Juvenile Salmonid Use of Thermal Refuges in the Klamath River 2016

Salmonid Research, Monitoring, and Evaluation (RM&E)

Monitoring Research
Project IDYUROK-2015-6
Recovery DomainsN CA - S Oregon
Start Date06/01/2016
End Date09/30/2017
Last Edited05/08/2024
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Snorkel surveys were conducted on a weekly basis at five to seven different tributary confluence areas on the lower Klamath River between river kilometer (rkm) 26 and rkm 80 to enumerate the number of juvenile salmonids using associated thermal refugia areas.. We also used these funds to monitor adult salmonids (Chinook and steelhead) that were using thermal refugia in the Klamath River. We deployed our PIT tag antennae array at the Cappell Creek thermal refugia for a limited time on a trial basis. We also tagged a number of fish that were using said refugia. Data generated from this project was used in near real time by river managers to assess disease conditions on the lower Klamath River. The majority of this work took place in 2016, a small percentage was undertaken in 2017.

Project Benefit    

Recent research in the Klamath Basin, indicates that both summer and winter refuges associated with the lower reaches of Klamath tributaries are critical for the survival of juvenile salmonids, and in particular, juvenile coho. Fisheries surveys have identified consistently high numbers of juvenile salmonids in habitats that function both as summer and winter refugia. The Yurok Tribe has conducted direct snorkel observation of thermal refuges sites for fifteen years, and has an extensive data set on the location and usage of these areas.

In this project, the Yurok Tribe proposes to conduct a study that ascertains a much more comprehensive picture of thermal refugia use on the Klamath River. Data collected will add further detail to the multitude of snorkel observations already contained in the Tribe’s data set. We will capture (via seine netting operations) numerous juvenile salmonids at various thermal refuges or closely situated riverine habitats. Captured fish will be injected with Passive Integrated Transponders (PIT Tags) and released. Various thermal refuges will be equipped PIT tag antennae listening arrays which will detect tagged fish as they enter and exit the thermal refugia. This information will allow us to establish exactly how long juvenile salmonids are using these thermal refuges, how they interact with the river while in the refugia, and the migrational timing and relationships between different thermal refuges. These listening stations would also have the ability to detect any PIT tagged fish from other studies within the Klamth River Basin including the ongoing study looking at the migration of juvenile ESA-listed SONCC coho salmon.

All data collected can be compared to a range of environmental and biological river conditions. Temperature is probably the leading factor regarding salmonid thermal refugia use however other aspects of water quality may be involved. One very important biological aspect of Klamath River ecology is related to the Myxozoan parasite (Ceratomyxa Shasta) C. Shasta. This disease kills numerous juvenile salmonids in the Klamath River each year. Juvenile salmonids may be inadvertently using thermal refuges as a refuge from this river borne pathogen as well. There are a number of ongoing studies looking at various aspects of the life history of C. Shasta. Klamath River water and juvenile salmonids are constantly being tested for the presence of the disease during summer months. Data collected from this study could be used to augment any ongoing C. Shasta studies as well as any C. Shasta modeling projects.

PCSRF Goals, Objectives addressed:
This project will enable the Yurok Tribe to participate in the development of scientific information that will be used to affect water management on two important tributaries to the Klamath River; the Shasta and Scott Rivers.

Outcomes & Benefits
• Ascertain the length of time juvenile salmonids are holding in thermal refuges.
• Establish how these tagged fish interact with the river while holding in the thermal refuges.
• Gain a better understanding of the migrational timing between different thermal refuges.
• Determine any relationships between study results and river conditions.


Metric Completed Originally
Research and Monitoring
  Stream Miles Monitored 44.00

Funding Details

Report Total:$27,000

Project Map



  • Worksite Identifier: 6003
  • Start Date: 06/01/2016
  • End Date: 09/30/2017
Area Description

No Area Description data was found for this worksite.

Location Information

  • Basin: Klamath (180102)
  • Subbasin:
  • Watershed:
  • Subwatershed:
  • State: California
  • Recovery Domain: N CA - S Oregon
  • Latitude: 41.26104589588896
  • Longitude: -123.78054495239056


  • Southern Oregon / Northern California Coastal Chinook Salmon ESU
  • Southern Oregon/Northern California Coast Coho Salmon ESU
  • Klamath Mountains Province Steelhead DPS




  • E.0 Salmonid Research, Monitoring, and Evaluation (RM&E)Y (Y/N)
    •      . . E.0.a RM&E Funding 27,000.00
    •      . . E.0.b
      Complement habitat restoration project
    •      . . E.0.c
      Project identified in a plan or watershed assessment.
    •      . . E.0.d.1 Number of Cooperating Organizations 0
    •      . . E.0.d.2
      Name Of Cooperating Organizations.
    •      . . E.0.e.1 Number of reports prepared 0
    •      . . E.0.e.2
      Name Of Report
      Salmonid use of Thermal Refugia in the Klamath River
    •      . . E.1 MonitoringY (Y/N)
      •      . . . . E.1.a Monitoring funding 27,000.00
      •      . . . . E.1.b.1 Stream Miles Monitored 44.00
      •      . . . . E.1.b.2 Acres of Watershed Area Monitored 510,000.0
      •      . . . . E.1.c.1 Adult salmonid population monitoringY (Y/N)
        •      . . . . . . E.1.c.1.a # miles (to nearest 0.01 mile) monitored for adult salmonids 44.00
      •      . . . . E.1.c.2 Salmonid smolt or fry monitoringY (Y/N)
        •      . . . . . . E.1.c.2.a # miles (to nearest 0.01 mile) monitored for Salmonid smolt or fry 44.00
        •      . . . . E.1.d
          Name Of Comprehensive Monitoring Strategy/Program
      •      . . E.2 ResearchY (Y/N)
        •      . . . . E.2.a Research Funding .00
        •      . . . . E.2.b.6 Wild salmonid tagging/marking studyY (Y/N)
          •      . . . . . . E.2.b.6.a
            Key issues addressed by wild salmon tagging/marking study
            We would like to ascertain how long juvenile chinook salmon are using thermal refugias. This is being done on a pilot basis.
          •      . . . . . . E.2.b.6.b Number by species of wild salmonids tagged/marked (LOV)