by Matthew Kaylor (CRTFC) and Evan Booher (ODFW)

MFIMW partners including Oregon State University (OSU), Oregon Department of Fish and Wildlife (ODFW), the Columbia River Inter-Tribal Fish Commission (CRITFC), and the Confederated Tribes of Warm Springs (CTWS) are investigating when Chinook Salmon fry leave spawning gravels (emergence) across the Middle Fork John Day River (MFJD). This is important to evaluate because emergence timing determines the conditions fish first experience (temperature, food availability, flow, habitat accessibility) and the amount of time fish have to grow. Differences in emergence timing across the watershed may translate to differing experiences in growth and survival as well as differences in their ability to access floodplain habitat.

Staff from the Oregon Department of Fish and Wildlife sampling for Chinook Salmon fry in inundated floodplain areas of the Middle Fork John Day River.

Researchers first modeled emergence timing throughout the MFJD using data on the timing of spawning and water temperature. They found that emergence was earliest upstream near Bates State Park and was progressively later downstream. This is the opposite pattern of what they found for other NE Oregon rivers in the Grande Ronde River basin, and may be attributed to upstream groundwater inputs which are warmer in winter compared to colder surface water. To evaluate these predictions, ODFW and CTWS began capturing fry at multiple locations along an upstream to downstream gradient throughout the MFJD during spring 2021. They sampled fry at these locations every week from March through May and will examine the size of fish over time to determine when peak emergence occurred, which will then be compared to modeled predictions. Lastly, in collaboration with the National Oceanic and Atmospheric Administration (NOAA), researchers are modeling when and where floodplains are flooded across the MFJD using historical flow records and satellite imagery. Floodplains provide important habitat to juvenile salmon by providing abundant prey and refuge during high flows. The researchers are determining when fish emerge relative to when floodplains are flooded to determine how fish may use these habitats, and where floodplain restoration may be most impactful for juvenile Chinook Salmon.

Chinook Salmon fry captured in the Middle Fork John Day River to evaluate emergence timing from nests.
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Inundated floodplain in a restoration area of the Middle Fork John Day River during early spring runoff in 2021. Floodplains are important habitat during the early life stage of juvenile salmon, providing refuge during high flows, abundant prey, and thermal conditions conducive for fish growth.

by Matthew Kaylor (CRTFC) and Evan Booher (ODFW)
      
Once the warm temperatures and low flow conditions of summer arrive, juvenile Chinook Salmon hunker down and move little until flows increase in the fall. However, we know little about movement in spring because fish are too small to mark with PIT tags and challenging to capture as high flows make sampling inefficient. It is important to determine patterns of fish movement during this early-life period because it sets the stage for where juveniles spend the critical summer period. This information can provide guidance for prioritizing and locating restoration projects to maximize juvenile salmon use.
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Using genetics as a tracer, MFIMW partners including Oregon State University (OSU), Oregon Department of Fish and Wildlife (ODFW), the Columbia River Inter-Tribal Fish Commission (CRITFC), and the Confederated Tribes of Warm Springs (CTWS) are quantifying movement from redds (salmon nests) to summer rearing habitats in the Middle Fork John Day River (MFJD). In September of 2020, genetic samples were obtained from 111 adult salmon after they spawned, which represented roughly a third of the spawning population. In addition, the location of each fish was recorded. During the summer 2021, the offspring of these adults will be captured from locations throughout the MFJD and fin clips will be collected for genetic analysis. Sampled juveniles can then be matched to previously sampled parents through genetic parentage analysis, which then provides a location of where juveniles originated. The project will occur over an additional year (adults from 2021; juveniles from 2022), with a greater focus on sampling Chinook fry from floodplain habitats to determine dispersal patterns shortly after they emerge from redds.

​The Chinook Salmon life cycle comes full circle in streams and rivers of the Columbia River basin. The locations at which adult Chinook Salmon spawn and ultimately perish (left) could play an important role in determining habitat use of the next generation of juvenile Chinook Salmon (right). 

By Evan Booher

​In August, 2020 ODFW staff installed a new type of fish detection antenna at a site on the Middle Fork John Day River (MFJDR) near Ritter, OR. These new antennas, designed by ODFW employees, are made of loops of low-power electrical wire encased in PEX plumbing tubing. Their low profile will enhance their durability during flood and ice events that often damage previous designs. The antennas detect fish that were tagged with passive integrated transponder (PIT), radio frequency tags when they were either juveniles in the river or as adults at Columbia River Dams. This detection site will provide valuable information for counting and estimating survival of salmon and steelhead benefitting from the restoration work being implemented in the John Day River. This site is also part of the Middle Fork John Day River, Intensively Monitored Watershed (IMW) and complements other data being collected to monitor salmon and steelhead. Multiple interrogation sites will allow managers to estimate the return of adult chinook and steelhead prior to spawning and estimates derived from these monitoring efforts provide real information for tracking the recovery of these populations.

