Trinity River Animal Spotlight – February

Freshwater Mussels in the Trinity River

Freshwater mussels are considered to be one of the most sensitive and threatened aquatic species within Northwestern watersheds. In North America, there are 297 known freshwater mussel species. Nearly three-quarters of these are considered imperiled, and more than 35 species have gone extinct in the last century. Eight species are known to exist west of the Continental Divide. Mussels have a fascinating life history strategy, which involves parasitizing on fish during their larval stage, and can live to be over 100 years old. They are considered an indicator species, like the good ole canary in a coal mine, as they require pristine water quality to thrive.

Photo Credit: Western pearlshell Mussel photo by Roger Tabor USFWS

Life History, Strategy and Anatomy

To the unknowing eye, freshwater mussels look very similar to saltwater mussels as they are both bivalves, meaning they have 2 shells connected with a hinge. They are also both filter feeders and both belong to the class Bivalvia in the phylum Mollusca. Despite being named and shaped similarly, saltwater mussels, are however more closely related to oysters and scallops than they are to freshwater mussels, and thus have developed different evolutionary strategies. Saltwater mussels use a byssus thread to attach themselves to underwater structures, while freshwater mussels use a foot to move short distances and bury themselves. There are also differences in their sexual reproduction strategies. Saltwater mussels reproduce by ejecting the sperm and the eggs into the water column, where they fertilize and develop. With freshwater mussels, on the other hand, the sperm is ejected into the water column and inhaled by a female mussel downstream. The egg is then fertilized within a special part of the female mussel’s gills, and she exhales the baby mussels (called glochidia) after they are developed.

All freshwater mussels have:

  • a hinge, which connects the two shells
  • a raised, rounded area along the dorsal edge called, a beak
  • a foot used for motion and feeding
  • a thin sheet of tissue that envelopes the body within the shell, called a mantle
  • and inhalant/exhalant features along said mantle

Some mussels have pseudocardinal teeth, which are short, stout structures below the beak. There are many more features with very technical names, but these are the most useful anatomical structures for identification in our region.

Western pearlshell mussel (Margaritifera falcata)

In the Trinity River, there is one confirmed species of freshwater mussel – the Western pearlshell mussel (Margaritifera falcata), which have very prominent pseudocardinal teeth. The Klamath River has also documented populations of the Western ridged mussel (Gonidia angulata), which have an obvious ridge on the outside of the shell, and floaters (Anodonta spp.) which are small and have neither teeth nor ridges.

Check out this article from the Mid-Klamath Watershed Council to learn more about Klamath’s freshwater mussels.

Photo Credit: Klamath River mussel bed above Rock Creek on 7-5-18. Mid-Klamath Watershed Council.

Western pearlshell mussels are known as being the longest-lived and slowest-growing mussel species in North America. In fact, they are the oldest freshwater invertebrates in the world. Their age can be estimated by counting the growth rings on their shells, similar to the growth rings on trees. The black, concentric rings are thought to represent winter rest periods. Some Western pearlshells have been documented to live over 100 years, meaning that some of these mollusks may have been in our river since it was buzzing with dredgers and mining activity in the early 1900s.

Western pearlshell mussels. Akimi King/USFWS

The foot on freshwater mussels aids in movement, but mussels are still very limited in their ability to transport throughout a stream. In order to colonize different parts of a river system, particularly upstream, after being released by the female as described below, the larvae (called glochidia) attach to fish passing by becoming parasitic. In the case of the Western pearlshell, the glochidia are released into the water where they clamp onto the gills of salmonids (particularly chinook salmon and steelhead) to hitch a ride upstream. After a short period (typically between a week and a month), the glochidia drop off into existing mussel beds (see the diagram borrowed from the Mid-Klamath Watershed Council).

Similar to salmonid migration, in which the salmon return to their natal stream, mussels can identify ideal locations to drop from their host and landing in existing beds of freshwater mussels. This life stage is one of the most fascinating aspects of this species. Originally the larval stage mussels were thought to be an entirely different parasitic invertebrate species yet scientists recently realized they are actually freshwater mussels in an immature life phase. Other species of mussels may parasitize different parts of their host fish, with some sending worm-like tendrils into the fish’s gills to sap vital resources. However, it is not thought that the mussels have a significant impact on the health of their host fish.

Pearlshell species can release their glochidia in aggregates, called conglutinates, which are bound by mucus. They seem to reproduce in spring and summer, though few studies have been conducted on the life cycle of our Western pearlshells. Though there is no scientifically defined relationship between water temperature and spawning (due to a lack of study), it has been observed in a study conducted in the state of Washington that mussels in warmer waters spawn earlier than those in cooler waters.

An example of conglutinates containing mussel larvae being released out of mussel gill. Credit: Rachel Mair U.S. Fish and Wildlife Service Northeast Region

Ecological Benefits

Freshwater mussels have many benefits to stream ecology and have a major influence on the aquatic food web. They are filter feeders and they have separate orifices for inhaling and exhaling, which is how they derive nutrients. They filter tiny, suspended particles, including sediment, algae, bacteria and zooplankton out of the water column. Some of these particles are bound to larger particles within the mussels and expelled, where they sink to the bottom and feed benthic macroinvertebrates. Individuals in some species of freshwater mussels can filter up to 15 gallons of water per day, reducing turbidity and improving water quality. This cycling of nutrients also supports the growth of emergent plants, fostering a riparian habitat that benefits salmonids, which mussels are dependent upon. To be cliché, it’s all connected.

An example of a high-density freshwater mussel bed in the Trinity River near Junction City.

