Central Valley Hatchery Salmon Production Is Being Wasted A Tale of Two Hatchery Salmon Smolt Release Groups

There are two common strategies for releasing juvenile salmon from  state and federal salmon hatcheries in the Central Valley.  One strategy is the release of hatchery salmon smolts at or near the hatchery where they are produced.  The other strategy is trucking the smolts from the hatchery and releasing them into the Bay.  There is much controversy and argument over the relative merits of the strategies.  There can be little argument that release into the Bay generates far more adult salmon than release near the hatcheries.

Consider what occurred with two American River release groups after their release in May 2018 and return as adults in 2020.  Release group #061465 was 669,000 fall-run smolts (3-4 inches long) that were transported 20 miles downstream from the American River (Nimbus) Hatchery and released into the mouth of the American River under the Jibboom Street Bridge.  Release group #061467 was 650,000 fall-run smolts transported approximately 100 miles downstream to net pens at the Wickland Oil Terminal for release into eastern San Pablo Bay, about 20 miles from the Golden Gate Bridge and the Pacific Ocean.

The estimated percent survival based on tag recoveries was 0.04% for group #061465 (released near the hatchery).  The estimated percent survival was 2.20% for group #061467 (released in San Pablo Bay).  The returns by locations are shown in Figures 1 and 2.  These relative results are common.

Figure 1. Returns for tag group #061465.

Figure 2. Returns from tag group #061467.


The Demise of Sacramento River Spring-Run, Fall-Run, and Late-Fall-Run Chinook Salmon

We all know the story of the demise of Sacramento River winter-run Chinook salmon below Shasta Dam over the past several decades (Figure 1).1 But what has happened to the other three Chinook runs: the spring, fall, and late-fall runs? They too have declined (Figure 2-4). Just 50 years ago, 300-500 thousand Chinook salmon ascended the Sacramento River to spawn. This was decades after most of the big Central Valley dams were built. Today, less than 10,000 Chinook salmon return to spawn near Redding. Most of these are Battle Creek and Livingston Stone hatchery fish, plus strays from Feather, American, Mokelumne, and Merced hatcheries. Wild, native Chinook are becoming increasingly rare with each decade.

There are many factors that have led to the demise of Sacramento River Chinook salmon. No doubt, the two major droughts (76-77 and 87-92) had major roles. There was bad management and lack of regulatory protection on many levels. Today, the details of a post mortem are of less value than recognizing the problem and doing something about it.

Much has been tried and accomplished (three of the four runs substantially improved around the turn of the century). A decade of effort and wet years achieved much. However, the three major droughts since (07-09, 13-15, and 20-22) have undone much of those gains and more.

What needs to be done now to bring the salmon back from the brink of extinction is the following:

  1. Recognize and acknowledge the problem (we haven’t)
  2. Develop a single integrated, comprehensive plan to solve it (there isn’t one)
  3. Overhaul the massive salmon hatchery program (we spend huge sums raising and releasing over 30 million salmon smolts each year – the price per pound is astounding – most never reach the ocean)
  4. Overhaul our salmon fisheries program managed by the Pacific Fisheries Management Council (it’s not working – the stocks are in a constant state of over-fishing – and the fishery is not the most important problem – shutting fishery gates after fish have escaped the corral doesn’t solve the problem)
  5. Overhaul the Central Valley water supply management system (it’s taking all the water for humans and leaving none for the salmon – don’t let folks blind you, it’s true)
  6. Overhaul the Central Valley water quality management system (drought “emergencies” routinely bring weakening of standards, wiping out annual salmon runs)
  7. Rebuild salmon habitat from the ground up (much is gone and what is left is degrading fast, as past and present efforts at watershed restoration literally burn away each year).
  8. Implement the comprehensive plan with prioritized short- and long-term goals, objectives, and actions.

The sooner we implement these actions the better – Sacramento River salmon are facing a “Passenger Pigeon” moment. The longer we wait, the tougher it is going to be and the less chance there is we will succeed.

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1970-2021 In-River Winter Chinook

Figure 1. Sacramento River Winter-Run Chinook

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1969-2021, In-River Spring Chinook

Figure 2. Sacramento River Spring-Run Chinook

Graph of Adult Escapement (fish/year) Mainstem, Keswick Dam to Red Bluff Diversion Dam spawn years 1952-2021, In-Rier Fall Chinook

Figure 3. Sacramento River FallRun Chinook

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1971-2021, In-River Late-Fall Chinook

Figure 4. Sacramento River Late-Fall-Run Chinook


How did Winter-Run Salmon do in Summer 2022? Not Good.

