BAY DELTA SCIENCE CONFERENCE: Harvest, Hatchery Returns, and Straying of Salmon Released at Bay and Delta sites during California’s Drought

The U.S. Fish and Wildlife Service’s Coleman National Fish Hatchery is the largest salmon hatchery in California, annually producing 12 million fall Chinook Salmon smolts that substantially contribute to California’s ocean and inland fisheries. Standard practice at Coleman NFH is to release smolts on-site into Battle Creek; however, during the severe drought of 2014 and 2015, degraded water quality throughout the Sacramento River and Delta raised concerns that fish released on-site would not survive their emigration to the ocean.

Consequently, the decision was made to transport a large percentage of fall Chinook salmon smolts for release at off-site locations in the Delta and San Pablo Bay to increase smolt survival by bypassing poor in-river conditions. However, an unintended consequence of releasing juvenile salmon off-site is decreased returns to the hatchery because of increased straying.

At the 2018 Bay Delta Science Conference, Sarah Austing from the US Fish and Wildlife Service gave a presentation on where ultimately the fall chinook salmon ended up that were trucked offsite during the drought.


The Coleman National Fish Hatchery is the largest of the Central Valley hatcheries and is located on Battle Creek, a tributary of the upper Sacramento River.  Annually, the hatchery targets to raise about 12 million fall chinook smolts.  The fish are spawned during October and November at the hatchery, and then reared through the winter months.  They are released the following spring once they reach a target release size of about 75mm and have been tagged at a rate of 25% with an adipose fin clip and coded wire tag.

The management goals for the hatchery are to provide about 1% of their production or about 120,000 fish from each brood year to the ocean fishery, the freshwater sport fishery, and returns to Battle Creek for brood stock, all while trying to reduce negative impacts on naturally spawning fish.


Note:  I asked Ms. Austing to explain why salmon straying is a problem.  She responded with this next section which is written by herself and her associate Kevin Niemela (and not myself).  It was not part of the original presentation.

High rates of straying are an unintended consequence of transporting juvenile hatchery salmon from Coleman National Fish Hatchery downstream to the Bay-Delta for release.  This occurs because fish that do not naturally emigrate through the river system lose the opportunity to imprint properly and may be unable to locate their natal area when they are ready to spawn.  Hatchery fish that stray into natural spawning areas can detrimentally affect natural fish populations through genetic, ecological, and behavioral mechanisms.

Salmon have existed for millions of years, and have adapted to changing environmental conditions through the process of natural selection.  Genetic diversity, within and among salmon populations, provides the ability for salmon to adapt to localized environments and respond to changing environmental conditions.  Thus, maintaining genetic diversity at the landscape scale is considered an important consideration for management and conservation, and protecting the remaining natural salmon populations is believed to provide the best chance for long-term survival of the species.  Increased straying by hatchery fish may reduce genetic diversity within and among salmon populations.

Likely due to the prevalence of off-site release practices at Central Valley hatcheries, Central Valley fall Chinook Salmon have lost locally adapted genes and become one large, genetically homogeneous population (see Johnson et al 2012).  Furthermore, salmon that are spawned and reared in fish hatcheries may become quickly adapted for characteristics that favor their survival and reproductive success in the hatchery environment while, at the same time, diminishing their ability to survive and reproduce in the natural environment.

Stray hatchery fish may also compete with natural fish populations for limited resources, including competition for preferred spawning areas by adults and competition for food resources and habitat by juvenile fish.  To address these concerns, fish production programs at Coleman NFH attempt to maximize the proportion of fish returning to the Battle Creek (the location of the Coleman NFH) and minimize the proportion of fish straying to other areas.

When hatchery fall Chinook Salmon from Coleman NFH stray at high rates, the freshwater fishery may be redistributed to other parts of the Central Valley and sport fishing in the upper Sacramento River fishery is negatively impacted.  Likewise, high stray rates of trucked hatchery fish may impact the ability of Coleman NFH to meet its annual fish production targets.  For example, in 2017 (which corresponded to age-3 adult returns of fish that were 100% trucked), less than 350 adult salmon returned to the hatchery.  At a minimum, Coleman NFH needs to spawn 2,600 pairs of adult salmon to meet the production target of 12 million juveniles.  As a result, Coleman NFH released less than 6 million juveniles in the spring of 2018, which will result in fewer fish available to achieve our management goals in future years.

The decision to transport juvenile fall Chinook Salmon to the Bay-Delta for release during the recent period of extreme drought considered how this action would impact the multiple management goals for fall Chinook Salmon at Coleman NFH; including (1) providing fish for the ocean commercial and sport fisheries, (2) providing fish for the freshwater sport fishery, with a focus on the upper Sacramento River, (3) to have a sufficient number of salmon return to the hatchery for use as broodstock, and (4) to reduce impacts to naturally spawning fish.  While it appears that there was an increased availability of fish for the ocean harvest, there were also negative impacts on the upper Sacramento River sport fishery, the ability of Coleman NFH to meet its production goals and straying into non-natal areas.