Patterns in the movement and survival of threatened salmon and steelhead stocks are essential information for their management in Oregon watersheds. PIT tags are widely used throughout the Columbia River basin to assess these population characteristics by multiple fishery agencies and these data are stored in a centralized database: the PIT Tag Information system (PTAGIS). Detections of PIT-tagged fish at Columbia River dams and throughout the Pacific Northwest, are used to monitor migrating salmon at multiple stages of their life cycle. This data is used as a standard for adult performance in NOAA’s Biological Opinion for the recovery of federally-listed salmon and steelhead in the Columbia and Snake River basins.

By Kasey Bliesner

​MFIMW partners recently completed Phase II of the Vincent to Caribou habitatdisrupted natural channel migration patterns, were removed.

To improve and increase more natural instream fish habitat, some of the The project installed or placed 700 cubic yards of gravel, and added roughly 600 trees across 80+ structures. 20 pilot channels were also excavated to better allow the river to access the flood plain during high flow events. For this project, CTWS employed innovative, low cost, low impact methods to place and anchor these large wood structures, replacing the more invasive practice of burying portions of the wood in streams banks for anchoring. Burying portions of the wood in stream banks isn’t natural, is slow and expensive, creates a lot of turbidity, and exposes disturbed ground to weeds and erosion. With the Phase II methods, most wood is simply placed on the ground without excavation (as natural tree-falls would occur), and wood structures are stabilized with posts. These posts are intended to stabilize wood structures in the short-term, while allowing for more natural large-wood movement and function processes in the long-term.

This project also consists of several riparian enhancement elements. Several studies performed throughout the MFIMW over the last 12 years have identified elevated summer stream temperature as the largest factor limiting productivity of salmonids in the Middle Fork John Day River, and that this factor is mostly facilitated through solar exposure due to lack of shade relief from riparian vegetation (See Shading Out Climate Change: Planting Streamside Forests to Keep Salmon Cool). In effort to improve riparian condition and function, CTWS will be installing three riparian vegetation enclosures to protect over 55 acres of riparian area, as well as planting approximately 3,000 sedges and over 4,000 woody species such as Cottonwood, Alder and Willow in 2020. The lead for this project is the Confederated Tribes of Warm Springs and partners include the Bureau of Reclamation, Bonneville Power Administration, Pacific Coastal Salmon Recovery Fund (NOAA), and Oregon Watershed Enhancement Board.

High stream temperatures in the Middle Fork John Day continue to be a limiting factor for salmon and steelhead. Research into keys factors for reducing stream temperature in the Middle Fork John Day IMW area led by Steve Wondzell (research ecologist, USFS PNW Research Station) was recently highlighted in the June 2020 edition of the USFS PNW Research Station publication PNW Science Findings. Wondzell and his team used water temperature modeling to study and predict how stream temperatures could change in response to future changes in air temperature, stream discharge, and the amount of shade provided by riparian vegetation.  Modeling results showed “the effect of restoring riparian forests on streams where shade is currently lacking could be so large that future stream temperatures could be colder than today, even under a warmer climate with substantially lower late summer streamflow.”

Follow this link to read more…

By Kasey Bliesner

In the initial 10-year period (2008-2017) of the MFIMW, over 100 active and passive restoration projects of varying size and scope were implemented. 20 organizations participated in monitoring activities resulting in over 14 scientific reports. A comprehensive Final Summary Report synthesized results and represents 10 years of work by agencies, organizations and individuals conducting restoration, research, and monitoring activities. In order to quickly share results of the report with restoration practitioners, the MFIMW workgroup recently produced a fact sheet distilling findings. It features the MFIMIW’s goals, key findings and lessons learned from 10 years of paired restoration and monitoring. The fact sheet is available in two formats:

1. a two-page 11x17 PDF or
2. a four-page fold-over 8.5x11 PDF

By Emily Davis

After ten years of hard work, the Middle Fork IMW Working Group is celebrating the completion of its Final Summary Report. 

The Final Summary Report summarizes data collected from 2008 to 2016. This report represents 10 years of work by numerous agencies, organizations and individuals conducting restoration, research, and monitoring activities in the upper Middle Fork John Day River. Each principal investigator and their co-authors wrote a final report, which represents the culmination of their research and monitoring. The reports were compiled, along with pertinent background information, into this final Summary Report. An extensive overview of MFIMW activities, key findings, and recommendations can be found in the Executive Summary.

 For full details about a specific monitoring project including methods, analyses and results, readers can refer to Appendices B-M, which are compiled in a separate document. Links, bookmarks, and navigation have been provided, where possible, to ease in viewing this document electronically.

Final Summary Report

Access the Appendices

More is in store for the Middle Fork IMW in 2018. Be sure to check back for additional news items, and meanwhile, enjoy perusing the Summary Report! 

By Emily Davis
 
The summer of 2016 was a chaotic one at Oxbow Conservation Area. Excavators, fencing crews, scientists, and Tribal staff all hurried to finish the last phase of the five-year Oxbow Mine Tailings Restoration Project before season’s end. Amid the hustle and bustle, you might have observed something a little different: two women with microphones and film cameras, dodging in and out of the hubbub to get the best shot, or herding someone away from the racket for a quiet interview in a meadow.
 
