In the Salmon Subbasin, ISEMP focuses on steelhead (Oncorhynchus mykiss) and spring/summer Chinook salmon (Oncorhynchus tshawytscha) populations in the Lemhi and Secesh Rivers. Implementation of ISEMP in the Salmon River Subbasin was designed specifically to meet the data requirements of the Watershed Model. The program has the following major components:

  • Watershed Model: Develop and apply the ISEMP Watershed Model as a means to relate freshwater productivity of anadromous salmonids to habitat conditions in order to evaluate habitat restoration while controlling for hatchery effects, local and large-scale climatic drivers, and background habitat degradation.
  • Monitoring and Evaluation: Provide the data needed to run the Watershed Model. This includes the design and implementation of improved monitoring and analytical methods for describing salmonid populations, habitat, and fish-habitat relationships.
  • Infrastructure: The Salmon Subbasin ISEMP: a. fully funds the operation of a rotary screw trap on the lower Secesh River (SubReport 1); b. partially funds the operation of two rotary screw traps in the Lemhi River Subbasin, one on the lower mainstem, and the other in Hayden Creek (SubReports 2 and 3); c. operates and maintains 32 Instream Passive Integrated Transponder (PIT) Tag Detection Systems (IPTDS; Sub-Reports 4 and 5).

Subbasin Name:  Salmon River

Lemhi (ID)
South Fork Salmon (ID)

Project Contact: 
Chris Beasley,  QCInc



IN-STREAM PIT TAG DETECTION SYSTEMS (IPTDS) Significant effort has been put into the installation and operation of IPTDS, which provide data for survival estimation, abundance, and distribution of juveniles and adults (Table 4). These data are directly used by the Watershed Model and address Reasonable and Prudent Alternative (RPA) 50.5, which requires productivity and abundance monitoring for a majority of Snake River B-run steelhead populations. In the Lemhi River, IPTDS are located in both mainstem and smaller tributary streams, allowing age- and sex-structured abundance estimates to be reported for the population and at finer scales useful for evaluating habitat action effectiveness in a treatment/reference context. Automated data management systems have been developed by QCI to efficiently process the large volumes of data generated by IPTDS and to assist data managers with remote monitoring of these systems. These IPTDS data are uploaded into regional databases (e.g., PTAGIS) in near realtime.


During remote site surveys, captured fish are counted and measured, and spring/summer Chinook salmon and steelhead are PIT tagged and sampled for age and sex. Tagged fish are recaptured or resighted during subsequent remote site surveys; at rotary screw traps in the lower Secesh River, lower Lemhi River, and Hayden Creek; and at numerous IPTDS located strategically to assess movement patterns. Mark-recapture techniques are used to estimate population size and life-stage specific growth and survival. These various sampling efforts provide estimates of sex ratio, age structure, growth, abundance, survival, migration probability, and habitat associations for parr to smolt life stages, at broad (population) and fine (individual treatment and reference sites) scales.


In order to estimate adult escapement to Snake River tributary streams, adult natural origin spring/summer Chinook salmon and steelhead are PIT tagged and sampled for age and sex using scale and tissue samples as they ascend Lower Granite Dam (LGD) on the Snake River. Tagging goals are set at a minimum of 4,000 natural origin individuals of each species. Adults are detected upstream at IPTDS. These data are used in a Bayesian patch occupancy model and a 6 branching model to provide precise age- and sex-structured adult escapement estimates (typically with a coefficient of variation <15%). Reproductive potential is estimated based on the number and age of escaping females. A detailed description of methodology and the escapement estimates will be reported in collaborative report expected to be released by the Idaho Department of Fish and Game, and will be available at their website.


Habitat data are used to estimate stream habitat quantity and quality and provide data to populate the Watershed Model. Habitat surveys are conducted from June – October annually. Collaborators involved in habitat sampling include ISEMP, CHMP, IDFG, and the Nez Perce Tribe. Since 2011, habitat sampling has been conducted using CHaMP monitoring protocols (Bouwes 2011). Previous (2009 – 2010) habitat data were collected using ISEMP protocols and are compatible with CHaMP data (Bouwes 2010). Habitat data are available available on In the Lemhi River watershed, the main goal of habitat monitoring is to characterize habitat in restoration/treatment and reference areas. In the SF Salmon River watershed, the main goal of habitat monitoring is to relate habitat status and trends to freshwater productivity of steelhead and spring/summer Chinook salmon. Spatial overlap in fish and habitat data allows for description of fish-habitat relationships at site, tributary, and population scales. ISEMP analysts are evaluating the utility of several complementary approaches for describing fish-habitat relationships, including: 1) correlations between fish and habitat metrics (e.g., habitat suitability indices, regression models, and structural equation models); 2) mechanistic models such as bioenergetics models and production function models; and 3) watershed experiments. A better description of fish-habitat relationships will facilitate the recommendation of habitat actions that are most likely to benefit fish populations.

Available Data:

Geospatial Data

2009-2010 Habitat Monitoring Data stored in the STEM Databank


  • Increase in juvenile rearing conditions by opening up additional areas. The potential impacts of future restoration should focus on lower mainstem Lemhi restoration efforts to improve conditions for rearing and overwinter survival.
  • Predictions showed the greatest population changes are influenced by a combination of improved conditions for rearing and spawning.
  •  Currently there are only a few potential areas that Chinook adults can access; however, water quality (Big Springs, lower mainstem Lemhi), channelization (lower mainstem Lemhi) and the lack of hydraulic connection (Texas Creek) preclude additional production from spawners.