Freshwater mussels also help increase the exchange of nutrients, including oxygen, between sediments and the water column, in a similar mechanism to earthworms in the soil. They increase sediment porosity and allow the sediment to retain more organic matter. This ultimately improves the quality of aquatic habitat, allowing for a higher diversity of benthic macroinvertebrates.

Though not known for being a delicious treat to humans, mussels are an important food source for otters, raccoons and skunks. Healthy mussel populations are unaffected by natural predation, but low populations may be at risk of extirpation, and overly high populations may encourage excessive predator populations.

Trinity River Mussel Surveys and Conservation

In 2020, the Bureau of Land Management conducted a qualitative study of freshwater mussels on the Trinity River. A crew surveyed the upper 40 miles below Lewiston Dam and identified mussel beds as high, medium, and low density, and marked their locations on a map. This effort helps inform necessary conservation actions on project sites. If a mussel bed is known to be directly or indirectly affected from restoration activities, the Best Management Practice is to relocate a percentage of the population to an existing mussel bed upstream of their current location.

Mussels were relocated from a TRRP project in 2017 to an existing mussel bed. The green tags are for monitoring relocation success.

Relocation of freshwater mussels can be a tricky business. The species are incredibly sensitive to temperature and water quality conditions, so efforts must be conducted with efficiency and special care. It’s important to avoid moving mussels during certain times of the year when they are the most sensitive, which is when they are in their reproductive stages between December and July.

Mussels being tagged as part of a relocation effort on a TRRP construction site in 2017

The long lived and sensitive nature of freshwater mussels is one reason it’s important to manage the Trinity River for long term impacts. Since mussels cannot move quickly to escape suboptimal conditions, their population fluctuations can reflect cumulative effects of environmental conditions, so studying and understanding freshwater mussels can be indicative of some aspects of riverine health. Despite being rather uncharismatic and tremendously understudied, the role that freshwater mussels play within aquatic ecosystems is invaluable.


Veronica Yates, Riparian Ecologist

Hoopa Valley Tribal Fisheries Department, Weaverville

Featured Article – Sediment, the Building Blocks of the Trinity River

When you go down to the river, it’s hard to ignore the assortment of sediment on the bed and banks – from sand and silt, to gravel, to larger cobbles, to the largest of boulders. Seeing rocks that contrast so strongly with the rough, jagged ones in the surrounding hills might beg the question – how did these get here, where did they come from, and how long ago did they arrive?

Photo: Riparian area along the Trinity River above Trinity Reservoir showing an assortment of sediment, vegetation and large wood. [TRRP]

If a rock is rounded, more likely than not [1] it was transported by the river in a series of floods, originated from higher up in the watershed. Depending on the size these rocks may have arrived recently – perhaps as recently as the last flood. Large, rounded boulders that appear to be too large to have been rolled down the river on their own may have been in place since the last natural 100-year or 500-year flood and may remain there forever, or at least as long as Trinity and Lewiston dams are in place.

[1] Gold miners washed much sediment into Trinity River valleys from ancient riverbeds created from tectonic lifting that are presently high up on mountain slopes.

A river’s function

Besides the ecological benefits that rivers provide us, they have two pivotal functions in nature – to move water and to move sediment from the mountains to the ocean (the process is illustrated below). As both water and sediment flow downstream, they interact with each other to create a mosaic of pools, riffles, runs, islands, meanders, bars, and all of the other physical features that draw people, plants, and animals to a river.

“Conveyor Belt” conceptual model of sediment transport. Rivers move water and sediment from the mountains to the sea.

The Trinity Watershed is situated in a relatively young, steep, and highly erodible mountain range, and is therefore blessed with a plentiful supply of sediment. A healthy sediment supply is beneficial to fish, invertebrates, and floodplain vegetation. However, due to the placement of two dams in the Trinity River’s upper watershed an important element of restoration is giving gravel to the system below a dam since the river’s natural sediment supply is blocked. We know rivers below dams need a replenished sediment supply, however, a key question that geomorphologists continue to study is how much sediment, and what size distribution of sediment should be added? These factors are difficult to determine and are constantly being re-evaluated as part of our adaptive management program.

How we calculate amounts for placement

Gravel augmentations to the river are first determined using a defined sediment budget specific to the Trinity. Also, at some point below most dams, a river’s tributaries provide a sufficient supply of sediment to support the physical processes and biologic populations in the river. On the Trinity, that point is considered to be just below the junction of Indian Creek. In years past, during floods, the amount of sediment moving along the bottom of the river (called ‘bedload’) was directly measured with large strainers placed on the riverbed. Data obtained from the strainer monitoring station have indicated that minor floods may move 2,000-3,000 tons of bedload (the monitoring station that is nearest to Indian Creek is located just upstream of Douglas City campground). At this same location, larger floods may move 15,000-30,000 tons of bedload past the monitoring station. The Trinity Record of decision provided the program with a framework of how much sediment should be applied to the river below the dam with the expectation that geomorphologists study current conditions through time and then adapt management based on results found.

After many years of physically sampling bedloads, program scientists switched to a more efficient and safer technique called acoustical monitoring. This method uses underwater microphones to quantify the amount of sediment during floods by measuring the amount of noise generated by rocks rolling on the bed. The physical data collected from the past is then compared to the measured volume of noise and produces a calculated volume of sediment rolling past. Scientists then scale annual sediment augmentation projects to these measured amounts. Additionally, the riverbed is periodically surveyed below sediment augmentation sites to determine whether the effects of placements are positive or negative. If too much sediment is noted, this information is used to scale back future sediment augmentation plans. If you were to compare the original amounts of sediment proposed in the Trinity Record of Decision to what we add today, ROD volumes were 2-3 times higher!

Above Photo: a 2023 gravel augmentation site pictured prior to high flow. Right Photo: the same site pictured after the gravel was dispersed by high flow.

