Featured Article: Algae, Food-Webs, and Flows

Posted on January 12, 2024January 29, 2025 by Kiana Abel

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 https://www.trrp.net/library/document/?id=2549. 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

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]

Diatoms

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!

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.

Return to the January Newsletter

Flow Variability in the Trinity River

Posted on September 18, 2023January 29, 2025 by Kiana Abel

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.

Return to the September Newsletter

Featured Article: A Brief Introduction to Thermal Ecology of the Trinity River

Posted on August 7, 2023January 29, 2025 by Kiana Abel

This image shows the Bucktail channel rehabilitation site in April 2019, three years after construction. This image illustrates a pond with a beaver dam analogue in the location of a former gravel quarry that is connected to the river by a perennial side channel (lower right), a main channel that reoccupied a channel that filled in after Trinity Dam was completed (top of photo), and an alcove with perennial flow (second channel from top). The variety of water depths, velocities, and temperatures resulting from the project are intended to provide good rearing conditions for all anadromous fish species that may use the site. Photo by A. Martin, Yurok Tribal Fisheries Dept., 2019.

A Brief Introduction to Thermal Ecology of the Trinity River

Rivers, particularly those in Mediterranean climates, are extremely complicated systems (see figure 1). Water temperatures in unregulated rivers vary over time and space. They tend to be warm in the summer, cold in the winter, colder in the headwaters than in downstream reaches, and colder at the bottom of slowly moving, deep pools. Temperatures in tributaries often differ from mainstem rivers and create even more variability in the system. This complexity ‘muddies the water’ when the topic of water temperatures comes up in conversation or when making flow management decisions. To complicate matters more, dams and diversions strongly affect water temperatures, especially how they change over time and space, so river managers have invested heavily [1] in understanding riverine thermal patterns to better maintain water temperatures needed by fish and wildlife.

Figure 1. Reproduced from: J. Eli Asarian, Kyle De Juilio, David Gaeuman, Seth Naman, and Todd Buxton. (2023). Synthesizing 87 years of scientific inquiry into Trinity River water temperatures. 80 p. + appendices. Prepared for the Trinity River Restoration Program, Weaverville, California.

It is well known that native Trinity River salmonids – Coho, spring and fall Chinook, and winter and summer steelhead – generally require ‘cold’ water. However, Trinity River ecology is more complex than that, as salmonid temperature needs vary by species and life stage. When speaking in generalities, there are a few truths. Mortality is likely if daily average water temperatures reach 73°F (23°C) for young and mature salmonids alike, however, if adult salmonids can access cooler water and don’t encounter other stressors they can survive. When salmonids are young and food is unlimited, optimal growth in freshwater occurs between 55°F-65°F (12°C-18°C), and seasonal runs of adult Chinook salmon stop migrating upstream when temperatures exceed about 68°F (20°C). Among salmonids, Coho eggs are the most sensitive to temperature while they develop in the gravel during the winter months. Optimal temperatures range from 36°F-44°F (2.5°C-6.5°C). Survival rates begin to decline at temperatures above 50°F (10°C).

When a river is dammed, water pools behind it and is exposed to sunlight and warm air, and the water inevitably warms. Water that is too warm directly kills salmon. Conversely, with cooler water, salmonids also have a threshold as low temperatures slow growth and can enhance conditions for some diseases, and mask environmental cues for migration. Since cooler waters do not directly kill salmonids and since the degradation of cooler temperatures affects out migrating young salmon vs adult salmon, managers have been conserving salmon in dam-regulated rivers as cold as possible. Doing this is straightforward: release water from deep in the lake (where water is colder than at the top), and release as much of this cold water as is necessary to keep the tailwater at the desired temperature downstream to the desired point. However, from empirical data, we know that rivers within a Mediterranean climate warm in the summer. In fact, the seminal fisheries investigation on the Trinity River [2] documented summer surface water temperatures of about 80°F (27°C) in the Lewiston area, and simultaneously salmon were present and thriving in this environment. Anecdotal reports from long-time Trinity County residents also suggest that very low flows, “to the point that one could walk across the river”, in places, without getting wet – were frequent and salmonids were able to handle these conditions just fine. Coincidentally, these warmer, slower flows were also needed by other aquatic species that co-evolved with salmonids such as the foothill yellow-legged frog and western pond turtle whom we have seen decline in dammed rivers due to higher summer flows and colder temperatures.

Fish biologists will tout the natural warming of a river found in Mediterranean-climates as a benefit because warm summer waters stop upstream salmon migration. Thermal barriers separate the spring and fall Chinook runs and minimize interbreeding between the runs. This is important because when individuals from these two runs interbreed, their adult offspring are rewired to begin their upstream migration in the hottest months of the summer [3] and depending on the year these re-wired fish can enter into poor to very poor river conditions.

Managers can achieve a cold river by one of two ways. Using the current system they release lots of water (450cfs) from the deep in the reservoir and keep the river cold. This large mass of cold water gradually and uniformly warms as it goes downstream. The second management system would be to release less cold water to promote stratification, and have both warm and cold water in close proximity to each other for a long ways downstream. For many years, public opinion and legal requirements, informed by our limited understanding of how rivers work, has favored the former strategy. In the future, an ever-shrinking water supply, a better understanding of thermal ecology, and perhaps a need to conserve other species along with salmonids, requires each of us to explore the latter.