First the bad news. The production in 2022 of winter-run salmon fry in the upper Sacramento River near Redding was at record low levels, similar to the disaster years 2014 and 2015, maybe worse (Figure 1).

Next, more bad news (there is no good news). Most of the fry are now in the 100-mile reach below Red Bluff, with only a small proportion to date (November 7) reaching Knights Landing below Chico (Figure 2). Flows (Figure 3) remain too low for good fry survival, with little flow increase following late October and early November rains. Clear water conditions make it easy for the tens of thousands of striped bass and smallmouth bass residing in the 100-mile reach to pick off migrating juvenile salmon. Up till late October, water temperatures above 60ºF kept bass active (also Figure 3). With conditions expected to be similar to last year, one can only expect this year’s production to be similar to last year’s poor production (Figure 4).

Some might say increased hatchery winter run production in 2022 is good news. Higher than normal numbers of hatchery fry are being raised in the Livingston-Stone Fish Hatchery for release next winter. But last winter’s hatchery releases during critical drought conditions did not fare well, as shown by the very small numbers that reached the Delta (Figure 5). To compensate, Interior began increasing egg-taking1 for the hatchery and transporting adults and hatchery smolts to upper reaches of Battle Creek. While these actions are worthwhile, the problem remains that drought year release returns (harvest plus escapement) average about 0.2%, compared to 2% returns in wet years.2

The prognosis for the winter-run salmon from all these sources of recruitment during the 2020-2022 drought to return as adults into fishery catches and the spawning runs is grim.3 The population does recover after wetter year periods (2016-2019, Figure 6), but not without the support of the hatchery. More needs to be done to improve wild and hatchery fry survival and smolt production to safely recover the winter-run salmon population. Flow pulses and enforcement of the state water temperature standards are needed. Vitamin injections, more hatchery egg-taking, and taxi rides alone will not do the job.

Graph showing Run Size from 2007 through 2022

Figure 1. Annual catch of unmarked juvenile winter run salmon in screw traps near Red Bluff as of November 13, 2022. (Source)

Graphs showing Water Temperature and Daily Estimated Passage

Figure 2. Juvenile winter-run salmon catch in Red Bluff and Colusa screw traps in 2022. (Source)

Graph showing flow CFS and Temp

Figure 3. Water temperature and flow rate below Keswick Dam (KWK, RM 300), at Bend near Red Bluff (BND, RM 250), and below Wilkins Slough (WLK, RM 120) in 2022. (Source)

Graph of Cumulative Catch per Brood Year

Figure 4. Annual catch of unmarked juvenile winter run salmon in screw Chipps Island trawls near Pittsburg, CA. Red arrow shows 2021 catch. (Source)

Graph of Observed Chinook Salvage at SWP and CVP Delta Fish Facilities

Figure 5. Salmon salvage at south Delta export facilities in 2021. Salvage of hatchery release groups is color coded. Red arrow shows winter-run hatchery smolt release group and the subsequent capture/salvage of two smolts from the group in late March. (Source)

Graph California Central Valley Population Database Report CDFW GrandTab Adult Escapement

Figure 6. Winter run salmon escapement 1970-2021. (Source)

Wild Salmon Sanctuaries

In a 2014 blog post, Peter Moyle wrote about the Blue Creek Salmon Sanctuary on a large tributary of the lower Klamath River.  The Blue Creek effort is one of the most important initiatives toward saving salmon in California, and also serves as a demonstration and an inspiration.  California needs more salmon sanctuaries to preserve the state’s wild salmon heritage.

There are many potential salmon sanctuaries throughout California.  In this post, I list highly recommended rivers plus and few new ones.  I include only those I personally know well, but there are likely more that fit the paradigm.

My suggestions come from two major watersheds that deserve special mention and attention.

Klamath River Watershed:

 The Salmon River is a wild, natural tributary of the lower Klamath River that retains the last wild population of endangered spring-run Chinook salmon. Its watershed now suffers from the ravages of recent forest fires.  The river is a special place to the Karuk Tribe.