Size matters

As for size, the high end of the size distribution of sediments is the grain diameter that salmon can move to construct redds, or nests in which they place their eggs for incubation. Salmon can spawn in gravels with a median diameter up to about 10% of their body length. This leads to gravel being placed in the river that was filtered through a 4-inch screen. The lower end of the size distribution of sediment for redd building is considered to be in the size range of small gravel, and so the sediment mixtures for placement in the river are also screened to remove sand and silt. If the sediment is too small, it just flushes all the way down the river during floods and doesn’t remain to provide any benefits. If the sediment is too large, it stays close to the augmentation site and causes the riverbed to become coarser there. The need for small to large gravels for placement makes considering the size distribution between these end points important. Too many small gravels make the riverbed overly mobile and easy to scour, which endangers salmon eggs incubating in the bed. However, a grain-size distribution that is skewed towards larger particles makes the riverbed too stable, so that salmon are unable to move the sediment when attempting to construct a redd. These considerations make the size class of sediment another subject of adaptive management, and over time TRRP has reduced the size of sediment that is added to the river. Studies have also pointed toward ways that coarse sediments (gravel and cobble) interact with fine sediment (sand and silt), and restoring a natural balance of these grain sizes is an objective of the sediment augmentation program at the TRRP.  In the future you may hear of sediment with a more natural size distribution (e.g., “bank run material”) being used in sediment augmentation projects.

Salmon spawning in gravel in the Trinity River.

Filling deep pools

When you observe a river during typical baseflows, pools are calm while riffles are noisy, turbulent and swift. From an above water view, its natural to think that sediments would settle from these active riffles to its calmer neighboring pools. During low flow, if you look underwater, the river only has the power to move finer sediments, like sand and silt. Conversely, coarse sediment, such as gravel and cobble move only when the hydrology of the river is powerful with high flow or flooding.

When rivers flood, we see something that river scientists call a “flow reversal”. Flow reversal is when deep pools transition into a high-energy environment where flow velocity is more vigorous than on riffles. In this instance water meets the pool (and its surrounding environment, like bedrock) with force and activates sediments of different sizes within the pool. These sediments are “scoured” from the pool and placed on the riffle below it typically expanding a pool’s depth and also building the riffle below. Next time during a high flow, check out the way a pool churns and take note to notice the way water interacts with the riffle that lye underneath. During high discharges, flows on riffles are comparatively slow because the surface is not as deep. This interaction causes the water to “feel” the bed and slow due to its rough texture. These interactions cause sediment to deposit on riffles and scour from pools during high flows. The size of sediments that move are directly correlated to the amount of water flowing down the river and these events are the force behind building the riffles and pools of the Trinity River.

Dave Gaeuman, Senior Geomorphologist for the Yurok Tribe talks about the importance of variable flows and and how sediment transports from riffles to pools

TRRP sediment augmentation projects have sometimes been thought to contribute to the filling of deep pools in the river and there have been cases where pool depths have decreased in areas that the TRRP has worked to restore the river. However, TRRP studies have shown that this tends to occur where stream power decreases in the channel from lowering the elevation of adjacent floodplains and vegetation, which causes the flow to spread out instead of concentrate in the channel. In many areas of the Trinity River, lowering floodplains is necessary to reconnect them with the river during floods for the benefit of the fish, wildlife and plants that live there. This conundrum is another subject of adaptive management, and TRRP often avoids actions that would have a strong likelihood of affecting pool depths so that holding habitat for over-summering fish such as spring-run Chinook salmon remains available.  

The next time you visit the Trinity River, take a close look at the sediments that you see. Depending on the time of year, you may see salmon redds constructed of gravels.  You will also most likely find aquatic invertebrates and biofilm living on the gravel and cobbles surfaces. Dig into a sand and silt deposit along the channel margins and you might find juvenile lamprey wriggling around in these materials. You will certainly see how sediment forms the shape of the river. And hopefully you’ll come away with a greater appreciation of sediments that are the building blocks of the Trinity River!

Trinity River Plant Spotlight – January

Water fern (Azolla filiculoides)

There are various native plant species that cover the surface of stagnant or slow-moving water. One of these species is called water fern (Azolla filiculoides). Not to be confused with algae, Azolla is an aquatic vascular plant with a very shallow root system that grows on the water surface rather than in the water column. True to its name, it is a type of fern. Typically, the plant is bright or dark green, making the water appear to be covered in “pond scum”, but this plant is anything but scum. As a stress reaction, Azolla can turn a deep red-amber color, appearing dead or dormant. Despite the discreet and unassuming nature of this unusual plant, it has some mind-blowing properties, including the ability to purify water and fix nitrogen.

Nitrogen is often a limiting nutrient for primary producers because atmospheric nitrogen (N2) is not readily utilized by plants. As a result, many plants (such as those in the pea family, Fabaceae) have evolved the ability to “fix” nitrogen by converting it to an accessible form of nitrogen (NH4+). Some plants do this with the help of bacterial partners, as is the case with red alder (Alnus rubra) and specific bacteria, which partner to produce root nodules. In return for providing a home, the actinomycetes share some of their usable nitrogen with the red alder. While this activity occurs in the roots of the host plant, excessive nutrients are leaked into the surrounding environment, thus providing bioavailable nitrogen to other plant species and improving soil fertility within the red alder ecosystem. Instead of partnering with a bacteria like red alder does, Azolla has a symbiotic relationship with a cyanobacteria (blue-green algae) species called Anabaena azollae. The Anabaena is housed within the leaves of Azolla, and in return, Azolla receives fixed nitrogen which is ultimately shared with the surrounding environment.