In order to increase the number of fish that return to the upper river and hatchery and reduce the rate at which they stray into other areas, the hatchery prefers to release its fall run on-site straight into Battle Creek; they are able to do this under typical environmental conditions, but it’s not always possible in all years.

California’s drought had some negative impacts for Coleman National Fish Hatchery.  Ms. Austing presented a slide showing the conditions for the first week of April for years 2012 through 2015, noting that the darker colors indicate worse conditions.  This is significant because the first week of April is around the time that the first of the fall-run from Coleman have already been tagged and are ready for release.  However, the conditions were very poor in the spring of 2014 and 2015; these years were both classified as critically dry water years.

Under normal conditions at Coleman, we’re under a pretty tight time crunch to get all of our fish to release size and then released into the river before in-river conditions start heating up each spring,” she said.  “That problem was further magnified during these two drought years.  During these two critical drought years, the fish management agencies were concerned about the survival of fall run from Coleman Hatchery if they were released on-site into Battle Creek.”

Real-time decisions were made on environmental thresholds such as high water temperatures and low flows throughout the Sacramento River and Delta.  Various Delta water operations were also factored into the decision whether or not to truck.  Predictions were showing exceptionally poor conditions within the river and were expected to continue to degrade as the fish took their time to move downstream through the nearly 300 mile emigration corridor.  Exceeding any of those thresholds was expected to be detrimental to their survival.”

Brood Year 2013 fish were released in the spring of 2014.  Conditions were such that they were able to release 4.5 million fish onsite into Battle Creek on a large storm event; however, the positive impact of that storm was short lived and the in-river conditions degraded while the remaining fish were growing to release size.  So about 2.5 million fish were trucked to Rio Vista and about 4.8 million fish were trucked to San Pablo Bay.  Two different offsite locations were used so return rates and stray rates could be compared between the two locations.

Brood year 2014 fish were released in the spring of 2015, the second of the severe drought years.  No fish were able to be released onsite that year as the fish management agencies determined that based on the poor conditions, there would have likely been poor survival if they had released the fish onsite, so about 11 million fish were trucked to Rio Vista, and nearly 1 million fish to San Pablo Bay.


The fish were tracked using expanded coded wire tag recoveries.  Ms. Austing reminded that the target of the hatchery is to provide about 1% or about 120,000 fish from each brood year to the ocean, commercial, and recreational fisheries, to the freshwater sport fishery in the Upper Sacramento River, and to have fish return to the hatchery for brood stock to continue our mitigation program.  An additional goal is to reduce straying into non-natal areas to reduce impacts on naturally spawning fish.

Ms. Austing then showed the tracking data for the fish, noting that some of this data is still preliminary and may change somewhat once it’s finalized.


Brood Year 2013 fish were released in the spring of 2014 with only 4.5 million fish released onsite into Battle Creek.  Ms. Austing presented a slide (lower, left) showing how the fish contributed to the hatchery goals, with the fish released at Battle Creek shown in blue, the fish released at San Pablo Bay shown in red, and fish released at Rio Vista shown in green.

For the two upper river components, the upper Sacramento River sport fishery and returns to Battle Creek, you can see this fish are mostly from onsite releases and there are overall lower numbers of fish,” she said.  “For the ocean harvest, the valley wide sport fishery, and inland strays, you can see that there are overall more fish and that these are mostly from San Pablo Bay releases followed by fish released at Rio Vista.”

She next presented a slide (upper, right) showing where the geographic location of where the fish ultimately ended up, based on where they were released.  “For the onsite releases at Battle Creek, we can see that these are mostly recovered in the Upper Sacramento River and its tributaries with a few fish ending up in the Feather River,” she said.  “For the San Pablo Bay releases, we see that they are more widely distributed and largely seen in the Feather and American rivers.  The Rio Vista releases are also more widely distributed than the onsite releases and seen mostly in the Feather River, with only a few fish in the Upper Sacramento River and its tributaries.


Next she presented the same data for Brood Year 2014, which was released in spring of 2015; it was the height of the drought, and so there were no onsite releases that year.  San Pablo Bay releases are shown in red and Rio Vista releases shown in green.  The slide on the lower left is the contribution the fish made to the hatchery’s goals.  “Since there were no onsite release for this brood year, we can see that the upper river component is lacking compared to the previous brood year,” she said.  “There were no coded wire tags recovered during creel surveys of the upper Sacramento River and we only had 164 of nearly 12 million fish released return to Battle Creek.”  (Note: The term creel survey is applied to sampling surveys that target recreational anglers.)

The slide (above, right) shows the distribution of these fish that strayed inland.  “We can see that the San Pablo Bay fish are spread throughout the Central Valley and largely seen in the American River,” she said.  “The Rio Vista fish have a fairly similar distribution to previous brood year.  One thing I want to draw your attention to is that there were 11 million fish released at Rio Vista, and less than 1 million fish released at San Pablo Bay, so there are comparatively lower numbers of Rio Vista fish overall.”


Ms. Austing then presented a slide that shows how well the fish contributed to the management goal of 1% contribution to the fisheries and Battle Creek returns.  The bottom graph shows brood years and release location; the vertical bars represent the number of fish recovered divided by the number of fish released, or the percent contribution.  She also noted that she added in Brood Years 2011 and 2012 as these fish were raised during the early years of the drought as well.

