a low gradient valley where it spreads out over a marshy floodplain (Tucquala Lake) for a distance of about 2.75 miles before the channel once again is confined. Three miles above Cle Elum Reservoir Lake the Cooper River enters the upper Cle Elum River, while the Waptus River comes in 2.5 miles further upstream. Several smaller tributaries enter the upper Cle Elum River along its course; the largest of these are Fortune and Boulder creeks.

Population Information

Population Distribution and Life History

Both adult and juvenile bull trout have been found in the upper Cle Elum River (see Population Monitoring section below) but not a single confirmed bull trout redd has ever been documented in the river or any of its tributaries. Redd surveys have been sporadic and incomplete (a detailed description of the survey efforts is presented in Population Monitoring section below). It is probable that adfluvial bull trout were present in Cle Elum Reservoir Lake following construction of the dam, however confirmation of this has been elusive. The National Marine Fisheries Service (NMFS) reportedly captured 17 bull trout in floating Merwin traps set in the lake during a 1990-91 Cle Elum Reservoir Lake sockeye restoration feasibility study (Pasley 1993). Some believe that these fish may have been misidentified lake trout, which are relatively abundant (Eric Anderson, WDFW, pers comm).

Since that time no attempts have been made to capture bull trout in the lake and no anglers have reported encountering them (Eric Anderson, WDFW, pers comm). In 1996, biologists from Central Washington University observed several adult bull trout during a snorkel survey below Salmon la Sac bridge (Craig 1996). Due to their size (reported as “large”), the observers speculated that they might be migrating adfluvial fish (Paul James, CWU, pers comm). In 2002, two adult bull trout were observed by USFWS snorkelers just below the potential barrier mentioned above (Mallas 2003), however these fish were not of the size characteristic of adfluvial adults. In summary, it is uncertain if a viable adfluvial bull trout population still inhabits Cle Elum Reservoir Lake; it is also unknown if a resident component exists in the upper Cle Elum River, although that is possible. Further investigation is warranted.

Natural Barriers limiting distribution

A series of steep cascades is present about ten miles upstream of the lake (locally known as China Falls). These present a potential barrier to fish migrating upstream.

Population Genetics

No genetic samples have been taken from this population to date. Connectivity and thus the potential for genetic exchange with downstream populations in the Yakima River fluvial system was eliminated by the construction of Cle Elum Dam in 1933.

Population Monitoring

Prior to the 1990-91, NMFS study mentioned above, Cle Elum Reservoir Lake was sampled with gillnets by WDFW in 1978-79. Among other species captured was lake trout. No bull trout were included in the catch (Mongillo and Faulconer 1980). Although not targeting bull trout, none were collected in gillnets set by WDFW in a mid-1990s assessment of the pygmy whitefish population in the lake (Eric Anderson, WDFW, pers comm).

The upper Cle Elum River has received considerable attention over the last two decades by biologists conducting day and night snorkel surveys and electrofishing surveys. In 1992, the Forest Service conducted night snorkel surveys at several locations throughout the Cle Elum drainage and found no bull trout (USFS 1992). In 1996, the Forest Service conducted stream surveys, which appear to have employed electrofishing as the primary method, finding mostly rainbow and brook trout but no bull trout (USFS 1996). As mentioned above, biologists from Central Washington University observed two adult bull trout in the upper Cle Elum River in the fall of 1996 (Craig 1996). WDFW biologists snorkeled the upper Cle Elum River in September 1997 and observed rainbow trout and brook trout (Anderson 2001).

