Habitat for the Joseph Creek Population of Snake River Summer Steelhead Has Been Impacted

Draft October 23, 2006 - Wallowa/Lostine Chinook LF/T

Grande Ronde/Imnaha River MPG

Wallowa/Lostine Spring Chinook Population

Limiting Factors and Threats

Habitat conditions for spring Chinook vary considerably within the area inhabited by the Wallowa/Lostine population, ranging from nearly pristine conditions in high-elevation reaches within the Eagle Cap Wilderness to the valley floor where streams have been highly modified by agriculture, grazing, and urban development. The primary in-basin factors limiting spring Chinook populations in the Wallowa and Lostine River systems are water temperature, sediment, altered hydrologic function, predation, and habitat complexity (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). Altered hydrologic function primarily is the result of irrigation water management, which results in reduced instream flows, reduced quality of return water, elevated stream temperatures, and passage barriers. Habitat complexity issues primarily are due to reduced wetted widths and a lack of pools and large woody debris (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). Other factors limiting spring Chinook production in the Wallowa-Lostine system relate to passage barriers and non-temperature water quality issues, e.g., reduced dissolved oxygen levels (NPCC 2004; Huntington 1993).

Several stream reaches in the Wallowa system are on the Oregon Department of Environmental Quality’s 303(d) list for temperature (Wallowa River and Bear, Little Bear, Fisher, and Howard Creeks), sediment (Wallowa and lower Lostine Rivers and Bear, Hurricane, and Prairie Creeks), coliform bacteria (Wallowa River, Prairie Creek, and Spring Creek), dissolved oxygen (Prairie and Spring Creeks), and pH (Wallowa River; ODEQ 2006). Another potential concern for wild Chinook salmon production is the documented presence of Myxobolus cerebralisin the WallowaRiver system, an introduced protozoan that is the causative agent of whirling disease in salmonids (Lorz et. al. 1989).

Past and present land use activities have altered habitat conditions for the Wallowa-Lostine Chinook population. Most of the limiting factors listed above may be attributed to irrigation water withdrawals for livestock and agriculture, stream channel modifications, draining of wetlands, and riparian zone degradation (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). Road construction, grazing, animal feeding operations, residential development, and timber harvest(primarily in tributary areas not inhabited by Chinook) are the primary threats contributing to degradation of riparian areas in the system (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). Roads run along many of the streams within the watershed (with some exceptions, e.g., the upper portions of the LostineRiver and Bear Creek are in designated Wilderness), providing access for timber harvest and recreation high up into their watersheds. Other reaches have been channelized to accommodate road construction, homesteads, and irrigated agriculture; many of these streams have water diversions, e.g., channel spanning weirs and other impediments to fish passage. Past removal of beavers and large wood from stream channels contributed to poor quality and frequency of pools. Changes in upland vegetation as a result of past timber harvest, grazing practices, fire suppression, road construction, and introduction of noxious weeds contribute to sediment loads, elevated stream temperatures, and alterations of hydrologic function (NPCC 2004, Wallowa County – Nez Perce Tribe 1999). A 35-foot impoundment built on WallowaLake in 1918 has also altered the natural hydrograph of the system.

The ICTRT has identified three MaSAs and two MiSAs in the Wallowa/Lostine spring/summer Chinook salmon population.

In the following discussion, we grouped areas of the Wallowa-Lostine watershed with similar habitat conditions, land use, ownership, and stream morphology as well as similar use by spring Chinook. Much of this discussion is adapted from discussion of limiting factors contained in the Grande Ronde Subbasin Plan (NPCC 2004) and other references as cited.

LowerWallowaRiver(WLC1) – Mouth to MinamRiver (RM 0 -9.8)

The WallowaRiver from its mouth to the confluence of the MinamRiver(RM 9.8) flows through a confined canyon with limited access. A railroad parallels the east bank of this reach for its entire length. Apublic road that provides access to MinamState Parkis located next to the river along the reach’s upper two miles; private roads in its lower three miles provide access to the WallowaRiver’s confluence with the GrandeRondeRiver. Privateland, primarily used for timber and grazing, and a small amount of BLM land surround this lower portion of the river(NPCC 2004).