The two filmmakers were Michelle Alvarado and Jen Rule, who make up two-thirds of the talented Bend-based company Wahoo Films. Their short film Náimuni: Connecting Oxbow Conservation Area celebrates the completion of one of the biggest river restoration projects ever to take place in the State of Oregon. Along the way, the film explores the history of the upper Middle Fork John Day River, and its journey from damaged dredge-mined ditch to thriving salmon stream via the lengthy restoration process.  The theme of connection is woven throughout— as heavy equipment works to reconnect the river to its floodplain, we see how improving salmon habitat will also benefit the myriad other interconnected pieces in the ecosystem. ‘Náimuni’ means ‘connecting’ in Ichishkíin, one of the languages of the Confederated Tribes of Warm Springs, who own the conservation area and led the restoration effort.
 
Enjoy—and for more information on the project or to see past films exploring different aspects of this restoration effort, be sure to visit our video gallery, read more in-depth articles, visit the Warm Springs’ Fisheries web site, or come visit the Oxbow yourself!

By Emily Davis
 
Below the surface of the water, there’s a whole other world wriggling and crawling in the sand, mud, and gravels of the riverbottom. Fly-fishermen have known for years that learning the secrets of stream creepy-crawlies gives a great return on investment when it comes to catching fish. As it turns out, studying these water-dwellers is useful for more than just tying great flies. It’s also an effective strategy for tracking the progress of watershed restoration.
 
These stream “bugs”—known as aquatic macroinvertebrates to those who study them—can tell us a lot about the health of our streams, rivers, and lakes. ‘Macroinvertebrate’ refers to an animal that’s big enough to see without a microscope (‘macro’) and lacks a backbone (‘invertebrate’), and can include many categories of what are colloquially called “bugs”. The term ‘aquatic macroinvertebrate’ actually includes a variety of aquatic animals like snails, clams, and worms, in addition to insects like mayflies, caddisflies, and midges.

Because macroinvertebrates are sensitive to stream conditions like water temperature, pollutants, and sediment, we can use them as a barometer for water quality. Keeping tabs on abundance and diversity of macroinvertebrates is important for helping the Middle Fork’s juvenile salmon and steelhead thrive, because they are the main food source for these fish—along with other animals like lamprey, mink, otters, and so on. Tracking which groups of macroinvertebrates are present also help us track changes in stream habitat after restoration projects are completed. For example, if a project planted lots of streamside trees and shrubs to help shade the stream, over time we might see more cold-loving macroinvertebrates moving in to the neighborhood.
 
Justin Rowell, Public Lands Project Coordinator for the North Fork John Day Watershed Council (NFJDWC) explains further: “The various bugs each have a survivability threshold which means if we begin to not find certain bugs, or other bugs start moving in, then we know that stream conditions are changing. Or we can ID reaches that are in need of restoration compared to others.”
 
Rowell and his colleagues at the NFJDWC, based in Long Creek, OR, are well-acquainted with the secret riverbottom world of aquatic macroinvertebrates and why it matters for stream restoration. As part of their work for the Middle Fork John Day Intensively Monitored Watershed (MFJD IMW), Watershed Council staff travel around the Middle Fork John Day watershed collecting macroinvertebrate samples.
 
NFJDWC staff use two methods to collect aquatic macroinvertebrates: drift nets and benthic samples. A drift net is a net staked in the middle of the water column to catch whatever is floating downstream on the current—the random bits and pieces of debris that scientists call ‘the drift’, which includes both bottom-dwelling macroinvertebrates, and land-dwelling (terrestrial) ones that have fallen into the stream.

What does the Watershed Council collect? “Bugs we collect vary,” says Rowell, but “we expect to see a lot of caddisflies—which locals usually call periwinkles—stoneflies, dragonflies, various worms, crayfish, and others. We also find what we call 'water pennies' which are pretty neat little creatures.”
 
After samples are taken, they are sent to a lab where professionals identify the contents. Once samples have been processed, other scientists, from university researchers to Oregon Department of Fish and Wildlife biologists, can use the data to help answer questions about watershed health, stream restoration and fish populations.  
 
What does the data from the Watershed Council’s aquatic macroinvertebrate monitoring tell us about how stream restoration is changing the Middle Fork watershed? Stay tuned for results!

By Emily Davis

Have you heard? After five years and as many project phases, the Oxbow Mine Tailings Restoration Project is finally complete! This ambitious project  on the Oxbow Conservation Area sought to restore a large area of the Middle Fork John Day River severely damaged by gold dredging in the 1940s. Project leaders from the Confederated Tribes of Warm Springs worked together with partner US Bureau of Reclamation to re-meander the river, reconnect it to the floodplain, restore habitat complexity such as side channels, and plant native riparian vegetation.
 
See photos and read more about the project on the Warm Springs Fisheries website:
http://wsfish.org/2016/12/31/oxbow-restoration-project/
 
If you’re local, you may also want to come out to the Middle Fork and see the project for yourself! The restored area is visible along County Road 20, but for a closer look, the Oxbow Conservation Area is open to the public. Directions and more information are here.