  • The Scott River, the eastern neighbor to the Salmon River, features the last significant wild population of Coho salmon in California. While nearly ruined by logging, fires, and ranch development, the Coho hang on almost belligerently with the help of the Trinity and Marble Mountains and from some of the ranching community.  The river begs for the return of its beaver, so it can again be called “Beaver Valley.”  Some of the ranchers deserve credit for keeping the river and its fish on life-support.
  • The Shasta River is the next neighbor to the east of the Scott River. The river sustains the Klamath’s largest population of wild fall-run Chinook salmon, thanks in large part to the efforts of the Nature Conservancy.  The river has hope for the return of the Coho salmon with the help of ranchers, Sierra Pacific Industries, the tribes, and Crystal Geyser.  Ranchers, please no more revolts.
  • Deming Creek, among the headwaters of the Sprague River, a major Klamath River tributary in Oregon that drains into California, is a historical remnant of a creek that once supported wild spawning Klamath spring-run salmon and steelhead (really). It still has the southernmost extant population of endangered bull trout, which once occurred in California but are now extirpated in this state.  If the Klamath dams are removed, will the salmon return to Deming Creek?  I suspect the salmon will need some help getting to this beautiful place.

Sacramento River Watershed:

  •  The upper McCloud River above and below McCloud Falls is one of the most beautiful places in California. The McCloud once sustained winter-run and spring-run salmon below the falls.  Above the falls on the south flank of Mt. Shasta is the McCloud Redband Trout Refuge.  If part of the strategy is for trap-and-haul sanctuaries, this is a great place to put winter-run or spring-run salmon.
  • Upper Mill Creek and Deer Creek on the south flank of Mt. Lassen are two gems that retain small populations of spring-run Chinook salmon at the highest elevations known for the species.  Ravaged by fires in recent years, they too need help.  At least salmon in theses streams do not need a taxi service.
  • To the south of Deer and Mill creeks, Butte Meadows on upper Butte Creek upstream of falls and water diversions has much potential as a sanctuary. This location needs a taxi service only for adult spawners, but not their offspring should be able to migrate downstream volitionally.
  • Upstream of Lake Almanor, the upper North Fork Feather River drains the southern flank of Mt. Lassen, eventually finding its way past a series of dams into the Central Valley and the Sacramento River. This is another trap-and-haul sanctuary with strong potential, though it was severely affected by the recent Dixie Fire.
  • The upper North Yuba River above Bullards Bar Reservoir is a gem of a stream that once supported spring-run Chinook salmon. Again, this would be a trap-and-haul option.
  • The Middle Fork American River well upstream of Folsom Reservoir, another historical spring-run salmon stronghold, is also a good candidate. Badly damaged in the 2022 Mosquito Fire, the Middle Fork American is in need both of help with the forest and of a two-way taxi service for reintroduced salmon.

One thing common to many of these potential sanctuary locations is a legacy of massive fires in recent years.  A substantial effort is needed to restore these Klamath-Trinity and Sierra ecosystems to make them sustainable once again for California salmon and steelhead.

I also advocate for Chinook salmon sanctuaries below all our major Central Valley rim dams.  The dams were built with the promise of mitigation for the salmon runs.  It is time these many-decades-old promises were kept.   Though most of the lower rivers have escaped the direct ravages of fire, the consequences to their upper watersheds still affect the Valley reaches.  Without the remnant Valley salmon, there would be few salmon left in California.

Time has taken a toll on the Valley salmon below the rim dams.  To weather the effects of droughts, fires, and climate change, and to restore viable populations in the major salmon-bearing rivers, sanctuaries in both the upper watersheds above the dams and downstream of the dams are necessary.

For more information on California’s Chinook salmon see: https://wildlife.ca.gov/Conservation/Fishes/Chinook-Salmon

San Joaquin Salmon Population Status – End of 2021

Following some improvement in the numbers of adult fall-run Chinook salmon returning to spawn in the Stanislaus River and the Merced River from 2012-2017, overall escapement in 2020 and 2021 to San Joaquin River tributaries was severely depressed.  Better flows and water temperatures could help reverse this decline.

In February 2017, I wrote about the fall Chinook salmon runs on the San Joaquin River’s three major tributaries over the previous six years.  Salmon counts in San Joaquin tributaries showed an increase in returning adults in the 2012-2015 drought compared to the poor returns in 2007-2009 drought (see Figures 1 and 2).   The numbers of spawners in 2012-2015 were still well below the returns in the eighties and nineties that corresponded to wet water year sequences, but the increase seemed to suggest progress.