In addition to being able to contribute nutrients to the environment, Azolla has the ability to uptake metals as well as organic and inorganic pollutants from water. This process, known as phytoremediation, can take place via 4 different mechanisms. I’ll exclude the chemistry details here, but the important takeaway is that this little plant can extract toxic pollutants from water. Researchers are investigating the use of this plant in wastewater treatment facilities. There are countless more benefits and potential applications of Azolla to modern human civilization – including the potential to split water molecules and create energy. Azolla is endlessly interesting.

So how does Azolla affect our ecology here along the Trinity River? By covering slower moving bodies of water like ponds and backwater areas, it helps regulate water temperatures and provides habitat for cover-loving species. By the same mechanism, it also decreases habitat for mosquitos. It also serves as a food source for a wide variety of wildlife, from western pond turtles to waterfowl. These properties, combined with the ability to fix nitrogen and remove pollutants from water, make this easily over-looked water fern an important constituent of riparian and aquatic habitats.


Veronica Yates, Riparian Ecologist

Hoopa Valley Tribal Fisheries Department, Weaverville

Featured Article: Algae, Food-Webs, and Flows

Photograph by Thomas Dunklin
Filamentous algae found near Indian Creek, a tributary to the Trinity River. [Thomas Dunklin]

Algae are an important component of a natural river ecosystem.  They photosynthesize, converting light into sugar for usable biological energy that forms the foundation of most foodwebs.  Cold, oligotrophic (nutrient-poor) rivers such as the Trinity are generally not perceived as having a lot of algae.  Back in 2018 a bloom of algae in the ‘restoration reach’ of the Trinity (roughly Lewiston to Helena) raised concerns; the bloom brought greater visibility of algae than we had seen in the Trinity in recent memory. 

For TRRP scientists, those concerns translated to numerous questions.  But questions that should be overlaid on the large body of literature from countless scientific studies done elsewhere.  That literature shows (repeatedly) a number of fundamental patterns: 

  • A broad diversity of algae is natural in cold rivers like the Trinity.
  • Young salmonids feed on small invertebrates that come both from the terrestrial environment and from within the river where algae is a primary food source. 
  • In the river, algae grow primarily on the river bottom (it is “benthic”) while algae suspended in the water column (“planktonic”) is prevented from becoming thick by the swift outflow of the water. 
  • Algae can be scoured from the river bottom during large floods, forming a reset for the benthic environment (what ecologists call a ‘disturbance’). 

Studies by Dr. Mary Power (U.C. Berkeley) and her associates, primarily in the nearby Eel River, had gone further with the studies of disturbance.  They found that while floods scour algae, they also scour some of the larger benthic invertebrates, particularly caddis fly larvae.  Caddis fly larvae consume large amounts of algae and build cases around themselves from wood and sand to prevent fish from eating them. Their studies found that floods are necessary for controlling caddis fly populations so that algae may rebuild, that chironomid larvae (nonbiting midges) then become more abundant, and then young salmon have more food available.

Prior to 2018, TRRP scientists had their hands full with issues higher up the food chain and thus more directly related to salmon production; algae had not been specifically studied within the Trinity restoration reach from an ecological point-of-view.  Questions arose… Was the bloom inappropriate for the Trinity? How much algae ‘ought’ the Trinity have?  Are the types of algae in the Trinity appropriate for producing chironomid larvae and thus fish food?  How does the abundance of algae in the Trinity correspond to natural flows or scheduled dam releases? 

In 2020 I began monitoring algae with a simple method to address these questions while not detracting from the ongoing focus on salmon.  I have been regularly measuring an index of algal abundance based on their visibility in underwater photography.  I have also been sampling the algae in winter and summer to identify the types of algae present.  A report from the first year of sampling is available at A second, multi-year report should be completed in 2024.

An algae monitoring site near Steiner Flat.  Filamentous algae are washing up along the edge of the river while most of the bed has a coating of diatoms.  [Eric Peterson, TRRP/Reclamation]

The algae in our focal reach of the Trinity River can be roughly placed into 3 groups: cyanobacteria (once known as ‘blue-green algae’), filamentous algae, and diatoms. 

Pondlife, Episode #2 – Blue-green Algea (Cyanobacteria)


Cyanobacteria are commonly found in summer and winter; they are a regular component of Trinity algae. This can sound scary at first, as some cyanobacteria produce cyanotoxins that make water dangerous. Calothrix is common in several tributaries where it forms a brownish skin-like covering over rocks, but is not considered dangerous for water quality. Others that can be problematic for water quality if they build up in abundance are found frequently in the river and tributaries.  However, I have only seen them in large quantity once, in standing water of a tributary stream that had essentially stopped flowing and heated up during summer.  Cyanobacteria are known to be most problematic in warm, still water and that seems to fit the Trinity where nuisance blooms have been confirmed in the lower river in relatively still edge-waters and last summer in Lewiston Lake, also with edge waters that can warm substantially.

Cladophora Algae.  [Eric Peterson, TRRP/Reclamation]

Filamentous algae

Filamentous algae (photos to right and at top of page) are generally the most visible, forming long swaths that wave in the current.  The predominant filamentous algae in the Trinity and its tributaries is Cladophora, a type that is well known from many aquatic environments.  While Cladophora is a direct food source for some invertebrates that become food for fish, it also hosts abundant diatoms, which I will get to in a moment.  Other filamentous algae are commonly present as well, although they provide less value for the food-web that supports salmon. Places on the Eel river that have been described as productive for Chinook can have far more algae than I have ever seen in the Trinity River, so blooms like we saw in 2018 may be ecologically healthy even though they look disconcerting to us humans.

. . .

