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.