This reach is managed as an Oregon State Scenic Waterway and a federal Wild and ScenicRiver with a “recreational” designation. This lower portion of the river receives considerable recreational use by float boats in spring and early summer, steelhead anglers in early spring, and trout anglers in summer and fall. There have been some impacts to habitat in this reach from cattle grazing, recreational use, and the road and railroad; however, most of the water quality issues in this reach are a result of activities upstream in the WallowaValley(NPCC 2004, Wallowa County – Nez Perce Tribe 1999).

This portion of the WallowaRiver is 303(d)-listed for E. coli, fecal coliform, temperature, sediment, and pH (ODEQ 2006). Additionally, the subwatersheds of the two main tributaries within this reach, Howard and Fisher Creeks, are highly impacted, have high levels of fine sediment, and are 303(d)-listed for temperature(ODEQ 2006, NPCC 2004).Timber harvesting activities combined with access roads (roads parallel the entire length of HowardCreek) deliver excess sediment and warm water to the mainstem WallowaRiver (NPCC 2004).

StreamNet (2006) reports this reach as being used for rearing and migration. Its primary limiting factorsinclude low summer flows, poor water quality (temperature and sediment), predation, and a lack of habitat diversity (lack of pools and woody debris) (NPCC 2004, Wallowa County – Nez Perce Tribe 1999). Elevated summer temperatures, low flows, and lack of thermal refugia (primarily pools) likely are affecting abundance, productivity, and spatial structure ofspring Chinook in the lower WallowaRiver. No completed restoration projects are reported in the Grande Ronde Model Watershed restoration database within this reach of the WallowaRiver(GRMW 2006). However, restoration actions on tributaries have included:

• Seeding of 45 acres of wet meadows
• 2 stream crossing structures modified
• 22.5 miles of upland fence to improve livestock management
• 72 off-channel livestock water developments

MiddleWallowaRiver(WLC2) – MinamRiver to Rock Creek (RM 9.8 – 17.6)

From its confluence with the MinamRiver(RM 9.8) to its confluence with Rock Creek (RM 17.6), the WallowaRiver flows through a confined canyon. Oregon Highway 82, located along the north bank, and the Wallowa Union Railroad, located along the south bank, further confine the river. Privateland, primarily used for grazing and timber, surrounds this reach,very little of which is in public ownership (NPCC 2004, Wallowa County – Nez Perce Tribe 1999). Highway 82 provides easy access to the WallowaRiverfacilitating a popular sport fishery for trout and steelhead.

The mainstem and watersheds of the major tributaries within this reach are composed primarily of private land used for timber production and livestock grazing, the two primary threats in this reach (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). These activities combined with access roads (some located along stream channels) deliver excess sediment to the mainstem WallowaRiver (NPCC 2004). The NPCC’s 2004 Grande Ronde subbasin plan identifies WaterCanyon as being a tributary of particular concern.

StreamNet (2006) reports spawning (beginning at mile 28.75, the mouth of Parsnip Creek), and migration occurring in this reach. The primary factors limiting spawning and migration in this reach include an altered hydrologic regime (upstream irrigation withdrawals that decrease summer low flows,and storage at Wallowa Lake that reduces flows in winter and spring), poor water quality (temperature, excess fine sediment, and contaminated irrigation return), predation, and a lack of habitat diversity (lack of pools and woody debris) (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). This portion of the WallowaRiver is 303(d)-listed for E. coli, fecal coliform, temperature, sediment, and pH (ODEQ 2006). None of the other streams in this reach are on the 303(d) list (ODEQ 2006).