Photo: Cladophora Algae.  [Eric Peterson, TRRP/Reclamation]

A variety of diatoms under a microscope, including Cymbella and Fragilaria.  [Eric Peterson, TRRP/Reclamation]


Diatoms are amazing single-celled algae…  They form cell walls of silica (glass) with intricate patterns that look almost like spirograph art under a microscope, and many are actively mobile!  Some also are capable of capturing nitrogen, making them a particularly valuable food source for invertebrates, which then become a food source for young salmon.  These diatoms tend to have an orange color, so when aging Cladophora looks orange in the river, it actually is becoming covered with nutritious diatoms.  Diatoms also live directly on rocks, where they can build up to form a slippery surface.  When this “scum” of diatoms is removed from a river rock and placed under a microscope, not only is the beauty of those glass cell walls revealed, but also bazillions (OK – not a scientific term) of Chironomid larvae… fish food! 

Chironomid larva living in Cladophora and diatoms. [Eric Peterson, TRRP/Reclamation]

The timing of algae in the Trinity River seems to be in an unnatural state.  Algae tend to build up until a flood scours them away.  Most of my studies have been in critically dry years without out sufficient flooding to remove algae.  Algae may be seen by most people in summer, but have been peaking in abundance in winter… early winter for tributaries, late winter for the river.  However, in 2023 I was able to monitor algae before and after several significant floods. The first scoured algae from tributaries, but only scoured algae in the mainstem river below Canyon Creek (because releases from the dam remained low and the river didn’t flood sufficiently above Canyon Creek).  Where scoured, algae typically redeveloped within my two-month sampling cycle.  Similarly, when floodplains are inundated for several weeks, productive algae communities form.

. . .

Photo: A floodplain in the Junction City area that remained wet for several weeks allowed diatoms (the brownish color on these rocks) to thrive. 

While I lack specific data on the effect on invertebrates (and thus fish food), the pattern corresponded well with the studies by Dr. Power as well as observations from an ongoing invertebrate study being done in the Trinity. Indications are that Trinity and Lewiston dams, which prevent floods in winter, are preventing the ecological disturbance that builds algae communities to feed chironomid larvae for an optimal food supply as young salmon hatch and emerge from gravels.  Traditional ROD flows that don’t flood the river until April leaves an overly mature algae community (and invertebrates) in place while salmon fry emerge, then scours away the algae (the base of the food chain) when young salmon populations are peaking.  A shift in flow management to provide those scouring flows in winter should set the stage for more natural algal growth as well as optimal food supplies for emerging young salmon. 

Dr. Eric Peterson – Data Steward

Eric grew up in Weaverville, hiking in the Trinity Alps and exploring East Weaver Creek. A natural biologist from an early age, he completed a B.S. in biology and botany at Humboldt State University in 1995, and a Ph.D. at Oregon State University in 2000 in plant ecology with a focus on lichens and forestry. Eric worked as the vegetation ecologist for State of Nevada’s Natural Heritage Program for about 8 years, covering all corners of the state and developing techniques for mapping invasive annual grasses with satellite imagery. Eric joined TRRP in 2009 to manage Trinity River data and coordinate its use across the many offices of our partnership but also works with a focus on river ecology and is conducting a study of algae growth in the river and tributaries.

Implementation Branch Update – Jan 2024

With winter fully here and the holidays behind us, the Implementation Branch is moving forward with some exciting restoration proposals.  In recent past the TRRP publicly scoped two proposed channel rehabilitation projects, the Upper Conner Creek Rehabilitation Project in Junction City and the Sawmill Gravel Processing Site Project in Lewiston. A draft environmental assessment (EA) will be released in the coming weeks, and then the Implementation Branch and those involved in the project will host a public meeting to discuss the proposed designs and restoration activities. Keep an eye on our calendar or our facebook page for notification of that meeting. We hope to see you there.

Photos of the two proposed channel rehabilitation sites currently under Environmental Assessment, Upper Conner Creek (left) and Sawmill Gravel Processing Rehabilitation (right).

Proposed Upper Conner Creek rehabilitation project

The proposed Upper Conner Creek project designs were prepared by the Hoopa Valley Tribal Fisheries Department and McBain Associates.  Long term assessment of past restoration work nearby and adaptive management have led program partners to determine that the lowered surfaces of these early projects were not inundating (providing low floodplain habitat) frequently enough.  Improvements in floodplain connectivity to the mainstem, as well as course sediment additions and large wood features will open opportunities for the river to rework its form to provide long-term channel complexity and high-quality salmon habitat.  The recreational aspect of this area is appreciated by many and was an important feature to consider for this project. Through consultation with local residents and river users, project designers have worked to maintain the Junction City Campground’s river access for boating and swimming.  The proposed Upper Conner Creek Project first phase of restoration will begin in the spring of 2024.

Aerial shot of the proposed Upper Conner Creek rehabilitation site [Kenneth DeCamp]
Aerial image of the proposed Sawmill Gravel Processing site. [Ken DeCamp]

Proposed Sawmill Gravel Processing Site Rehabilitation Project

The proposed Sawmill Gravel Processing Site Rehabilitation Project, prepared by the Yurok Tribal Fisheries Department, the California Department of Water Resources, and the California Department of Fish and Wildlife, seek to decommission a portion of a long-used sediment processing site and do so in an ecologically beneficial way.  The proposed project also intends to address a floodplain breach on river right that has dewatered a side channel complex. Repairing this breach will allow adult salmon to spawn throughout the side channel as they have historically. 