In the most concentrated effort to date, in 2002 the USFWS surveyed 19 randomly selected sampling units using the presence/absence protocols established by Peterson et al. (Peterson et al. 2002). Fourteen additional opportunistic sampling units were also snorkeled and limited hook-and-line sampling was conducted in Hyas and Tucquala lakes. In all 4.9 miles of the river was snorkeled between the Waptus River confluence (~RM 5.5) and Hyas Lake (~RM 19). Twenty-four juvenile (<150 mm) bull trout observations were documented although it was acknowledged that some might have been brook trout (or hybrids). Juvenile brook trout, often difficult to differentiate from bull trout while snorkeling, were abundant and no genetic samples were obtained to confirm field identifications. Two larger bull trout (>220 mm) were observed and identified with certainty (Mallas 2003). Survey crews coordinated by the Forest Service in the fall of 2008 revisited the area where the juvenile observations were made. Working at night, snorkelers surveyed approximately two miles of the river. No bull trout were found, although brook trout and introduced coho salmon juveniles were abundant (Reiss 2008).

Fortune Creek, which enters the river at about RM 12, has also been the focus of fish surveys. The Forest Service employed various methods in 1991 and reported the presence of rainbow and brook trout only. In 2000, the Forest Service snorkeled a portion of the creek and reported the presence of three bull trout (life stage unavailable but assumed juvenile). They also observed brook and rainbow trout. Returning in the fall of 2008, snorkelers working at night surveyed about 0.5 miles of Fortune Creek and did not observe any bull trout (Reiss 2008). About 0.7 miles of the creek was snorkeled by the USFWS in their 2002 effort. This surveying was done during the day and produced no bull trout observations.

ADD INFO ON LAKE TROUT NETTING AND REMOVAL

Redd Surveys

Spawning surveys have been conducted sporadically in the upper Cle Elum River since 1996. With 19 miles to cover, the task is difficult. An index area has not been established, and none of the surveys can be described as complete. Habitat reconnaissance since 1999 has revealed that the most suitable spawning habitat exists above the Fortune Creek confluence (excluding the Tucquala Lake area) where the river has less gradient and the most suitable gravels. Nevertheless, no confirmed redds have been found in eight redd surveys conducted since 2000 (2000-2003, 2006-2009). The most promising “redds” observed were found by biologists from the USFWS and WDFW in September 2002 in the short (<0.7 mile), very low gradient reach directly below Hyas Lake (Jeff Thomas, USFWS, pers comm). Possible bull trout redds had been reported in this reach the two previous years. Seven large excavations that appeared to be redds (i.e., well defined pit and tailspill) were present in close proximity to each other but no fish were observed in the vicinity. The site was visited three additional times over the next month and subsequent investigation revealed no eggs present in the tailspill gravels of any of the redds. It was hypothesized that the redds might be those of spring spawners, possibly large rainbow or cutthroat trout, that had dropped down from Hyas Lake to spawn (fry emergence would have occurred several months previous). It is also possible that the excavations were not redds at all. It remains unknown what species produced these redds. The area was revisited the following two years and nothing similar was found (Reiss 2009).

The USFWS conducted a single redd survey in Fortune Creek in early October 2000. Thirteen redds were observed but the species responsible for the excavations is unknown since no fish were present on or near any of them (Judy Neibauer, USFWS, pers comm). There are strong brook trout populations throughout the Cle Elum drainage, and they are also fall spawning fish. In the fall of 2002 the USFWS conducted bull trout redd surveys (single-pass) in Fortune, Paris, Camp, and Big Boulder creeks. No redds were found in any of them.

Other Distribution Data (eDNA, etc.)

In 2017, Mid-Columbia Fisheries collected 32 eDNA samples in the Cle Elum River, 3 samples in Big Boulder Creek and 6 samples in Fortune Creek. Samples were collected between July and September with the intention that they would contain bull trout DNA from any adults staging to spawn. None of the water samples were positive for bull trout DNA (Parrish 2017). No other eDNA samples have been collected in the Cle Elum River or its tributaries. <--- CONFIRM SKYLARS SAMPLE MAP

Population Status and Trend

This population was last officially rated in combination with the Waptus Lake population. The USFWS (USFWS 1998) considered the Cle Elum/Waptus population depressed, decreasing, and at risk of stochastic extirpation. WDFW rates the status of this stock as unknown (WDFW 2004). For the purposes of this document the status of the Cle Elum River population should be considered unknown. As of 2015, the Cle Elum population of bull trout is considered functionally extirpated.

