Fish Biologists Turned Farmers: Growing Food for Juvenile Salmonids in a Regulated River System

Modern river science related to salmon restoration is everchanging due to the complex interplay of factors affecting their life cycle. There are man-made issues including habitat degradation, barriers to migration, harvest; as well as environmental, such as climate change, and ocean conditions. This makes it difficult to isolate and address specific issues as they are all interconnected. There is also intricacy in finding patterns to mimic regarding the complexity of change that our system presents us from year to year (think wet year vs dry year).

For many years river restorationists followed the mantra of “if you build it, they will come” thus resulting in habitat reconstruction efforts along identified areas within the 40-mile Trinity River Restoration Reach. This combined with increased releases from Lewiston Dam (starting in the year 2004) are thought to have led to the doubling of natural origin juvenile Chinook Salmon populations in the Trinity River (Pinnix et al 2022).
Even though we have seen a doubling of juvenile Chinook Salmon outmigrants from the Trinity River, adult returns remain lower than in the past. A decline of adult Chinook Salmon returns along the entire West Coast indicates there may be other issues than just in the rivers alone. Chinook Salmon have many limiting factors to survival and the Program can significantly influence only a portion of the Chinook Salmon’s life history – the riverine stages (returning adults to juvenile outmigration). Trinity River ecologists have been evaluating changes to restoration techniques to understand how to produce more robust juvenile salmon, and hopefully more returning adults, within the limited area and timeframe they inhabit the mainstem Trinity River.
One clue from decades long data collection is that the juveniles, although more in quantity, are smaller now than in the past– potentially leading to the indication that growth rates might be inhibited during their rearing period. This indication has led program scientists to conduct a multi-year monitoring effort aimed at shedding more definitive light on how food sources for juvenile salmonids interact with flow, temperature, scouring floods, and floodplain inundation on the Trinity River. Trinity and Lewiston dams, which until recent management changes did not release additional flows in the winter months. The lack of releases has prevented several ecological processes like scouring floods and floodplain inundation. Proper seasonal floods build and break down algae communities to feeding benthic macroinvertebrate communities which are the food supply for young salmon hatch and emerge from gravels.
Read on to explore the significance of algae, and the fish food within (benthic macroinvertebrates) alongside key functions of scour and inundation and how these important functions build the foodscape to aid juvenile salmonids within the Trinity River.
Trinity River Juvenile Salmonids

Salmonids are a keystone species meaning their presence and activity have a disproportionately large impact on their ecosystem. Juveniles specifically play a crucial role in ecosystem health by serving as food for various predators in the river system, including other fish, birds, and mammals. As they grow into adults salmon are critical to support recreational, commercial and Tribal harvest as well as delivering important marine derived nutrients from the ocean back to inland ecosystems.
Trinity River salmonids that are native to our watershed each have unique life histories as well as habitat needs within the river system. Due to their cultural, economic and environmental influence the three native species of interest to the Program are Steelhead (Oncorhynchus mykiss), Coho Salmon (O. kisutch), and Chinook Salmon (O. tshawytscha). There are also two additional native anadromous species to the Trinity that have specific cultural and ecological significance; the Pacific Lamprey (Entosphenus tridentatus) and the Green Sturgeon (Acipenser medirostris).
Despite unique habitat needs these species do share common life-history requirements that are considered when making decisions regarding restoration of the fisheries. At the juvenile stage these requirements include;
- Sediment vital in just the right amount. Spawning gravel that has a low amount of fine sediment helps water flow through the spaces between the eggs, which increases the chances of eggs hatching and young fish survival. However, too much sand and silt can suffocate both the eggs and fry, making it harder for the young fish to emerge successfully.
- Diversity in temperature and flow. When digesting they require low-velocity, shallow habitats that provide temperatures for prime digestion. As they grow, a variety of habitat types are required that include faster, deeper water and instream cover;
- Overwintering habitat. Coho salmon and steelhead must have abundant overwintering habitat composed of low-velocity pools and interstitial cobble spaces; and
- Food availability. abundant food sources can increase their chances of survival during their migration to the ocean and ultimately, as adults, to return to spawn.
Regulated river systems, shaped by dams, levees, and other infrastructure, significantly disrupt the natural processes that support juvenile salmonids. Most significantly, habitat availability below a dam is limited by the loss of natural processes of rivers. Thus, the Program has been given five main tools to mitigate for the presence of the dam. Flow Management, Channel Rehabilitation, Sediment & Wood Augmentation, Watershed Restoration, and finally Adaptive Management.


