Central Valley Spring Run Salmon – Record Low Run

Posted on November 14, 2018 by Tom Cannon

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

Posted on November 11, 2018 by Tom Cannon

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

http://calsport.org/fisheriesblog/?p=1052 ↩
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

Posted on October 28, 2018 by Tom Cannon

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.

https://cdfgnews.wordpress.com/2018/10/10/upper-klamath-river-quota-met/ ↩

Delta Smelt Resiliency Strategy – Update Fall 2018

Posted on October 22, 2018 by Tom Cannon

A summer pulse flow through the Yolo Bypass via the Colusa Basin Drain (Figure 1) was implemented in September per the Delta Smelt Resilience Strategy’s North Delta Food Web Action (Figure 2). I reviewed the initial application of the action in July 2016, concluding then there was no evidence that the action would meet its overall goals, but that the approach had potential.

The basic concept is this:

– By routing agricultural drain water through Yolo Bypass instead of the Sacramento River, DWR scientists predicted that a flush of plankton-rich water would provide a “seed” for the downstream Delta, enhancing food resources for Smelt. (Note: Historically, summer drain water from Colusa Basin rice fields was discharged into the Sacramento River at Knights Landing.)

– A similar managed flow pulse was generated in July 2016 with the help of Sacramento Valley water users, which helped transport plankton to the Delta. (Note: additional Sacramento River water was diverted near Red Bluff to the Colusa Basin Drain to supplement rice field drainage. There was no evidence that plankton blooms in the Yolo Bypass reach the Delta in meaningful amounts.)

– The action is designed to maximize the environmental benefits of water. Water isn’t “consumed” by the action–it is directed down a different and more productive path to the Delta. (Note: The basic concept is simple. The nutrient-laden drain water stimulates Yolo Bypass productivity, and the added river water flushes it through to the north Delta. Taking some of the Sacramento River at Red Bluff and routing it through the Colusa Basin irrigation and drainage system, then on to the Yolo Bypass tidal channels, should stimulate biological productivity and flush it, along with excess nutrients and organic debris from rice fields into the Delta at the end of the Bypass (Cache Slough – Rio Vista area). The Delta (and smelt) would benefit from the added biological productivity (phyto-zoo plankton) and nutrients (nitrogen, phosphorous, and organic carbon).

Does the concept work, and does it come without complications?

During implementation in 2018, there was an 60% uptick in aquatic plant productivity in the lower Yolo Bypass (Figure 3).
There was no increase in productivity as of early October in the north Delta at Rio Vista (Figure 4).
The water routed through the Bypass was initially warm (>70^oF, Figure 5), high in salts (Figure 6), lower in turbidity (Figure 7), and low in dissolved oxygen (Figure 8).
Warm water and the high organic load resulted in poor dissolved oxygen levels (3-5 milligrams-per-liter) that violate state standards and are potentially lethal to salmon migrating through the Bypass¹.

On a positive note, routing drain water to the Bypass does keep the poor quality drain water out of the Sacramento River below Knights Landing.

In sum, the benefits of the action remain questionable. Waiting to conduct the action until fall when waters are cooler could alleviate high water temperatures and low dissolved oxygen in the water. It might also create more Delta benefits by delaying nutrient use until nutrients reach the Delta. Further research is warranted into the water quality of the drain water, especially its oxygen-depriving, high-organic load and its chemical constituents (salts, herbicides, and pesticides). Otherwise, it may be that the action is little more than an augmentation of the current practice of dumping what might be described as polluted agricultural drain water into Central Valley rivers and the Delta.

Figure 1. Stream flow (cfs) in Yolo Bypass below Colusa Basin Drain outlet. The pulse flow reached the Yolo Bypass on or about August 28 and ended on September 25.

Figure 2. Project scheme and map of key features.

Figure 3. Chlorophyll concentration in lower Yolo Bypass at Lisbon in late summer 2018. There was a 50% increase in late September to about 8 micrograms per liter, although below the target of 10 or higher.

Figure 4. Chlorophyll concentration in north Delta at Rio Vista in late summer 2018. There was a slight decline after September 1 to about 1.25 micrograms per liter, well below the target of 10 or higher.

Figure 5. Water temperature in lower Yolo Bypass at Lisbon in late summer 2018.

Figure 6. Salt concentration (EC) in lower Yolo Bypass at Lisbon in late summer 2018. The drain water entering at the end of August had a high salt concentration.

Figure 7. Turbidity (NTUs) in lower Yolo Bypass at Lisbon in late summer 2018.

Figure 8. Dissolved oxygen (mg/l) in lower Yolo Bypass at Lisbon in late summer 2018. The drop in DO at the end of August reflects the high organic load of the drain water.

Migrating adult salmon are common in the Bypass in September, possibly being attracted to rice drainage flows with the chemical signal of the upper Sacramento River. ↩

Reclamation releases final environmental documents for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project

Posted on October 19, 2018 by Tom Cannon

A September 24, 2018 Reclamation press release announces:

The Bureau of Reclamation has issued final environmental documents for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project. The project’s purpose is to determine if the addition of nitrogen can stimulate (fish food organisms) production in a section of the ship channel, which is isolated from the Delta in terms of water flow.

The project is an initial step in a broader effort to determine if, through the repair of the West Sacramento lock system, Sacramento River flows could be used to move fish food organisms through the Sacramento Deep Water Ship Channel to the Delta. This step seeks to benefit delta smelt and the Bay-Delta System.

The press release and project Final Environmental Assessment (EA) are misleading in representing existing conditions and future project benefits.

Reclamation fails to explain the high EC (salt levels) in the project reach of the upper ship channel (Figures 1 and 2). Figure 1 includes three black arrows added to the project figure. These arrows represent large municipal/agricultural drains from the adjacent West Sacramento “island basin” that add salts, nutrients, and other wastes to the ship channel on a seasonal basis (generally early spring). The poor productivity in late summer may be at least partially due to these “waste” discharges.
The EA says: “This will restore nitrogen levels that occur naturally earlier in the season before drawdown by phytoplankton growth.” However, high nitrogen levels are not “natural.” They are man-made.
The EA says: “The fertilizer to be used for this experiment contains 1% ammonium nitrogen (NH4-N).” The press release and EA fail to mention billion dollar efforts to remove ammonium nitrate inputs to the north Delta from the Sacramento Regional Wastewater Treatment facility.

The press release acknowledges that repair of the ship channel gates would allow seasonal pulses of high plankton productivity to be flushed into the north Delta. Effective operation of these gates (selective opening and closing) would move existing blooms in the upper Ship Channel down into the Delta, likely eliminating the need for the addition of nitrogen. It would also reduce the temperature of the water in the Ship Channel. For more on these issues, see a previous post.