Habitat

Habitat Overview

Elevations in the upper Cle Elum River range from 2,240 feet at its mouth (Cle Elum Reservoir Lake) to 3,460 feet at the outlet of Hyas Lake about 19 miles upstream. For all but the upper mile the river flows through the Okanogan-Wenatchee National Forest. For almost all of this distance, the river is easily accessible by a Forest Service road, which is paved for the lower four miles. The watershed has a long history of grazing, timber harvest, and mining (Haring 2001). Some scattered small-scale gold mining still occurs in a couple of tributary creeks but grazing and logging are no longer significant activities at this time. CONFIRM. The watershed is a very popular recreation area. Four heavily used Forest Service campgrounds exist next to the river in the lower five miles, and road densities are high (3-4 miles/sq. mi.). There are numerous dispersed campsites upstream. Most of these are between Fortune Creek and Tucquala Lake. Many are located on the banks of the river, although the Forest Service has been working over the last decade to relocate and/or restrict access to some of the more problematic of them. There are just a few private residences located on land leased from the Forest Service; most in a small cluster near Big Boulder Creek (~RM 8).

Much of the upper Cle Elum River is confined in a canyon reach about eight miles in length beginning near RM 4.0. Large substrate materials dominated by boulders, high stream gradients and high water velocities characterize this reach. A series of steep bedrock cascades at RM 9.7 present a potential barrier for fish migrating upstream. Below the canyon reach the river channel displays alluvial characteristics, which could provide good spawning conditions for bull trout. Above Fortune Creek (~RM 12), the channel is also alluvial and physical habitat conditions for spawning and rearing are much better than were available in the canyon reach. This was the only portion of the river that approached meeting Forest Plan standards for pool quantity and LWD (USFS 1996). The riparian corridor is basically healthy except in areas where concentrations of dispersed campsites are present. In the mid-1990s fine sediment levels (in riffles) met standards, but concerns were raised that increased delivery of fine sediments was likely from dispersed recreational activity. Forest roads are not considered to be a leading contributor of fine sediment in the watershed (Haring 2001).

Elevated water temperatures in the upper Cle Elum River could be a problem for bull trout. The river is on the CWA 303(d) impaired water quality list for water temperature and investigators have recorded maximum temperatures exceeding 15^o C for extended periods in the summer (Mallas 2003). This is most likely a natural condition probably due to the presence of Hyas and Tucquala lakes as well as the fact that there are large segments of the river where the riparian canopy is naturally sparse.

Detailed habitat information is not available for smaller tributaries of the upper Cle Elum River. Redd survey notes compiled by the USFWS in 2002 provide some general descriptions of habitat conditions in several of these creeks (Fortune, Camp, Big Boulder, Paris). All of them had very steep gradients (>5%) and substrate materials dominated by small and large boulders; suitable spawning gravels were limited and found primarily in small pockets. Steep cascades and small waterfalls were prevalent, many of them at least potential barriers to fish migration. Fortune Creek has the longest stream length available above its mouth, approximately 2.5 miles, before a definite passage barrier is encountered. The distance from the mouth to a barrier waterfall in Big Boulder Creek is approximately a half-mile, but the creek is essentially a continuous steep cascade for this entire distance. The other two creeks have barrier waterfalls located within 100-200 yards upstream of their mouths. All four of these streams are subject to extremely low flows in late summer and early autumn.

If a viable adfluvial bull trout population still exists in Cle Elum Reservoir Lake, FMO habitat for that population is provided by the Reservoir Lake. Neither the sparse shoreline development or water sports activities on the Reservoir Lake are believed to impact habitat quality. Cle Elum Reservoir Lake is the largest storage reservoir in the Yakima Basin. Although it does experience extreme drawdown in the summer, a 265,000 acre-foot conservation pool (i.e., dead storage) cannot be accessed. This is the only body of water Lake in the Yakima Basin with a strong population of lake trout, which has been identified as a major limiting factor for bull trout populations in Montana (Donald and Alger 1993; Martinez et al. 2009).

