Mokelumne River Salmon Update – Fall 2018

Dan Bacher’s report on 2018 salmon returns to the Mokelumne River Hatchery provides continuing good news for the Mokelumne River salmon run.

When I last reported on the fall run of Mokelumne River salmon, I described strong runs from 2010-2016. The 2017 run was exceptionally strong (Figures 1 and 2), despite being the product of the 2013-2015 drought. This success story is in large part due to the management of the Mokelumne River Hatchery, as reported in the Bacher article. Trucking hatchery smolts to the lower San Joaquin in the western Delta near Jersey Point greatly improves survival over releases of salmon in the lower Mokelumne River.

Best returns from the spring 2015 releases were from smolts barged and released near the Golden Gate. That group of 101,000 smolts (tag code #060593) had a good return of 1.35 percent compared to 0.06-0.80 % from smolts released in the west Delta and 0.01 % released in the lower Mokelumne River. In early May 2015, soon after river and Delta smolt releases, water temperatures reached 68oF in the west Delta and 72oF in the lower Mokelumne in the central Delta, levels stressful to smolt salmon. Delta outflow in early May 2015 was critically low at ~5000 cfs. Net flow in the lower San Joaquin River in the west Delta, with the Delta Cross Channel closed, was near zero.

The returns from tag group #060593 (shown in Figure 3), which represented only about 3% of the total smolts releases from the Mokelumne Hatchery in 2015, exemplifies the kind of return pattern that can be achieved by a progressive hatchery program. The majority of the adults returning from this tag group to the Central Valley were to the hatchery (192), although a significant number strayed to the neighboring American River (82) and San Joaquin River and its tributaries (40). In previous years, the California Department of Fish and Wildlife achieved similar success barging smolts from the Feather River Fish Hatchery.1

Figure 1. Mokelumne River in-river fall Chinook returns (escapement) 1975-2017.

Figure 2. Mokelumne River hatchery fall Chinook returns (escapement) 1975-2017

Figure 3. Mokelumne River fall Chinook tag returns through 2017 from 101,000 Mokelumne River Hatchery smolts, tag group #060593, barged to and released near the Golden Gate Bridge.

Sacramento River Salmon Science

A recent paper in the prestigious Canadian Journal of Fisheries and Aquatic Science discusses Central Valley salmon. The paper concludes: “Wild stocks in several California rivers are now dominated by hatchery fish (Barnett-Johnson et al. 2007; Johnson et al. 2012; Quiñones and Moyle 2014), potentially eroding the long-term resiliency of wild, locally adapted populations by disrupting selection for heritable traits that improve lifetime reproductive success in variable environments.”

First, wild or naturally spawning stocks or runs of fall-run Chinook salmon in Valley rivers are all dominated by hatchery salmon. Without hatcheries and straying of hatchery salmon to non-hatchery rivers (e.g., Yuba, Cosumnes, etc.), there would be almost no salmon runs of significance.

Second, there are hardly any significant locally adapted (wild) traits left to erode. River flows, water temperatures, gravel spawning beds, large woody debris, predators, and channel morphologies have become so limiting or compromising that wild salmon survival is nearly nonexistent.

Third, the “lifetime reproductive success” potential of wild fish is primarily compromised by water and fisheries management. Flows are too low, and fisheries continue harvesting much of the wild salmon production.

Fourth, the recent salmon population crashes of 2009 and 2016 are blamed by many salmon scientists on poor ocean conditions, with little regard for poor river habitat or water management as contributing factors, let alone hatcheries. By contrast, the federal Battle Creek hatchery managers knew they had to truck some of their smolt production to the Bay during the drought because of poor river conditions if they hoped for some survival and contribution to future runs.

The authors of the paper imply that hatcheries are the problem. No doubt the hatchery programs could be improved to lessen their negative effects and improve their contribution to salmon recovery. But for sure the fault is not with the hatcheries. Lack of support for hatcheries by scientists and resource agencies will dry up hatchery funding by water-user entities and make the problem worse.

The paper’s authors conclude: “There is a growing concern that salmon populations in the C[entral] V[alley] of California are becoming dependent upon hatchery supplementation, a conservation status recently identified as “mitigated extinction” Baumsteiger and Moyle 2017).” California salmon have been dependent on hatcheries for many decades. This is not a new development. Dams and diversions wiped out the wild salmon and their critical habitats, while hatcheries kept the dream going. Now scientists want to take the dream away.

Give the authors some credit for ending by saying: “Hatcheries can play a key role in the recovery of wild stocks, supplementing the fishery, and the reestablishment of natural areas, but only with cautious and appropriate management.” Despite the ambiguity, I had similar recommendations for improving hatchery programs in a recent post. 1

Fall Run Salmon Spawn 2018

In a past May 2018 post I described how fall-run salmon redd dewatering was a key factor in the poor wild salmon production in the Sacramento River during the two prominent salmon population crashes in the past decade. This problem is again occurring in fall 2018 (Figures 1-3). The close to 50% drop in flow releases from Shasta Dam since late October and the corresponding 2-to-3 foot drop in water level is causing redd stranding of spring-run and fall-run salmon in the spawning grounds of the Sacramento River below Shasta.1

Despite nearly filling this past spring, Shasta Reservoir was drawn down over the summer and fall (Figures 4 and 5). The decline is unprecedented and is more typical of critical drought years. I recognize the concern for Shasta storage, but Reclamation’s decision to provide 100% water allocations under low snowpack conditions has again compromised Sacramento River salmon production.

