Idaho’s Salmon River once produced some of the largest salmon and steelhead runs in the Columbia River Basin.  Mallet (1974) estimated that historically 55% of all Columbia River steelhead trout originated from the Snake River basin, which includes the Salmon subbasin.  Stream habitat in the Lemhi watershed has been altered by human activity much more than in other watersheds in the upper Salmon River (Loucks 2000). Key land uses that have had limiting effects on habitat in the Lemhi River and its tributaries are irrigation (diversions and water withdrawal), grazing, channelization, and road construction.  More than 95% of the known chinook salmon use of the river as a spawning and rearing area occurs along the upper 28 miles of the Lemhi, between Hayden Creek and the town of Leadore.   This section of river is bordered by private land, frequently lacks high quality pools and the bank stability provided by vigorous riparian vegetation, and apparently experiences high and widely fluctuating water temperatures during the mid-to-late summer (Servheen 2001).  Migration of adult and juvenile salmonids is impacted by dewatering in the lower reaches of most tributaries (Table 1).

Table 1 - Ranked impacts of altered ecosystem features impacting habitat quality and quantity for focal fish species in the Lemhi watershed. Degree of impact on habitat quality or quantity ranked as: P (component is functioning properly, needs protection), 1 (least influence), 2 (moderate influence), 3 (greatest influence-highest priority).

 Habitat

Riparian and aquatic habitats in the Lemhi watershed provide rich and vital resources to fish and wildlife due to their high productivity, diversity, continuity, and critical contributions to both aquatic and upland ecosystems. Riparian areas function as the transition zone between aquatic and terrestrial ecosystems, and aquatic and riparian habitat mutually influence and benefit each other. The Lemhi watershed supports twenty-two species of fish.  More than 75% of the Salmon subbasin’s terrestrial vertebrate species use riparian habitats for essential life activities. Properly functioning riparian habitats are critical in creating and maintaining instream conditions necessary for native fish stocks (NPCC 2005).

One of the primary limiting factors in the Lemhi watershed is adequate fish passage conditions between the Lemhi River and tributary habitats. Irrigation withdrawals that dewater stream segments and fish passage barriers (e.g. diversions and road culverts that block fish migration) effectively disconnect tributaries from the mainstem. These factors prevent access to historically available spawning and rearing habitat for anadromous species while isolating resident fish populations. Only four of the 30 tributaries to the Lemhi River are regularly connected to the mainstem (IDWR 2013).  There are 2,950 points of water diversion in the Lemhi watershed and 191 stream-alteration permits recorded. Low flows are a primary concern in the Lemhi, but channelization has also caused a loss of floodplain access and lack of habitat diversity in the lower reach. When State Highway 28 was constructed in 1952, approximately 5 miles (8 km) of the Lemhi River channel were altered and/or isolated from the river (Gebhards 1958). An additional 10 miles (16 km) of Lemhi River channel were altered in 1957 in response to significant flooding (Gebhards 1958). Altered riparian habitats are common in the drainage. High water temperatures in the Lemhi River downstream of Agency Creek and in Big Springs Creek impact habitat quality (NPCC 2005).

Section 303(d) of the Clean Water Act establishes requirements for states and tribes to identify and prioritize water bodies that are water quality limited (i.e., water bodies that do not meet water quality standards). States and tribes must periodically publish a priority list of impaired waters, currently every two years. For waters identified on this list, states and tribes must develop water quality improvement plans known as total maximum daily loads (TMDLs) that establish allowable pollutant loads set at levels to achieve water quality standards.  Seven creeks are included on the 303(d) list as sediment-impaired streams, and one is listed for fecal coliform. TMDL's have been developed to address sediment in Bohannon Creek, Eighteenmile Creek, Geertson Creek, Kirtley Creek, Sandy Creek, McDevitt Creek, and Wimpey Creek, and to address fecal coliform bacteria in the Lemhi River (http://www.deq.idaho.gov/water/data_reports/surface_water/tmdls/lemhi_river/lemhi_river.cfm).