J. Eli Asarian, Kyle De Juilio, David Gaeuman, Seth Naman, and Todd Buxton. (2023). Synthesizing 87 years of scientific inquiry into Trinity River water temperatures. 80 p. + appendices. Prepared for the Trinity River Restoration Program, Weaverville, California.
Moffett, J. W. and Smith, S. H. (1950) Biological Investigations of the Fishery Resources of Trinity River, California. Special Scientific Report – Fisher No. 12 from the U.S. Fish and Wildlife Service.
Neil F. Thompson, Eric C. Anderson, Anthony J. Clemento, Matthew A. Campbell, Devon E. Pearse, James W. Hearsey, Andrew P. Kinziger, and John Carlos Garza. (2020). A complex phenotype in salmon controlled by a simple change in migratory timing. Science, 370 (6516)
Buxton, T. H., Y. G. Lai, N. A. Som, E. Peterson, and B. Abban. 2022. The mechanics of diurnal thermal stratification in river pools: Implications for water management and species conservation. Hydrological Processes 36(11):e14749. DOI: 10.1002/hyp.14749.
Carter, Katharine (2008). Effects of Temperature, Dissolved Oxygen/Total Dissolved Gas, Ammonia, and pH on Salmonids – Implecations for California’s North Coast TMDLs.

Return to August Newsletter

Featured Article: Sediment and Summer Thunderstorms

Posted on July 19, 2023January 29, 2025 by Kiana Abel

Lightning strike in the Trinity Alps Wilderness during a set of summer thunderstorms in 2023. **[Photo credit: Anonymous]**

Sediment and Summer Thunderstorms

Thunderstorms and sudden cloudbursts are common in the mountains during the summer. Following a wildfire, they can have dramatic results, especially after a dry year without significant rainfall. A single downpour can set a mountain stream roaring, sending a puff of suspended sediment downstream to wash into the river below. Usually this passes quickly, leaving little trace. Significant rainfall and subsequent runoff normally occur in fall or winter. However, an unexpectedly intense storm directly following a wildfire in 2022 lead to a natural disaster on the Klamath River. In August, heavy rain flooded an area burned by the McKinney fire, California’s largest wildfire that started in July that same summer, resulting in an enormous plume of sludge and debris that killed thousands of fish.¹

Sediment is usually mobilized by the large storm systems that come in fall and winter during the rainy season, but a burned landscape is much more vulnerable. Wildfires cause loss of canopy vegetation as well as changes to soil properties. Storms can result in more water flowing over the land, leading to flooding and erosion, while delivering sediment, ash, pollutants, and debris to surface water.² All that mobilized debris can choke small creeks and block local drainages, turning rivers into muddy, churning maelstroms. And even after the water clears, the excess fine sediment can fill in pore spaces between cobbles where fish lay their eggs (redds), suffocating eggs and aquatic larvae on the bottom; it can also clog and abrade the gills of mature fish.³

While erosion is a natural process, its effects on rivers and streams are highly variable, and the increasing frequency and intensity of wildfires is changing that dynamic. Ongoing research by agencies like the U.S. Geological Survey is shedding new light on wildfire’s impact on soil and water.

Soil properties can change dramatically due to fire. For example, metals can be volatilized and rained down or deposited by ash, and the structures that burn can introduce all sorts of other materials into the mix. Each watershed reacts uniquely to wildfire. Topography, including slope, affects how much erosion occurs. The type of vegetation (or structures) burned and what was in the soil itself affect what ends up in the surface water. And the mechanics of the fire, like how hot the fire burned and how much of the watershed burned, affect what is in the runoff.⁴

When rains hit, the tremendous amounts of ash and sediment that wash into rivers and reservoirs cause physical disruptions. In addition to the large-scale runoff (landslides and debris flows), smaller-scale runoff increases the amount of fine sediment suspended in water. Sedimentation also decreases the water quality itself by changing the amount and type of dissolved organic matter (DOM). Fire releases nitrogen stored in plants and trees. Geochemists have also found that different trees release different metals, in different concentrations, when burned. For example, when a ponderosa pine burns it releases whatever metals it has absorbed from the soil and air, like iron and manganese. An aspen or spruce might emit more vanadium, lead, magnesium, or copper.⁵

Salmon redds are most vulnerable during and after spawning season, which starts in October. The first big storm in the Trinity Alps came in October of 2022. Deadwood Creek and Dutch Creek, tributaries to the Trinity River, dumped a ton of sediment into the mainstem that had failed to mobilize in the previous drought years. Deadwood Creek sits high up in the managed river system where some of the heaviest spawning takes place. At the time of the storm, the Trinity River itself was still at baseflow (300 cubic feet per second), so it did not have the momentum to carry the sediment very far and it settled closer to the mouth of the creek, smothering a number of redds.

The solution? Once the eggs have hatched out in the spring, most fish can usually swim away from pulse-disturbances and pollution as long as their movements are not restricted by barriers like road crossings, dams and culverts. TRRP is helping fund watershed projects that limit the sources of excess sediment and remove barriers to migration to give fish more ability to escape difficult conditions. These include the Supply Creek Berm removal project and the Carr Fire Recovery & Sediment Reduction Project, as well as the planned Oregon Gulch Culvert Replacement and East Branch East Weaver Creek Migration Barrier Removal.⁶ A proposal to synchronize winter storm events with flows out of the dam would help keep tributary sediment from piling up at creek mouths during storm events. The TRRP is also looking to support more projects that emphasize fire resiliency. Restoring the river and its watershed is the ongoing mission of the TRRP.