Habitat Monitoring

Field Habitat Surveys

Mongillo (1982) measured water quality parameters and zooplankton densities for Cle Elum Reservoir. Mongillo and Faulconer (1980) conducted limnological studies in Cle Elum Reservoir in 1978 and 1979. They recommended lake fertilization as one method to increase productivity. Mongillo proposed a Cle Elum Reservoir Lake fertilization implementation and monitoring study. Flagg et al. (2000) reviewed Cle Elum Lake productivity and fertilization potential. Lieberman and Grabowski (2007) conducted limnological studies in Cle Elum Reservoir from 2003-2005. They concluded that zooplankton densities may limit the lakes capacity to support resident fish as well as introduced salmonids and suggested the nutrient enrichment may be one method to increase both algal and zooplankton production.

Sediment samples were collected and analyzed for the Cle Elum River and Cooper River in 1990 (Mayo 1998). Cle Elum River samples were collected between the reservoir and Fortune Creek. This monitoring effort demonstrated a level of fine sediments in the substrate within the spawning reach (~3-9%), which would qualify as “functioning appropriately” (USFWS 1999) although this data are from only one year.

The Forest Service completed habitat surveys on the Cle Elum River in 2000 (lower reach) and in 2005 (upper reach) using Hankin and Reeves protocol (Hankin and Reeves 1988; USFS 1996). In these surveys, data was collected on pool/riffle frequency, riparian and channel condition, substrate, LWD, and temperature. In 2006 an Aquatic Species Environmental Baseline was completed for the Cle Elum watershed (USFS 2006d). In 2004, a Federal Roads Analysis was completed for the Cle Elum watershed, including an aquatic rating.

Stream Temperature Data

In 2001, the Forest Service contracted aerial thermal infrared remote sensing surveys on the Cle Elum River from Cle Elum Lake upstream to the outlet of Hyas Lake (Watershed Sciences 2002). Accuracy of temperatures was confirmed with instream sensors. The flights were completed in early September and stream temperatures ranged from 13.9-17.4 °C.

There are three long-term monitoring sites in the Cle Elum River drainage where thermographs have been deployed during the summer low flow period for numerous years: Cle Elum River above French Cabin Creek (2000-2011), Cooper River (1994-2011) and Waptus River (1994-2006) (USFS 2011b). There are a number of other sites throughout the system that have been monitored by the Forest Service for a period of time, mostly between the years of 2000-2005. ADD ANY NEW TEMP MONITORING SITES? SUMMARY DATA?

Restoration Actions

DISCUSS YN CLE ELUM RIVER PROJECTS, SOCKEYE, POOL RAISE?

Threats

Connectivity

Fish Passage Barriers

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Entrainment

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Dewatering due to flow management

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Land-use Issues

Forestry

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Agriculture and Grazing

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Recreation

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Roads and Development

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Mining

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Ecological Interactions

Brook Trout

Threat Severity:

Other Invasive Species

Threat Severity:

Diminished Prey Base

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Disease

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Water Quantity and Quality

Flow issues/dewatering

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Current and modeled future temperature conditions

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Fisheries Impacts

Angling Regulations/Fisheries Use/Poaching (Recreational)

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Management/Monitoring (Research)

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Other Threats

Low Population Resiliency

Climate Change

Summary of Primary Limiting Factors and Threats

2012 SUMMARY:

The highest severity threat to this population appears to be low abundance. It is uncertain whether bull trout are still present anywhere in the Cle Elum drainage as their presence was last documented in 2002. A high severity threat that appears to have contributed to this possible extirpation is the presence of strong populations of introduced species (brook trout, lake trout, and brown trout). Passage barriers have also likely contributed, both Cle Elum Dam, which has limited connectivity to other bull trout populations and precluded anadromy, and recreation dams that may limit migrations within the system. Other threats to the population include lack of marine derived nutrients, habitat degradation due to recreation and forest management and illegal angling.