For the ocean contribution rate, the offsite releases had a higher contribution rate for the most part than the onsite releases with San Pablo fish (shown in red) having a higher contribution rate than Rio Vista releases (shown in green).  The sport fishery is shown next with the dotted bars, and Ms. Austing noted again that there’s a higher contribution rate from the offsite releases, but the harvest of these fish was redistributed to the lower Sacramento River and other parts of the Central Valley and had a negative impact for the upper river fishery.  The next bars are returns to Battle Creek, shown in the light colors; while the contribution for the onsite releases was fairly low during the early years of the drought, enough fish came back to Battle Creek that they were able to meet our production goals in every year except 2017.

The stray fish are shown in the lined bars on top.  “Now we have the whole picture of what happened with these fish during the drought,” she said.  “The one percent contribution goal to the fisheries and returns to Battle Creek was not able to be achieved under the drought conditions.  The one group that came in closest was the San Pablo Bay releases in brood year 2014.”


Ms. Austing then discussed the management implications of trucking fish.

She presented the data for fish in the ocean harvest with the harvest year on the horizontal axis and the number of fish on the vertical axis.   Battle Creek releases in shown blue, San Pablo Bay releases shown in red, and Rio Vista releases in green.

Remember the onsite releases had a lower contribution rate to the ocean fishery than the offsite releases, so you can see that those trucked fish had value for the ocean fishery and they supplemented the catch,” she said.

She next presented the number of fish harvested in the freshwater sport fishery.  The upper Sacramento River which is emphasized in the hatchery’s management goals is shown in purple and the catch in the rest of the Central Valley is shown in orange.

We can see in 2016 and 2017, which correspond with 3 year-old returns from the trucked fish, that the overall numbers are up from the previous years, but that harvest was redistributed to other parts of the Central Valley and had negative impacts for the upper river fishery.”

Another negative impact was the increased number of strays in the Central Valley.  The number of strays for each release site is shown on the chart.  “We can see an increasing number in 2015 through 2017 with the trucked releases returning,” she said.  “Earlier, when we looked at the geographic distribution of those strays, they were largely seen in the American and Feather rivers.  When we look at the number of fish returning to Battle Creek, we can see there was virtually no contribution from the offsite releases to the point where you can’t really even see them on this graph.”

In 2016 and 2017, which correspond with the trucked fish coming back as three year olds, there were very low returns to the hatchery in Battle Creek. The hatchery was able to meet their production goals in every year except for 2017; the run that year was the lowest run on Battle Creek since the 1970s.

In a normal year, the majority of fish coming into Coleman are 3 year olds.  In 2017, less than 350 adults came into the hatchery, and only 24 of those were 3 year olds.  “For a hatchery that frequently handles tens of thousands of fish within a season, it’s pretty striking to only have 24 fish from our dominant year class,” she said.

Coleman needs to spawn a minimum of 2600 females in order to achieve their targets of producing about 12 million smolts.

We spawned less than half of that in 2017, the majority of those were H2 jills which have fewer eggs than adult females,” she said.  “In attempt to collect more eggs to meet our production goals, we operated the fish trap located at Keswick Dam located on the upper Sacramento River.  This trap is typically used to collect brood stock for other runs of salmon, but in 2016 and 2017, we used it to supplement the fall run spawning program.”

They also partnered with Nimbus State Fish Hatchery on the American River to collect additional eggs in 2017.  “We had coded wire tag data from the previous year that showed a high number of Coleman offsite released fish straying into Nimbus Hatchery,” she said.  “During spawning, we used real-time coded wire tag reading to target Coleman origin fish to reduce impacts of bringing non-Coleman fish into our production.  Despite our extra efforts to collect eggs at Coleman, Keswick, and Nimbus, we only met about half of our egg goals this year and released less than 6 million fish this spring.”

The way the fall run program at Coleman currently operates, Ms. Austin said they are in a time crunch to get fish to the 75mm release size and into the river before conditions start degrading during the spring.

Changing environmental conditions may only amplify this problem with a shortened rearing season due to later spawning or conditions becoming worse at an earlier date during the spring,” she said.  “But our program is not static and we’re continually looking at ways to improve.”

She noted that a few years ago, they began an experimental release study to determine the survival of fish released at an earlier date or smaller size and potentially on a storm event with the goal to get fish out of the hatchery before in-river conditions degrade during future drought conditions.


The drought conditions led us to truck some or all of our fall-run during 2014 and 2015,” Ms. Austing said.  “There were tradeoffs between the expected high stray rates with offsite releases and low survival with an onsite release.  With the trucked fish, we saw that they supplemented the ocean harvest, redistributed the inland sport fishery, had high stray rates, and low returns to Battle Creek.  Because of this, we saw the lowest run on Battle Creek in 40 years.”

Despite our extra efforts to collect additional eggs, we only met about half of our production target.  We’ve undertaken a study to assess fish survival under different release strategies.  This information will hopefully allow for adaptive management, based on changing environmental conditions and may give us some flexibility to release fish onsite to meet our multiple management goals in the future.”


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