Sediment and Wood Augmentation Environmental Assessment

Also working its way through the environmental compliance pathway is the TRRP’s Sediment and Wood Augmentation EA. The EA seeks to establish four new augmentation sites and allows for wood placement at the five existing sites in addition to sediment augmentation to address the sediment and wood deficiency upstream of Indian Creek.  The new augmentation sites are also located in the upper river near Lewiston and include Dark Gulch, Trinity House Gulch, Steel Bridge, and Vitzthum Gulch.  The wood component of the analysis is an exciting addition to the EA.  Wood is critical to a dynamic river system as its benefits include creating fish cover, adding hydraulic complexity, connecting the main river with important fish feeding grounds called floodplains, retaining sediment and aiding a variety of river species by creating more robust habitat. The EA wrapped up its public comment period on November 22 and the public draft is available on 

A rehabilitated side channel and large wood placement at the 2021 Chapman Ranch Rehabilitation site saw adult salmon building redds this past fall. [Todd Buxton, TRRP/Reclamation]

Trinity River Watershed Restoration Programmatic Environmental Assessment

Restoring the lands that surround the Trinity River is an important part of system restoration. [Trinity County Resource Conservation District]

Finally, the TRRP’s Trinity River Watershed Restoration Programmatic Environmental Assessment (PEA) is on track to be completed in 2024. The PEA focuses on improving the quality and quantity of accessible cold-water aquatic habitat throughout the lands which flow to the Trinity River. A goal of the PEA is to encourage more stream and riparian habitat restoration projects by providing National Environmental Policy Act (NEPA) coverage to organizations who propose areas in need of restoration.  

Program Update Jan 2024

Since the foundational 1999 Trinity River Flow Evaluation Report, decades of scientific research have poured into improving outcomes for Salmonids, both from within the Trinity River Basin and from rivers researched across the world. The cumulation of data has made scientists within the Program increasingly aware that shifting how the Program uses restoration flow allocation has the potential to lead to stronger and more resilient juvenile salmonids.

Survey crews monitoring the interaction between high flows and recently restored floodplain on the Trinity River in April of 2023.

Restoration releases continuing through late spring and into the summer keep water colder than optimal for juvenile salmon growth. With size of outmigrating salmon strongly tied to their survival in the ocean, the correlating smaller sized salmon has led scientists to question if a change in management actions would benefit juvenile salmon. Further, Program scientists have figured out that greater than 60% of young chinook salmon have already left the restoration reach by the time spring restoration releases start to interact with restored habitat created by the Program over the last 18 years. River restorationists believe that if floodplains and side channels can get wet when more juvenile salmon are in the upper river to use them, then they can take advantage of all the extra food that those habitats create and if the water meets a range of ideal temperatures for these cold-blooded creatures, they will grow faster.

A partial implementation of an initial proposal to shift a portion of the annual restoration flow allocation earlier in the year occurred in the winter/spring of Water Year 2023 (partial because only elevated baseflows were implemented. The synchronized pulse flow component was not implemented); in September 2023, Program scientists proposed the same action for Water Year 2024 to the Trinity Management Council indicating to the Council that the proposal was the best available science in improving results for salmonids. Unfortunately, the TMC requires near unanimous votes to approve actions and failed to approve that proposal, with six votes in favor and two opposed. However, all was not lost. A group including Trinity County brought in a retired USFWS biologist to review the proposal and findings from the Water Year 2023 and offered to work with program scientists to craft a proposal that was perceived to be less problematic for late winter/early spring river-based recreation and its associated economic benefits. Parties worked together busily behind the scenes, and the revised winter flow proposal will be presented to the TMC at a special meeting on Jan. 18. If approved, modestly increased winter base flows would begin in February.

Trinity River Surveys: Gravel Bar Mapping


Crews have been mapping gravel bars and fine sediment deposits on the Trinity River these past few weeks. The mapping was last done in 2013, and the updated measurements will indicate progress the Program has made in restoring these features on the Trinity River. Prior research on the Trinity River and elsewhere has shown the quantity of habitat for juvenile salmon rearing increases where sediment bars are present in the river – the more bars, the higher the ability for producing salmon. Results of the survey will be published in the coming months.

[Photo Credit: Jeanne McSloy, TRRP/Reclamation]

Gravel Bar Mapping Surveys


During the month-long survey, crews witnessed salmon actively spawning in areas recently rehabilitated by the Program. As shown in the photo to the left, a salmon redd is located where the riverbed is more brightly colored, which happens as a result of when periphyton is removed from river rocks as a salmon builds its nest. This particular redd is located at the lower end of Chapman Ranch, a channel rehabilitation site that was completed in 2021. As the survey crew approached the redd, a male salmon was found guarding the nest. The female salmon was not present and had either completed her spawning at this location and moved on to build another redd elsewhere (salmon sometimes construct several redds in one spawning season) or perished after constructing this one.  Either way, the male was left to guard this nest from other fish that may attempt to construct their nest near enough to this one to damage it. 

[Photo Credit: Todd Buxton, TRRP/Reclamation]

As the mapping work proceeded, the male salmon moved from the redd to a deep area that had scoured around the constructed wood jam shown in the picture (below). The male used the deep water and its overhead wood as protective cover and did not return to guarding the nest until the team moved far enough away for the fish to return to guard duty. 


Wood placement in rehabilitation projects and natural recruitment of logs from adjacent forests is an important element for restoring the Trinity River. Wood provides cover for fish, creates backwater areas for migrating fish, and helps river flows sort sediments for use by species that require mainly gravel (salmon for spawning) or finer sediments (sands for lamprey rearing), or a mixture of both (macroinvertebrates). It gives our team an immense amount of pride witnessing these efforts work in the river and for its inhabitants.

[Photo Credit: Todd Buxton, TRRP/Reclamation]

Trinity River Watershed: Animal Spotlight

The North American Beaver (Castor canadensis) is a true riparian specialist that is fairly common in the mainstem Trinity River below Lewiston Dam. Beavers attracted some of the first European explorers to the Trinity watershed, notably Jedediah Smith, who along with other mountain men traded with local tribes for beaver pelts in the early 1800s.