Figure 1. River flow (cfs) below Shasta/Keswick in the Sacramento River in fall 2018 along with long term average.

Figure 2. Water surface elevation in Sacramento River below Keswick Dam at upper end of prime salmon spawning reach in fall 2018.

Figure 3. Water surface elevation in Sacramento River near Red Bluff at lower end of prime salmon spawning reach in fall 2018.

Figure 4. Shasta Reservoir information in 2018.

Figure 5. Monthly Shasta reservoir storage 2005-2018.

Central Valley Spring Run Salmon – Record Low Run

In a 10/31/17 post, I described record low spring-run Chinook salmon runs in Sacramento Valley rivers in 2017, with emphasis on the Feather River, the largest component of the Central Valley spring-run population. In this post, I update information on Central Valley spring-run. The combined Central Valley runs of spring Chinook salmon were indeed at record low levels in 2017 (Figure 1). The run total includes escapement to all Central Valley streams that host spring-run salmon, including Battle Creek, Clear Creek, Butte Creek, Antelope Creek, Big Chico Creek, Cottonwood Creek, Mill Creek, Deer Creek, Antelope Creek, Feather River-Yuba River, and the mainstem Sacramento River.1

I plotted these numbers in a spawner-recruit relationship, with spawners being recruits three years earlier (Figure 2). The water year type during the first winter-spring following spawning is shown in Figure 2 by color. Winter-spring conditions reflect early rearing and emigration conditions in spawning rivers, as well as conditions in rivers downstream an in the Bay-Delta.

Factors contributing to poor recruitment in the eight critically dry years in the observed period include low river flows, high water temperatures, excessive predation, loss at water diversions, and low turbidity, all factors that are inter-related. Poor ocean conditions and hatchery operations also were likely factors, which may also be related directly or indirectly to river flows.

Most recent recovery efforts and planning have focused on habitat restoration.2 My own focus has been on poor river conditions (low flows and high water temperatures) and related predation.3 My reasoning is based on escapement trends over the past decade that indicate sharply dropping escapement during dry year low-flow conditions in most of the spawning rivers (Figures 3-5).

Figure 1. Spring run salmon in-river escapement (spawning run size) in the Central Valley from 1975 to 2017.

Figure 2. Spawner-recruit relationship for Central Valley river escapement of spring-run Chinook salmon. Recruits represent spawner escapement for that year. Spawners are recruits from three years prior. Numbers are log10 of escapement minus three. Red represents dry years during winter-spring after fall spawn. Blue represents wet years. Green represents normal years. Blue dotted line is statistical trend line. Yellow line is replacement level. Note eight points in bottom-right quadrant represent winter-springs of critically dry drought years (77, 89-91, 07-08, 13, and 15).

Figure 3. Battle Creek spring run salmon escapement from 1989 to 2017.

Figure 4. Deer Creek spring run salmon escapement from 1975 to 2017.

Figure 5. Mill Creek spring run salmon escapement from 1975 to 2017.

Tag Code #060448

In the spring of 2014, 11,791 Feather River fall run Chinook smolts with tag code #060448 were trucked from the Feather River Hatchery and released to net pens in northern San Francisco Bay near Tiburon, California and the Golden Gate Bridge.  It was the middle of the historic 2012-2015 drought.  Somehow, an estimated 323 of these fished survived (2.74%) to be recovered in fisheries, spawning grounds, and hatcheries, including 68 back to the Feather River Hatchery (Figure 1).  The return rate for the Tiburon released smolts was over ten times that of the Feather River releases, five times that of Delta net pens, and over twice that of eastern San Pablo Bay pen releases (Table 1).  Similar results occurred from 2013 and 2015 Tiburon releases.  Results were even better from smolts barged from the Feather River to the Golden Gate in 2013.1

One wonders whether trucking and barging millions of smolts reared at the Feather and American River hatcheries would lead to more salmon commercial and sport fishery catches and improved spawning runs in the Feather and American rivers, especially during droughts.  Salmon run collapses during the 2007-2009 and 2013-2015 droughts were often blamed on poor ocean conditions, as well as poor river conditions.  Concerns of potential straying are unfounded, as all the Bay releases of Feather and American hatcheries have low straying rates (see Figure 1 for example).  Do we want a better return on our Central Valley salmon hatchery investments?

Table 1.  Number released and estimated %return from 2014 Feather River smolt releases.2
Release Location Total Released Percent Return
Tiburon Net Pens 11,791 2.74
Lower Feather River 1,230,000 0.01-0.19
West Delta Net Pens 201,000 0.55
San Pablo Bay Net Pens 6,900,000 0.19-1.30
Lake Oroville 127,000 0.0
Total 8,400,000 0.0-2.74

Figure 1. Tag return locations from #060448 Tiburon release. Source:

  2. Note: not all returns have been analyzed and recorded; further returns are expected from various 2017 tag-recovery sources. Data source: