Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Sacramento River Salmon Science

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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

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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

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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

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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: rmis.org

  1. http://calsport.org/fisheriesblog/?p=1052 ↩
  2. Note: not all returns have been analyzed and recorded; further returns are expected from various 2017 tag-recovery sources. Data source: rmis.org ↩

Klamath River Fall Chinook Salmon – Fall 2018 Update

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The Klamath River is closed to salmon fishing again this fall after the number of fish caught reached the small allotted quotas1. Poor run size (escapement) continues to be a problem, especially for the Scott River, a major spawning tributary of the Klamath. The 2015-2017 Scott run was approximately 2000 spawners, as compared to over 12,000 in 2014. Few fall-run salmon have been counted in the Scott this fall, compared to 4500 on the Shasta River. A past post describes the problem in detail.

The key factor in the decline of Scott fall Chinook has been poor late summer and early fall flows. Low flows do not allow adult salmon to ascend the Scott from the Klamath. This not only hurts that year’s Scott run, but out-year Scott (and Klamath) returns two to five years later.

The problem is especially acute this fall, with flows less than 10 cfs, less than 20% of the historical average (Figure 1). In fall 2017, flows were near or above average (Figure 2), leading to a small increase in the run to 2500, despite poor flows during the 2013-2015 drought. The strong 2014 run also helped.

The solution is simple: stop irrigating pastures and hayfields in Scott Valley after September 1. Many ranchers do, especially for hayfields, but not all. If that is not possible, there are many idle wells of 5-10 cfs capacity each that could pump water into the river to keep the river adequately watered, with little threat to subsequent winter groundwater recharge. A battle is brewing over Scott River water use and the public trust salmon resources.

Figure 1. Scott River flows fall 2018.

Figure 2. Scott River flow in fall 2017.