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?

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.

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[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.

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!

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.

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.

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!

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.

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. 

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! 

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. 

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.