Transportation issues associated with the paved road along the mainstem Cle Elum River and active mining claims are present in this population area, but are not thought to be significant threats. Agriculture, altered flows, development, dewatering, grazing, and limited habitat are not present in this population area.

Recovery Strategy

Population-level Recovery Strategy

The Cle Elum River population has been identified as a “Monitor” population with a low priority for implementing bull trout actions beyond population monitoring actions used to determine whether there are extant bull trout remaining. If bull trout are found in this basin, the highest priority to recover this population would be to reduce the populations of brook trout, lake trout, and brown trout (to a lesser extent) which dominant this system. There is currently work being done to restore passage and reintroduce anadromous species including sockeye into the Cle Elum system. However, actions to provide passage (Passage at Major Storage Dams) recover salmon populations (Restore Healthy Salmon Populations), address riparian health, extend outreach to anglers and remove recreational dams will do little to benefit bull trout if there are none present. Supplementation will likely be necessary to recover viable populations of bull trout in this system in the future but issues with introduced species would need to mitigated first.

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Actions

Future link/ iframe to PowerApp will go in this section.

Completed Bull Trout Recovery Actions

• Cle Elum Dam fish passage facility final design and DEIS, which includes reintroduction of anadromous species, was completed in 2010.
• Cle Elum Dam fish passage facility was constructed and is functional for downstream juvenile migration as of XXXX (2025??). A trap and haul facility was constructed for adult passage upstream but has not been utilized yet, as of 2026? PLEASE CORRECT THIS INFO IF WRONG
• Dispersed campsites near the confluence of Cooper and Cle Elum rivers were closed or relocated by USFS in 2007 and 2008.
• Numerous dispersed campsites along the river from the northwest end of Cle Elum Lake to the Fortune Creek area were relocated and/or had vehicle access restricted by USFS in 1996.
• Roads in the watershed that were acquired over the last ten years by the Forest Service in land exchanges were decommissioned between 2006 and 2008 (most of these roads were in the upper headwaters of the Cooper River and Thorp and French Cabin creeks).
• Three segments of Forest Service Road 4330 (totaling one mile) located in the active floodplain of the Cle Elum River that are chronic sediment sources are scheduled to be relocated; old road prisms were decommissioned in 2012.
• Drainage and hydraulic improvements were completed along Forest Service Road 4330 in 2011 (1,000 feet of road treated).
• Motor vehicle use on the lakebed was restricted to a limited number of access points and for ingress and egress to shoreline only; off-road vehicle activity on the lakebed was prohibited by USFS in 1999.
• Fishing regulations have been implemented to protect bull trout in the Cle Elum and Waptus rivers (see Appendix F).

Recommended Actions

Relevant Multiple Population Actions

• Basin-wide #3: Evaluate supplementation (see Appendix D).
• Basin-wide #4: Monitor Yakima Basin Bull Trout Genetics Over Time (introgression with brook trout).
• Basin-wide #6: Outreach and Conservation
• Basin-wide #9: Habitat monitoring (temperature).

Cle Elum River Actions

• Cle Elum River #1: Provide connectivity at Cle Elum Dam
• Cle Elum River #2: Lake Trout assessment and removal
• Cle Elum River #3: Determine presence and distribution
• Cle Elum River #4: Determine presence and distribution in Waptus
• Cle Elum River #5: Riparian restoration
• Cle Elum River #6: Habitat Evaluation and Temperature Monitoring

Actions in the Yakima Steelhead Recovery Plan that benefit this population

• Upper Yakima #8: Provide passage at Cle Elum Dam

Update Notes

2012 BTAP text copied into Yakipedia and edited to match new format in July 2026 by Aimee Taylor. ADD LINK TO 2012 BTAP pdf placemark

Additional edits proposed by Alex Conley, Aimee Taylor and Cle Elum River population small group. Reviewed, and updated and approved by BTWG in XXXXXXXXXXXXX

Specific detail on out of cycle updates: