The Importance of the Bay-Delta Estuary to the Recovery of Wild Chinook Salmon

Common sense says salmon recovery efforts should focus on the most important factors that control fish population dynamics. In reviewing Central Valley population dynamics, I have seen each life stage and each individual controlling factor become important at one time or another. In my experience, the estuarine rearing and migrating stage is an essential component that is not given enough attention.

Central Valley salmon populations are nearly all “ocean-type” Chinook salmon, meaning they move to the ocean usually during their first six months of life, with substantial estuary rearing as fry, fingerlings, and pre-smolts. That is not to say that yearling smolts contributions are not important. It is that they are a minor contribution in “ocean-type” Chinook (note that late-fall-run are “river-type”).

I have always believed the survival of wild salmon fry in the Bay-Delta to be a key limiting factor in wild salmon production in the Central Valley. Hatcheries have kept smolt numbers to the ocean up, while the survival of wild salmon eggs, fry, fingerlings, and smolts has worsened. Fry-fingerling estuary survival is important, if only in the sense of sheer numbers and the resulting potential to increase overall smolt production. This is true for fall-run, spring-run, and winter-run populations. There is substantial evidence that returning wild adult salmon are predominantly from the estuarine-reared groups. Such evidence exists from fish surveys, scale analyses, and genetic studies. Thus, a recovery program for wild salmon should include a strong focus on estuarine rearing and survival.

My beliefs are shaped in large part from my personal experiences in conducting winter seine and screw trap surveys throughout the Bay-Delta and lower rivers. Young wild salmon classified as fry and fingerlings, 30-50 mm (1-2 inches), dominate the inshore landscape and screw trap collections. Millions of fry and fingerlings pour out of the spawning rivers and tributaries into the main rivers and into the Delta, where they dominate the winter fish community. Larger, more elusive pre-smolts, mostly winter-run, are also present in smaller numbers, but in numbers important to the winter-run population. Yes, there are millions of fry left to rear in highly regulated and disturbed river habitat, but their overall numbers are fewer, with less potential for ultimate survival to smolts entering the ocean than their estuarine counterparts.

One of the better indicators of the general pattern of estuarine use by salmon is fish salvage collections at the massive federal and state pumping plants in the south Delta. As shown in Figure 1, December is important in the estuary for winter-run and late-fall-run pre-smolts and yearlings, respectively. The January through March period is important for spring-run and fall-run fry/fingerlings. The April through June spring period is important for spring-run and fall-run pre-smolts.

To support juvenile salmon in the estuary, Delta habitat therefore needs protection from December through June. Natural flows and flow direction patterns are important habitat features. Water temperature is important in late spring. Exports affect such habitat, especially in dry, low-flow years.

The State Water Resources Control Board is in the process of revising water quality standards in the Bay-Delta watershed.1 Salinity, flow, water temperature, and export-limit standards need updates to protect salmon using the Bay-Delta through the winter and spring. Such protections will be key to wild salmon recovery in the Central Valley.

Figure 1. Salmon salvage at south Delta pumping plants in 2011. Note red-outlined groups of predominately wild salmon. Blue dots depict salvage events for hatchery salmon.


Shasta River Update – April 2019

A February 20, 2019 article in the Eureka Times-Standard reported continuing improvement of Klamath River fall-run Chinook.

“The number of natural area spawners was 53,624 adults, which exceeded the preseason expectation of 40,700. However, the stock is still in “overfished” status as escapement was not met the previous three seasons. The estimated hatchery return was 18,564 adults for the basin.

Spawning escapement to the upper Klamath River tributaries (Salmon, Scott, and Shasta Rivers), where spawning was only minimally affected by hatchery strays, totaled 21,109 adults. The Shasta River has historically been the most important Chinook salmon spawning stream in the upper Klamath River, supporting a spawning escapement of 27,600 adults as recently as 2012 and 63,700 in 1935. The escapement in 2018 to the Shasta River was 18,673 adults. Escapement to the Salmon and Scott Rivers was 1,228 and 1,208 adults, respectively.”

In a May 2017 post, I discussed an increasing contribution to the Klamath run from the Shasta River.  In Figure 1 below, I have updated my original spawner-recruit analysis from the prior post with 2017 and 2018 escapement numbers for the Shasta River.  The Shasta run in fall 2018 was third highest on record for the Shasta River.  The river’s fall-run population continues to benefit from improved water management.  Coho salmon and steelhead have yet to show significant improvements (Figure 2).