As Columbia River Basin anadromous fish runs began to decline, ranchers in the Lemhi Basin took action to prevent the extirpation of Lemhi salmon and steelhead runs. They sought the assistance of state and federal officials to help develop a conservation plan addressing the in-basin habitat needs of ESA-listed fish. The Northwest Power Planning Council’s (NPPC’s) Strategy for Salmon (NPPC 1992), issued a plan calling for the recovery of salmon runs in the Columbia River Basin, watershed-level planning efforts to effect that recovery, and cooperation between private landowners, government agencies, and other stakeholders in developing such efforts. These collaborative efforts led to establishment of the Model Watershed Project in Salmon, Idaho in 1993 (which has since expanded to become the Upper Salmon Basin Watershed Project); completion in 1992 of a plan by local irrigators to improve fish passage in the Lemhi River (the “Irrigator’s Plan”; LID and WD74 1992); and the Model Watershed Plan (ISCC 1995), which identified a range of fish conservation actions for the Lemhi, Pahsimeroi, and East Fork Salmon River watersheds. Based on the latter plan, numerous and significant conservation projects have been voluntarily implemented in the Lemhi Basin focusing on fish passage issues, fish screen improvements, protection of riparian habitat, and consolidation or modification of irrigation diversion works (Framework 2005).

Since the late 1980’s, numerous on-the-ground improvements to irrigation diversions (in conjunction with fish screening) and riparian habitat have been achieved through the voluntary actions of landowners and water users in cooperation with the USBWP; (formerly the Lemhi Model Watershed Project) and the IDFG Anadromous Fish Screen Program. Many of these habitat issues promoted by landowners were addressed by projects that were developed through the USBWP Technical Team.

Conservation measures are being developed by collaborators in the Lemhi River watershed to improve stream flow in the mainstem and dewatered tributary segments.  Other conservation measures include fish habitat improvements such as riparian protection/restoration, improving instream habitat, and diversion improvements.

The State of Idaho is in the process of developing a Lemhi Conservation Plan (LCP) and negotiating a Section 6 Agreement under the ESA with the federal regulatory agencies (National Marine Fisheries Service and the U.S. Fish and Wildlife Service) for the purpose of implementing habitat conservation actions throughout the Lemhi River watershed.

In 2005, Idaho completed a comprehensive water rights settlement between the U.S. government and the Nez Perce Tribe known as the Snake River Basin Adjudication (SRBA). This agreement provides a framework for the development and implementation of habitat conservation actions throughout the Lemhi River watershed. Priority habitat actions prescribed in these agreements include improving mainstem habitat in the Lemhi River where the majority of Chinook salmon production occurs, and establishing functional reconnections between the mainstem and tributaries. Significant progress has been made in completing some of these actions through the implementation of habitat projects. 

The Lemhi River Restoration project will provide either partial season or permanent stream reconnects for Lemhi tributaries.  Tributary reconnects benefit both resident and anadromous salmonids by providing access to historical spawning and rearing habitat. Chinook salmon do not have access to historical tributary habitats that would provide good quality spawning and rearing conditions, particularly in the headwater reaches that are generally unimpaired by irrigation withdrawals and land use.

Figure 1 - Lemhi River Basin Priority Tributaries (Idaho Department of Water Resources, 2013)

Depending on the snow pack and early season irrigation practices, dewatering of the lower river can delay anadromous smolt and adult migrations. The large number of irrigation diversions may also delay smolts on their seaward migration, thus potentially decreasing survival.  Tributaries of the upper Lemhi River above Hayden Creek (with the exception of Big Springs Creek) do not contribute to anadromous production because of low flows and irrigation withdrawals (Figure 1).

6.         Describe the nature of the relationship between the proposed habitat program and the Integrated Status and Effectiveness Monitoring Program ((ISEMP) including an explanation of whether ISEMP will be evaluating reach-level or impact-area responses of projects implemented by this program. Provide a complete description and examples of the adaptive management process.