Poor water quality (particularly elevated temperatures), low flows, excess sediment, and a lack of pools likely are affecting abundance, productivity, and spatial structure of spring Chinook in the midWallowaRiver. Restoration projects accomplished to date in this reach that directly or indirectly benefit Wallowa/Lostine Chinook salmon include (GRMW 2006):

• 0.25 stream miles of instream habitat improvements (boulder and large wood placement)
• 13 off-channel ponds developed for livestock watering
• 10.5 miles of road improved
• 0.5 miles of road closed
• 2 stream crossing structures installed

UpperWallowaRiver(WLC3) – Rock Creek to WallowaLake (RM 17.6 – 51.2)

The WallowaRiver from its confluence with Rock Creek upstream to the dam at WallowaLakeexists as a moderately confined, low-gradient channel. Some sections of road and railroad are adjacent to the river in this reach; the towns of Wallowa, Enterprise, and Joseph also are located on its banks. Private land, primarily used for irrigated agriculture, grazing, and residential development, surrounds this lower reach; very little of thearea is in public ownership (NPCC 2004, Wallowa County – Nez Perce Tribe 1999).

The primary factors limiting spawning and rearing in this reach include an altered hydrologic regime (irrigation storage and withdrawals that decrease, and sometimes eliminate,late summer and winter flows and reduced “flushing” flows, especially below the city of Joseph), poor water quality (temperature, excess fine sediment, contaminated irrigation return, nutrients), predation, food, and a lack of habitat diversity (lack of pools and woody debris) (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999). Altered hydrologic regime is primarily due to the impoundment at WallowaLake where river flows are controlled by the dam. Local fish biologists report that the reach between the mouth of Prairie Creek and WallowaLakeoften goes for several years without a high spring flow to flush sediment from spawning gravels and holding pools (Wallowa County – Nez Perce Tribe 1999). Cattle grazing, animal feeding operations, residential development, and irrigation withdrawals and returns are the primary threats in this reach, which is 303(d)-listed for E. coli, fecal coliform, temperature, sediment, and pH (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999, ODEQ 2006). Additionally, the watersheds of its tributaries, most of which are discussed individually below, are heavily impacted.

StreamNet (2006) reports the section of this reach upstream of Parsnip Creek (RM 28.75) is used for spawning and rearing; the remainder of the reach is rearing and migration habitat. Of the limiting factors outlined above, low flows and increased temperatures likely limit summer rearing while excess sediment/substrate embeddedness may limit survival during incubation. Additionally, reduced flows in the upper most part of this reach may prevent returning adults from accessing upstream spawning habitat and excess sediment may reduce the volume of pools used as holding habitat. Under a management agreement between ODFW and the Nez Perce tribe, excess adult hatchery springChinook have been trapped at the Lostine weir and outplanted in the Wallowa River; 177 fish were outplanted in 2004 and 94 fish were outplanted in 2005. None were outplanted in 2006 (J. Harbeck, pers. comm.).

Poor water quality, low flows/dewatering, excess sediment, substrate embeddedness, and a lack ofhabitat diversity (pools and habitat structure)likely are affecting abundance, productivity, and spatial structure of spring Chinook in this reach(NPCC 2004, Huntington 1993, Wallowa River Wallowa County – Nez Perce Tribe 1999). The EDT analysis within the NPCC’s 2004 Grande Ronde subbasin plan identifies this reach as having high potential for increases in abundance and productivity relative to other reaches within the Wallowa-Lostine spring Chinook population. Consequently, it should be strongly considered for restoration. Restoration projects accomplished to date in this reach that directly or indirectly benefit Wallowa/Lostine Chinook salmon combine to provide the following quantities (GRMW 2006):

• Under the CREP program, 5.1 acres of riparian habitat along 0.36 miles of stream have been treated
• 0.03 stream miles of log/rootwad streambank treatments
• 0.6 miles of stream benefited by irrigation modifications
• 0.93 miles of stream treated by large wood placement
• 5.43 miles of riparian exclusion fence protecting 39.1 acres of riparian habitat along 3.82 miles of stream
• 4.35 acres of riparian planting along 0.96 miles of stream
• 3 acres of planting in riparian/upland areas
• 2 spring water developments for off-channel livestock watering
• 1 stream crossing
• 1 acre of streambank planting along 0.19 miles of stream
• 10 streambank rock structures along 0.24 miles of stream
• 1 well water development
• 1 water development with ditch or stream as source

Hurricane Creek (WLC4) – Mouth to RM 7.6

Hurricane Creekflows out of the Eagle Cap Wilderness Area and enters the WallowaRiver at RM 41.3 near the town of Enterprise. The upper reaches are in the Eagle Cap Wilderness and are characterized by pristine, high-elevation forests and meadows. Recreational activity, although heavy in some areas, is the only land use within the wilderness area. The lower reaches of Hurricane Creek are private with some small areas of municipal ownership as well as the Joseph airport. Irrigated agriculture, grazing, and rural residences dominate private lands within the drainage (NPCC 2004, Wallowa County – Nez Perce Tribe 1999).

