Sep 12, 2025

September 2025 Field Updates: Increasing Our Understanding of Steelhead

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The Morro Bay watershed is home to a unique species called steelhead trout (Oncorhynchus mykiss). These fish are born in freshwater streams like Chorro Creek. Some spend their entire lives in the creek and are known as resident rainbow trout. Others, known as steelhead, spend a few years in freshwater and estuary environments before journeying to the ocean. Whether a fish becomes a steelhead trout or remains a resident rainbow trout depends on genetic and environmental factors. 

Steelhead require healthy creek, estuary, and ocean environments to support their life cycle. The Estuary Program works to protect creek habitat, water quantity, and water quality to benefit this threatened fish population. As part of an effort to better understand steelhead populations in the watershed, we recently embarked on a two-year steelhead growth and tracking study.  

This diagram provides an overview of the steelhead and resident rainbow trout life cycles. Some fish remain in fresh water to become resident rainbow trout, while others migrate downstream to the ocean as steelhead. After between one and four years, steelhead return to the streams of their birth to spawn. Adult steelhead may return to a creek to spawn up to twice in their lifetime. Diagram courtesy of Stillwater Sciences.

Understanding Migration and Movements

A key goal of this study was to determine how and when steelhead migrate between local creeks and the estuary. Understanding these patterns can help us identify times of year when fish need enough flowing water to migrate, which can lead to projects that protect surface water flows. It also tells us when to avoid certain activities that might interfere with fish movement. To answer these questions, we monitored the movement and growth of individual fish in Chorro Creek and San Luisito Creek, a smaller tributary that drains into it. 

This illustration shows two forms of steelhead trout. As the fish move from freshwater to saltwater habitats and prepares for a life in the ocean, they lose their speckled appearance and dark spots (above) and become more silver (below), a change known as smolting that allows for better camouflage in the estuary and ocean. Illustrations by Catie Michel. 

How Do You Track Fish Movement and Growth?

As you can imagine, tracking fast-moving, migratory fish can be tricky. For this study, we used a method called mark-recapture, where we implanted fish with a unique tag called a Passive Integrated Transponder (PIT), then recaptured them at a later date. To tag the fish, we used backpack electrofishers to temporarily stun and capture fish. We placed them in buckets with aerated creek water to keep them well-oxygenated, and then we counted and measured all fish.  

We anesthetized steelhead that were of sufficient size, implanted PIT tags, and then released them back into the creek. PIT tags are essentially microchips similar to the type used to chip dogs and cats.  

Passive Integrated Transponder (PIT) tags are small microchips that uniquely identify a fish. After the fish are anesthetized, the tag is inserted, and the fish are released unharmed to the creek.

We conducted this work at 17 sites along Chorro Creek stretching from Chorro Flats to just below the Chorro Reservoir behind the California Men’s Colony. The work was also conducted on two sites on San Luisito Creek. This fish capture and tagging work took place in fall 2023, spring 2024, and fall 2024. If we recaptured the tagged fish during subsequent fieldwork, we would again weigh and measure them to calculate their growth rate.

Once the tags are implanted, you need a way to track them as they move through the creeks. We installed stationary PIT-tag antennae in lower Chorro Creek, one just downstream of the South Bay Boulevard Bridge within the estuarine ecotone (transition zone from fresh to salt water) and one in Chorro Flats (near Quintana Road). As fish pass by an antenna, a reader scans the microchip in the tag to record a fish’s unique identifier.  

This paired swim-over PIT tag antennae in lower Chorro Creek detects fish as they swim over it and records the unique number associated with a specific fish based on the microchip in the tag. This paired antennae can detect whether fish are swimming downstream towards the estuary or upstream into the watershed.

What Did We Learn?

The data revealed interesting differences in fish density between creeks. In Chorro Creek, the density ranged from 4 to 102 fish per 100 meters of creek, whereas in San Luisito Creek it ranged from 44 to 263 fish per 100 meters of creek. As we collected limited data in San Luisito Creek, it’s not clear whether this higher density is a consistent trend until more data is collected.  

This photo shows a group of juvenile steelhead trout in the Morro Bay watershed.

We captured a total of 1,225 steelhead, and approximately 70% of them were large enough to PIT tag. Of the tagged fish, 7% were recaptured at least once, with only a handful recaptured at least twice. Juvenile fish (aged 0+) captured in Chorro Creek tended to have higher growth rates than those in San Luisito Creek. This is likely due to fewer fish present and warmer stream temperatures in Chorro Creek. There was no difference in growth rates for fish aged 1 to age 2+ between the two creeks. The higher density of juvenile fish on San Luisito Creek likely contributed to lower growth rates as there were more fish competing for habitat and food.  

The data also provided information on fish movement. A total of 201 fish were detected at the antennae between 2023 and 2025. Of these: 

  • 57% were detected only in the Chorro Flats area and are likely resident rainbow trout who will spend their entire lifespan in fresh water.  
  • 6% were considered to be one-way migrants from the creek to the ocean because they were originally tagged at an upstream location.  
  • 37% were detected at the estuarine ecotone antennae. Of these, 90% were one-way migrants, or smolts, that did not return after passing over the estuarine ecotone antennae, while the remainder were considered two-way migrants as they were later detected upstream at Chorro Flats.  

The typical pattern of fish movement was for age 2+ fish to migrate from higher up in the creeks to down past Chorro Flats, and then a few days later to continue downstream past the estuarine ecotone antennae. A few fish spent more time near the estuarine ecotone antennae and were detected in that location many times over several weeks. Based on fish movement, the window for smolting (transitioning from freshwater to saltwater habitat) in the Chorro Creek watershed was roughly January to April, but the start is typically dependent on a large rain event. 

This diagram shows approximate locations where fish were tagged and the locations of the antennae that track fish movement. The diagram shows that smolts (fish journeying from fresh water to salt water) would pass all three antennae without turning back. The resident fish never ventured into the lower parts of Chorro Creek or beyond into the saltwater habitat. And two-way migrants were fish that as part of their smolting journey spent time in the estuarine habitat (a mix of fresh and salt water) before venturing out into the open ocean. Figure courtesy of Stillwater Sciences. 

What’s Next?

This image shows a steelhead trout being released unharmed back into the creek following capture. We hope to continue our work tagging and tracking steelhead to learn more about how they use our watershed creeks and the estuary. Photo courtesy of Matt McKechnie.

This study provided fascinating new information on this iconic species. Next, we want to learn more about the role of the tributaries for steelhead trout in the watershed. We hope to undertake tagging work in San Bernardo, Pennington, and Dairy Creeks in the future. 

Help us protect and restore the Morro Bay estuary!