            The Idaho Department of Fish and Game (IDFG) coordinates and conducts several monitoring programs in the Lemhi River watershed. Monitoring was initiated in 2006 using PCSRF and Bonneville funds, Intensively Monitored Watershed (IMW) program funding from NOAA Fisheries was awarded beginning in 2007, and Integrated Status and Effectiveness Monitoring Program (ISEMP) funding from NOAA Fisheries was awarded in 2009.  (IDFG, 2012)  

            The IMW and ISEMP both implement components that were identified for implementation in the original ISEMP study design (QCI, 2005). This design uses an analytical framework for predicting fish population response to changes in watershed-level habitat quality and quantity resulting from restoration efforts. The framework uses baseline data, modeled and empirical habitat measurements, and empirical changes in fish survival, abundance, condition, and population distribution.  Emphasis is placed on generating stage-based survival estimates for anadromous and adfluvial species distributed in accessible habitat and reconnected habitat.

            The following is taken from Salmon Subbasin Pilot Projects Monitoring and Evaluation Plan, developed by Quantitative Consultants, Inc., 2005, p. 11:

            “The primary goal of the Lemhi ISEMP pilot project “is to identify and quantify the effects of habitat modifications on the productivity and survival of focal anadromous and resident salmonids within the Lemhi watershed. However, there are numerous obstacles   to directly quantifying the effects of habitat restoration on these vital rates. For example, even significant increases in the abundance and quality of freshwater habitat may not result in quantifiable changes in juvenile abundance if out-of-subbasin mortality limits the number of spawning adults, and therefore mutes the response in juvenile abundance.   Thus, this experimental framework includes the following components:

1. A watershed model that evaluates productivity and carrying capacity by life-cycle stage as a function of habitat availability and quality, and then simulates expected life-stage specific benefits from increased habitat availability or quality. 
2. Reach-specific empirical measures of juvenile productivity, survival, and condition to determine whether tributary reconnection has provided high quality habitat that benefits fish vital rates (survival, growth etc.).
3. Measures of the movement and distribution of anadromous and resident fish to address the following questions:

a)      Are anadromous fish using newly available habitat?

b)      Have the reconnections changed the distribution and connectivity of resident fish?”

            ISEMP, with support from IMW, is designed to evaluate changes in fish performance (e.g. survival) as a function of habitat change at multiple spatial scales. Early on, the study recognized that habitat actions, particularly land acquisitions and site-specific habitat restoration projects, can be problematic from an M&E standpoint. Each presume knowledge of factors that limit population growth, and that the habitat actions directly address limiting factors in the most efficient manner.

            Monitoring in the Lemhi assesses  juvenile production as a function of adult escapement, in terms of total production (standing crop), the sum of what survives to stay (residualization) and what leaves (anadromous emigration), and the distribution of juveniles. Most importantly, because ISEMP distributed the fish and habitat site-based monitoring effort in a probabilistic fashion, changes can be evaluated on multiple scales (e.g. a single site, or aggregate those sites to tributary, subwatershed, or watershed/population scale). This is accomplished by estimating adult escapement to watersheds and subwatersheds of the Lemhi, sampling and tagging juveniles probabilistically across the watershed, and sampling habitat continuously using green LiDAR and Columbia Habitat Monitoring Protocols (CHaMP) at sites that are coincidental to juvenile sampling sites.  ISEMP can state where juvenile fish reside, and how habitat condition influences their survival and growth, with some degree of uncertainty.

            The juvenile PIT tagging work in the Lemhi coupled with habitat surveys where fish are detected enables the ISEMP process to estimate the habitat quantity and quality needed to optimize survival and growth in a statistically correct fashion. Since sampling is replicated across 17 subwatersheds in the Lemhi, ISEMP can identify habitat features that limit survival and growth. This information can be extended to support or to refute the value of any given habitat action, whether it is site-specific or occurs at the spatial scale of a subwatershed (i.e., the reconnection of a tributary).  