In a December 2019 update, I  updated the earlier post with numbers from the 2016-2018 runs. The 2016 and 2017 runs were the product of poor rearing conditions in 2014 and 2015, both critical drought years, but with good fall adult migration conditions.  The 2018 run was a product of normal-water-year rearing (2016), but poor adult migrating conditions.  The 2016 and 2017 runs were strong in the Stanislaus and Merced rivers (see Figure 3), with both rivers benefitting from hatchery production and strays.  The markedly smaller runs in the Tuolumne (typical throughout the last decade) also benefitted from hatchery strays (Figure 4).  One strong component of the strays was the unusually high proportion of strays from the upper Sacramento River’s Battle Creek hatchery, whose managers’ strategy during the 2014-2015 drought was to truck their fall-run salmon smolts to the Bay, a practice that causes high straying rates, including to the San Joaquin tributary runs.

The 2018 San Joaquin run was lower, but still an improvement over the drought-influenced runs in 2007-2011 (Figure 2).  Spring rearing conditions in 2016 and fall adult migration conditions in 2018 were generally better than they were during the critical drought years, although still stressful.  Also, most of the Mokelumne and Merced hatchery smolts were released to the Bay and west Delta, respectively, in 2016, a likely positive factor in contributing strays to overall escapement.  A further explanation for this improvement was better hydrology-related habitat and migration conditions prescribed in the 2008-09 federal biological opinions that generally led to improved habitat conditions.

In the three years (2019-2021) since 2018, runs generally declined (Figure 3) despite being the product of two wet (2017 and 2019) and one normal (2018) year.  One reason for the reductions was that there were fewer strays from hatcheries. For example, the Merced hatchery smolt releases in 2017 were at the hatchery instead of in the Bay, and thus had poor returns.  Battle Creek hatchery returns were also lower, with less straying by smolts released near the hatchery.

The poor returns in 2020 in all three rivers are especially troubling, given they are the product of a good wet year run (2017) and reasonable rearing conditions in winter and spring of normal year 2018.  One factor in the San Joaquin watershed in late summer and early fall 2020 was unusually low flows and high water temperatures for a normal water year (Figures 5 and 6).  Based on the high number of returns of 2018 Merced hatchery smolt releases straying to other rivers (Figure 7), it appears that a compounding factor to these low flows and high water temperatures was high rates of straying by salmon sourced in San Joaquin watershed to the Mokelumne, American, and Feather Rivers.

The relatively high proportion of the Stanislaus River escapement in the 2021 San Joaquin run appears to be a result of attraction to the Stanislaus from a very warm lower San Joaquin River (Figure 8).  The Stanislaus is the first cool tributary encountered by salmon on their journey up the warm San Joaquin in late summer and early fall.

In summary, there is much straying to and from the San Joaquin salmon spawning tributaries.  Adult run size (escapement) is a function of straying, winter-spring flows and water temperature in the San Joaquin and its tributaries during the winter-spring rearing season, and streamflows and water temperatures during the annual late summer and fall spawning run.  The release locations of smolts from the Merced River hatchery and other hatcheries also plays a role.

Salmon runs to the San Joaquin and its tributaries could be improved with better streamflow and water temperature management.

Grandtab Table

Figure 1. Fall run salmon escapement to San Joaquin River and tributaries 1989-2021. Source: Grandtab.

Bar chart from Grandtab data

Figure 2. Plot of 1975-2021 fall run salmon escapement to San Joaquin River tributaries. Data source: GrandTab.

Stacked Barchart Grandab Data

Figure 3. Plot of 2015-2021 fall run salmon escapement to the San Joaquin River tributaries. Data source: GrandTab.

Pie chart rmpc.prg data

Figure 4. Returns of code-wire-tagged (cwt) salmon to Tuolumne River in 2016-2017 from five Central Valley hatcheries. Source: cwt return data in https://www.rmpc.org.

Line graph USGS data

Figure 5. July-December water temperature in San Joaquin River at Vernalis in 2020, and historical average.

Line chart USGS data

Figure 6. July-December streamflow in San Joaquin River at Vernalis in 2020, and historical average.

Pie chart rmpc.org data

Figure 7. Adult spawner returns to four hatcheries and spawning grounds in 2020 of 2018 Merced Hatchery tagged smolts released in Bay. (Note there were no records for Battle Creek returns.)
Source: cwt return data in https://www.rmpc.org.

Line graph and map

Figure 8. Water temperatures in the lower San Joaquin River at Vernalis (VNS), Brant Bridge (BDT), and Mud Slough (MSG), and Ripon (RIP) on the lower Stanislaus River in September 2020. Note adult salmon generally avoid 72°F water.