North American Beaver (Castor canadensis)

The fur trade led to the demise of beavers throughout North America, but they are making a strong comeback following the decline in demand for them. Beavers are still rare in Trinity River tributaries, especially streams draining the high meadows of the Trinity Alps. One of TRRP’s partners, the California Department of Fish and Wildlife, is making a concerted effort to restore beavers because their dam building and other behaviors benefit so many other species ( Perhaps because Lewiston Dam releases are so consistent, beavers do not build dams on the mainstem Trinity River, and in the Klamath Basin they rarely build lodges. Instead, they dig burrows in steep banks along the river.

Photo Credit: US Fish and Wildlife Service National Digital Library

In the wild, beavers can live for 10-12 years and reach weights of over 40 pounds. They like to live in colonies consisting of an adult pair and their offspring from previous years. These colonies tend to be distributed every mile or so along rivers and streams where the habitat quality and connectivity is good.

If you live near the river and are concerned about beavers falling your riverfront trees, it is a good idea to wrap the trunks with chicken wire to discourage beavers from gnawing on them. Otherwise, the work that beavers do is beneficial and appreciated by a wide variety of animals, including Coho salmon, willow flycatchers, deer, and humans.

James Lee, MS – Implementation Branch Chief

James Lee grew up near Redding, Ca, but his heart has always been in The Trinitys, where he chased tadpoles, salmon, deer, and gold nuggets for much of his youth. This love of the outdoors turned into an interest in managing fish, wildlife, water, timber, and other natural resources. 

Flow Variability in the Trinity River

Aaron Martin [Yurok Tribal Fisheries Department]

Imagine a winter storm brewing in the west, clouds accumulating over the mountain peaks dropping a dusting of snow and at lower elevations dripping down as rain. Waters accumulate and funnel toward low points in steep terrain running down stream paths catching sediment, leaves, and branches and delivering them into the tributaries of the Wild and Scenic Trinity River. Depending on the amount of precipitation or snow melt, creeks can daintily deliver cool mountain waters with smaller sediments while larger rain events can powerfully move tree logs and large rocks.

Between 1960 and 2022, when this wild pulse of storm-fed tributaries finally converged with the Trinity River, something peculiar happened; the mainstem did not match the same force of its smaller tributaries. The river’s flatlined flow left debris delivered by the tributaries stacked and settled at their mouths. In the wet winter of 2022-’23, the community witnessed Deadwood Creek deliver a plume of sediment from its wildfire-scarred upper reaches after a significant rain. The plume settled on a large group of salmon redds at the mouth of the creek, and the Trinity River, at its baseline winter flow of 300 cfs, couldn’t mobilize the sediments. The embryos developing in redds at the mouth of the Deadwood Creek likely died by suffocation.

As you are probably aware, the Trinity River has two dams which hold back waters from its upper watershed. In the absence of flow from those tributaries, the river then must rely on two hydrologic sources for river health: downstream tributaries and restoration flow actions released from the dam. Restoration flows have been managed by the Trinity River Restoration Program since 2004 and until quite recently, flow amounts during winter months were managed to maintain a consistent low flow (300 cfs) from October 15 through mid-April. Management was designed this way because the science of how flow influences the ecology of the river wasn’t as far along as the physical river sciences, and further, the water year type which establishes the volume of restoration flow is not determined by the California Department of Water Resources until April 15. Based upon that water year determination, program staff develop a hydrograph for its spring restoration release which intends to mimic an important ecological function of mountainous river systems – the snow melt flood.

As described in the first paragraph, the snow melt flood moves mountains, well the loose parts anyway. High flows during melt events benefit the river in form by moving sediments, logs and rocks which are critical in building habitat for salmonids. Logs slow upstream current, allowing migrating fish to rest and providing cover from predators. Rocks create oxygenation in riffles and provide nesting salmonids a place to dig their redds when spawning. Sediments, when settled and in healthy amounts, encourage proper algae and thus hatches of bugs, which feed fish on their path of migration.

With the snow melt restoration release the Trinity River began to heal from decades of dam-regulated flows. Data shows that the Program has been successfully sending more young fish to the ocean suggesting that habitat is increasing with more water in the system (Pinnix et al, 2022), but adult fish returns have not met expectations and scientists wanted to know why. In the mid-2010’s the Program began to explore the use of flows during winter months. A significant portion of rain events that trigger tributary flows happen from December to April and flows below the dam don’t match that pattern. Studies commenced on temperature, salmonid growth, food availability, habitat availability, redd scour, and geomorphic and hydrologic benefits of current and potential flow practices. The results from these studies became clear and culminated in the Trinity River Winter Flow Project report (Abel et al., 2022). The research led to a proposal of using some of the restoration flow volume earlier in the year by synchronizing a dam release with a winter storm between December 15– February 15 and then providing the river with an elevated base flow between February 15 and April 15; the balance of the restoration water volume would still be used to mimic spring snowmelt in the spring. The authors hypothesize that this change in flow management would more efficiently use the same amount of water to move rock in the river, while also increasing habitat and food availability for young salmon.

When you think about it, it makes sense. All the native species of the Trinity River evolved with winter storm flows, higher winter base flows, spring snow melt and dry hot summers. But for the past 56 years, water dispersal from the dam has been flipped and has largely disregarded vital variability in flow patterns outside of the spring and early summer. Key floodplain habitat that was once inundated for months during winter and provided an abundance of rearing areas and food production to Trinity River fish has been lost, unless flow patterns change. Catch data from downstream screw traps show that inundation of that rearing habitat does not occur until most juvenile salmonids are downstream of the restoration reach (Petros et al. 2017), meaning most juvenile salmon don’t have a chance to use all that habitat that has been created by restoration projects in the last 18 years, unless flow patterns change. We are also learning that water released from the dam can be so cold that it slows the growth of juvenile salmon and that the right temperatures and abundant food will translate into faster growth for salmonids (Lusardi et al. 2019).