            The IDFG monitoring program is a coordination operation of the IMW and ISEMP projects and relies on a suite of shared infrastructure located to estimate adult escapement using instream PIT tag detection systems and total juvenile production using rotary screw traps.  Instream PIT tag systems enable estimations of adult escapement to the Lemhi and subwatersheds (Hayden Creek and tributaries that are targeted for reconnection). Combined with probabilistically distributed juvenile capture and PIT tagging surveys this infrastructure estimates total juvenile abundance prior to emigration (standing crop) and estimates survival and emigration from key tributaries. Recapture information generated from rotary screw traps coupled with emigration timing provided by instream PIT tag detection systems allow estimates of growth as a function of the location where juveniles reared. (See Figure 1)

            The sample frame underlying remote fish capture and tagging surveys is also used for ground-based habitat surveys using the CHaMP protocol. These habitat surveys provide data on the distribution of habitat attributes in areas available to anadromous fish and in tributaries targeted for reconnection. (See Figures 2 & 3) These data are combined in a life-stage specific Beverton-Holt model that views fish abundance, survival, and growth as a function of habitat quality and quantity (QCI 2005). In short, the subwatersheds of the Lemhi provide contrast in habitat conditions that can be explicitly linked to juvenile production, survival, and growth.

Figure 1 - Locations of IPITDS and RSTs operated by the IMW and ISEMP projects and abundance estimates for juvenile Orcorhynchus mykiss generated by remote juvenile capture and tagging surveys.

Figure 2 - Distribution of a subset of habitat metrics in locations available to anadromous individuals prior to Lemhi River tributary reconnection work.

Figure 3 - Distribution of a subset of habitat metrics in tributaries available after reconnected to the Lemhi river mainstem.

The physical effects of site-specific habitat actions, such as channel realignment, are assessed using a Digital Elevation Model of Difference (DoD). The DoD quantitatively estimates changes in habitat attributes such as pool area. In turn, the biological benefits of these habitat modifications are estimated using the fish/habitat relationships developed by application of the watershed model described above.  (See Figure 4)

Figure 4   Example of a DoD generated by CHaMP habitat surveys prior to and following site specific habitat actions.

Adaptive Management            

            Adaptive management is an essential component of the Lemhi River Restoration effort to facilitate necessary refinement of actions/effort to meet conservation objectives. Adaptive management decisions use IDFG’s ISEMP and IMW project results to guide on-the-ground decision-making to implement measures in the most efficacious and efficient manner. A summary of three adaptive management events follows.

            Example #1:    Adult Chinook salmon have been radio tagged at Lower Granite Dam and tracked to the Lemhi drainage. Through this monitoring it has been established that adult Chinook salmon migrate directly to or very nearly to their spawning areas, arriving in June through early July; adults stage in those immediate areas until spawning in August.  The adaptive management response to this knowledge has been a shift in the timing for optimal water augmentation to benefit fish.  Efforts are now underway to acquire flow earlier in the year (June and July) to protect adult Chinook salmon.

            Example #2:    An irrigation ditch was closed near Leadore prior to 2009 to provide additional flow in the upper Lemhi River and facilitate reconnection of two tributaries, Hawley and Eighteenmile creeks. The expected outcome of this project was that there would be on average a three to six cfs increase in flow to the Lemhi River, dropping to two cfs during the irrigation season.  This added flow would provide a hydrologic reconnection of Hawley and Eighteenmile creeks to the mainstem Lemhi River, but would be insufficient to reconnect fully the streams to allow for fish passage into the tributaries.  Plans were developed to acquire additional flow to reconnect these tributaries fully; however, monitoring of flows after closure of the ditch showed flow increases in the range of 10 – 25 cfs during the irrigation season.  This increased flow adequately reconnects the tributaries and allows fish passage fully making flow augmentation unnecessary.

            Example #3:    A shallow spring-fed man-made pond was identified as a significant source of warm water (20 - 22°C) input to Little Springs Creek.  A project was implemented to construct a new channel around the pond so all of the cold spring flow goes directly to Little Springs Creek. Monitoring has demonstrated reduced water temperatures in Little Springs Creek; however, monitoring has also shown that the smaller pond, which still receives groundwater, is warmer than it was prior to the project.  This was unexpected. While the pond still releases warmer water into Little Springs Creek, the water temperatures in the creek have improved as a result of the project. As a result of this monitoring, alternatives plans are being evaluated to dredge and/or modify the outlet structure of the pond.