Several irrigation-related passage barriers exist within the lower portion of the watershed. Chinook access is limited to the lower 7.6 miles of Hurricane Creek downstream of the Upper Alder Slope Ditch and Moonshine Ditch diversion dam. A natural barrier (rock chute and cascade), within 0.5 miles upstream of the dam, was likely the historical upper extent of Chinook distribution. These passage barriers, located just upstream of the National Forest boundary, prevent salmon access to the wilderness area (NPCC 2004, Wallowa County – Nez Perce Tribe 1999). The upper 4.0 to 4.5 miles of this reach is often dewatered by irrigation withdrawals in late summer and early fall and is not available as year-round Chinook habitat. Some flow is maintained downstream of the dewatered reach as a result of irrigation return flow, springs, and diversion of water from the WallowaRiver into Hurricane Cr. via the Lower Alder Slope Ditch that enters at approximately mile 3.5. Two small campgrounds are located on this road. Numerous roads exist within the lower portion of the drainage; one road, running along the mainstem, extends into the upper watershed and provideshuman access to the wilderness area. Stream morphology in this lower portion of the river is characterized by low gradients, wide floodplains, and extensive channelization.

Primary land uses along lower Hurricane Creek are irrigated agriculture, grazing, and residential development. Most of the reach inhabited by spring/summer Chinook salmon has been channelized to accommodate agricultural and residential development. Much of the channelization occurred after large flow events in the 1940’s, 1960’s, and 1970’s (Huntington 1994; Wallowa County – Nez Perce Tribe 1999). As a result of development and channelization, most of the riparian zone along lower Hurricane Cr. has been altered and is in sub-standard condition (Huntington 1994; Wallowa County – Nez Perce Tribe 1999). There is also a general lack of pools, wood, and other instream structure as a result of low flows and modification of channels and riparian areas. In addition, Huntington (1994), WallowaCounty – Nez Perce Tribe (1999), and EDT analysis (NPCC 2004) all rated excess fine sediment as a high priority habitat attribute in lower Hurricane Creek. The lower 7.6 miles of Hurricane Creek are on Oregon’s 303(d) list for sediment and are listed as “water quality limited not needing a TMDL” for habitat modification and flow modification (ODEQ 2006). Wallowa County – Nez Perce Tribe (1999) also listed irrigation return flow and feedlot runoff as high priority water quality problems in lower Hurricane Creek. Hurricane Creek is 303(d)-listed for sediment from its mouth to RM 7.6 (ODEQ 2006).

Limiting factors Hurricane Creek below the National Forest boundary include irrigation withdrawals, excess fine sediments (creating water quality concerns and increasing substrate embeddedness), numerous physical barriers (primarily due to dewatering), and insufficient riparian vegetation, woody debris, and pool habitats (NPCC 2004, Huntington 1993, Wallowa County – Nez Perce Tribe 1999).

StreamNet (2006) reports the Hurricane Creek drainage as being used by spawning and rearing spring Chinook. Habitat conditions in Hurricane Creek have affected Chinook abundance, distribution, and spatial structure. Of the limiting factors outlined above, high levels of fine sediment would have the greatest effect on spawning and incubation life stages. Additionally, reduced flows and dewatered reaches may prevent returning adults from accessing upstream spawning habitat. Water quality (temperature, irrigation return flow and feedlot runoff) and low flow conditions would affect all life stages. Instream habitat conditions, poor riparian conditions, lack of wood, and reduced floodplain connectivity would have the greatest effect on juvenile rearing life stages.