Young fish need diverse habitats, appropriate temperatures and abundant food to thrive and survive as they travel down the river to the ocean. More natural flows, including winter floods, increased winter base flows, and spring snow melt better support a healthy ecosystem that many species depend upon. The system is a balancing act of physical processes like flow, seasonality, and a vast network of species that rely on each other to thrive.  The Trinity River Restoration Program is looking to give that power back to the ecosystem so that our cherished fish of the Trinity can be armed with bigger, healthier bodies when they meet the challenges of their harrowing migration to and from the ocean.

Highlights from the Trinity Management Council September Meeting

TMC Partnership Ring
TMC Partnership Ring

The last quarterly meeting of Fiscal Year 2023 was held in Weitchpec, CA on Wednesday and Thursday last week. Typical of the start to the first days agenda, is an approval of the June meeting minutes, however this was moved to later in the day due to a request from Justin Ly [National Marine Fisheries Service] who noticed an inconsistency between how a motion had been characterized and requested time to edit prior to approval. Following this decision, the TMC requested questions and discussion of non-agenda items and then moved into TRRP program updates. The TRRP Executive Director’s report can be downloaded by clicking here.

Comments on non-agenda items brought questions from the public regarding recent social media posts of non-native/introduced fish released into the Trinity River at a rehabilitation site in Junction City. Mike Dixon, [Trinity River Restoration Program] commented that office staff saw a social media post with a bullhead catfish and noted that bullhead are introduced as a sportfish into Trinity Lake and do occur in the Trinity River. The system does not have a robust population and their chance of surviving in the conditions of the river are slim. Interestingly Kyle De Juilio [Yurok Tribal Fisheries Department] also commented that bullhead can be found in the Klamath River as conditions are suitable for them, but they are not known to persist farther up in the Trinity River system. State officials attending the meeting also commented that the State does not have a specific policy regarding introduced game fish.

There were two presentations given to the TMC before and after the lunch hour. Max Ramos [Yurok Fisheries Department] presentation titled Modeling the reestablishment of Coho salmon in Klamath River tributaries following dam removal was postponed due to illness. In his place Kiana Abel [TRRP] presented on FY23 outreach accomplishments and early FY24 outreach plans. Following the outreach presentation, the TMC heard from Dr. Greg Courtice [Applied Ecohydraulics] presented Implications for wildfire-induced fine sediment loading within the Trinity Watershed. Slides from both presentations can be downloaded here: TRRP: Event Details

Post presentations, TMC members held a blind vote to replace the TMC’s vice chair vacancy. Some shuffling with responsibilities at the US Fish and Wildlife Service opened the Board’s Chair position. According to the TMC Bylaws a Chair vacancy mid-service is to be filled by the current Vice Chair and a vote is to be held to fill the open position. The TMC voted to place National Marine Fisheries Service Representative, Justin Ly into the position, he will serve as Vice Chair and Don Bader [Reclamation] will serve as Chair until the December 2024 meeting.

The final agenda item of the first day meeting was a decision item. TMC members voted to select, Dr. Daniele Tonina of the University of Idaho to join the Scientific Advisory Board in an advertised position to focus on hydrology. To learn more about the SAB, please click here.

Day 2 of the TMC quarterly meeting started with regular business in discussing non-agenda items. Thanks were given to the Yurok Tribe for hosting the meeting. There was no request from the public to comment on non-agenda items.

Seth Naman [NOAA Fisheries] reported on the latest synthesis report on temperature in the Trinity River, Synthesizing 87 years of inquiry into Trinity River Temperatures. Please download the report here: Asarian etal (2023) Temperature Synthesis 87 years.pdf

Ken Lindke [California Department of Fish and Wildlife] led the TMC’s final presentation, Water Year 2023 initial findings and WY24 flow recommendation from the TRRP Interdisciplinary Team Work Group. The TMC considered the WY24 flow recommendation from the Flow Work Group and Interdisciplinary Team and Justin Ly [National Marine Fisheries Service] made the following motion: “to approve the IDT’s recommendation to implement winter flow variability for WY24, to timely complete the NEPA process prior to implementation, and to inform the public at least two weeks prior to moving forward with winter flow. In addition, a monitoring plan will be provided to the SAB for their review prior to winter flow variability implementation to assess the effectiveness.” The motion failed 6-2 (TMC bylaws require 7/8 affirmative votes if 8 members are present).

After a discussion of what it meant for the TMC to not send a flow recommendation for the upcoming year to the Department of Interior, Justin Ly [National Marine Fisheries Service] made a second motion to, “recommend that TMC approve beginning October 1, implement 450 cfs baseflow through October 15, then reduce baseflow to 300 cfs from October 16 to April 15.” This motion also failed. The TMC failed to pass the flow recommendation and subsequently failed to pass a motion recommending that DOI implement status-quo winter base flows, so the TMC has not yet made a recommendation to DOI. The winter flow recommendation ruleset does not change flows until December 15, so there is still time for TMC to revisit this issue and make a recommendation to DOI one way or another. If no further guidance is provided by TMC, DOI will have to evaluate its obligations under the law and determine how to proceed.

The TMC will hold their first quarterly meeting for FY24 on December 6 & 7, 2023 at the Shasta-Trinity National Forest Service office in Redding, CA.