The Trinity River Restoration Program utilizes channel rehabilitation to return low floodplain habitat to the river and its aquatic species. In recent rehabilitation projects like Oregon Gulch, the designs are intended to follow the Stage 0 restoration concept. Stage 0 restoration is a method for restoring rivers that focuses on resetting the river to allow natural processes to shape the landscape. The goal is to recreate environments where river processes can improve connections within the ecosystem. This approach helps create vibrant and self-regulating riparian and stream areas that can develop on their own over time.
The Program also utilizes variable flow management to help shape habitat. Until recently due to forecast methods and limited data, variability was only utilized during one season, the snow-melt peak and recession period (April through June, July and in wetter years into August). In water years 2023 and 2025 Program partners came to agreement that changing variability by reallocating water to key growth periods during the late winter and early spring months could help juvenile salmon become more robust.
Scour and Inundation: Key to River Function in Mediterranean River Systems
Scouring floods and floodplain inundation are two important river processes influenced by river releases. Scour and inundation’s ability to support young salmon rely heavily on the physical structure of the Trinity River.
Scour occurs during large winter storms when fast-moving water erodes the riverbed, moving sediments and changing the channel’s structure. This process helps to maintain river functions by exposing and transporting sediments, logs, and nutrients throughout the river system. Combined with flow, these elements contribute to a dynamic river design and are crucial for all life stages of salmon. Logs and sticks create hiding spots from predators and provide areas with optimal flow conditions for feeding. Deep scoured holes provide temperature diversity throughout the year. The movement of sediments and other detritus transfer nutrients to floodplains which provides a suitable substrate for algae and benthic-macroinvertebrate populations.
Inundation refers to the seasonal flooding of riverbanks and adjacent floodplain habitats during higher flows during the spring. This flooding is vital for rejuvenating riparian zones and promoting the growth of riparian vegetation. Inundated areas often serve as nurseries for juvenile salmonids, providing preferred temperatures for digestion and shelter from faster areas of higher flow within the main channel. The nutrients deposited during flooding can enhance algal and macroinvertebrate production, further supporting the growth of juvenile salmonids.
The Role of Algae & Benthic Macro Invertebrates in Juvenile Salmonid Success
Algae play a significant role in primary productivity, providing essential food sources for various aquatic organisms, including benthic macroinvertebrates, the favored food of out-migrating juvenile salmonids. Through photosynthesis, algae contribute to oxygen production, an essential requirement for many aquatic species. Additionally, algae facilitate nutrient cycling within the ecosystem helping to enhance habitat health.
Read more about Trinity River Algae, Food Webs, and Flows

Benthic macroinvertebrates are tiny invertebrates that live on the riverbed. While young salmon feed on both terrestrial and aquatic invertebrates, these organisms provide an essential source of food for juvenile salmonids. Common examples of benthic macroinvertebrates that juvenile salmon consume include mayflies, stoneflies, midges, and caddisflies. Moreover, these organisms serve as indicators of ecosystem health; their presence, diversity, and abundance can offer valuable insights into the ecological status of a river system. In addition to being food for juvenile fish, benthic macroinvertebrates contribute to the breakdown of organic matter, aiding nutrient cycling and improving overall ecosystem productivity.
Read more about Trinity River Benthic Macroinvertebrates
Understanding the roles of algae, benthic macroinvertebrates, scour, and inundation in the Trinity River, a regulated river system, is essential for supporting juvenile salmonids. By recognizing the interconnectedness of these organisms and processes, ecologists can implement strategies that potentially promote a balanced ecosystem. Ensuring that algae and macroinvertebrate populations meet the demand of juvenile salmonids will enhance their health and survival contributing to the overall vitality of aquatic ecosystems.