An February 26, 2019 article from the publication Grist (posted in 2/26/19 Maven’s Digest) describes changes to water management in the Shasta River.  The Nature Conservancy, using public grant funds, purchased the nearly 5000-acre Shasta Big Springs Ranch for $14 million in 2009.  More recently, the California Department of Fish and Wildlife purchased the water rights of the Shasta Big Springs Ranch.  Now, more water is left in the Shasta River, and only a third (1500 acres) of the ranch remains irrigated.  The article in Grist states that the new allocation of water has negatively affected the ranch’s ability to support wildlife and threatened its ability to support ranching.  In addition, the article questions the benefits of the new management regime to fish: “[T]he fish don’t seem to be doing much better either.”

While some will argue the relative values of ranching and fish protection,  I see no grounds to argue that changes in water management have not been positive to the Shasta River and Klamath River salmon.  Summer flows in the river below the ranch appear to have improved over the long term average (Figure 3).  Many of the Shasta River’s Chinook and Coho salmon spawn in the Big Springs area and in the river below Big Springs, and depend on flow and cold water input from the springs.  Even with the contribution of this flow, water temperatures are marginal (>65oF) for young salmon from May to September (Figure 4).

From my perspective, the loss of several thousand acres of irrigated pasture out of roughly 25,000 acres in the Shasta Valley seems a small price to pay for a large step towards the recovery of Shasta and Klamath River salmon.

Figure 1. Spawner-recruit relationship for Shasta River. Escapement estimates (log10X – 2 transformed) are plotted for recruits by escapement (spawners) three years earlier. Year shown is recruit (escapement) year. The number is the year that fish returned to the Shasta River to spawn. The color of the number depicts the water-year type in the Shasta River during the year the recruits reared. The color of the circle depicts the water-year type in the Klamath River during the year the recruits reared. Blue is for Wet water-year types. Green is for Normal water-year types. Red is for Dry water-year types. Example: 90 depicts fish that returned to the Shasta River as adult spawners in 1990. These fish were spawned in 1987 and reared in winter-spring 1988. The red number shows that the 1988 rearing year was a Dry water year in the Shasta River; the red circle shows that the 1988 rearing year was a Dry water year in the Klamath River. Note very poor recruits per spawner in 1990-1993 drought period, compared with relatively high recruits per spawner from 2011-2018, even though the latter period included the 2012-2016 drought.

Figure 2. Shasta River salmonid runs from 1930 to 2017. Source:

Figure 3. Shasta River flows in the Shasta River below Big Springs 2016-2018 with 30 year average. Note summer base flow appears to have improved by approximately 10-30 cfs.

Figure 4. Water temperature in the Shasta River below Big Springs including summers of 2017 and 2018. Source: DWR CDEC.



Are Delta Smelt in Hot Water? Yes, and water management has been putting them there.

A March 14, 2019 post in Maven’s Notebook summarized a presentation at the 2018 Bay Delta Science Conference on Delta smelt growth factors in the Bay-Delta estuary. The main author, Dr. Hobbs, described UC Davis research on smelt growth rates from analysis of smelt ear-bone cross sections.

The research indicates that growth rate is related to salinity, water temperature, and water clarity (turbidity). Growth rates were depressed when salinity was above 3-4 parts per thousand (ppt),when water temperature exceeded 20-21oC, and when water clarity was relatively high.

Dr Hobbs also addressed the question: HOW WILL FLOW AUGMENTATION AFFECT THE DELTA SMELT?
“The answer generally is that it will have an effect if the flows will actually reduce salinity, increase turbidity or reduce temperature.” They found that flow affects salinity, but temperature and turbidity not so much.

  • “But from 2015-2017, we had an excessive period of time when it was above 22 degrees throughout the estuary.”
  • “The average temperature from 1999 to present shows that 2014 and 2015 were exceptionally warm and the water has been getting clearer throughout the estuary since the early 2000s. How are we going to manage freshwater flows to affect these other two important variables?”
  • “We’ve been thinking about how to manage freshwater flows for Delta smelt for the better part of 20 years, and what we need to be thinking about now is how do we manage temperature for Delta smelt? How do we manage temperature at all? Can we even manage temperature?”

My answer to the question about the effect of flow on Delta smelt is that flow is extremely important to salinity, water temperature, and turbidity, as thus Delta to smelt survival and population abundance.

  1. Dr. Hobbs implied that flow has little effect on water temperature, but he failed to mention that his two warmest years, 2014 and 2015, had the lowest spring-through-fall Delta inflows and outflows. Flow standards were relaxed in both years to save water in depleted reservoirs. He failed to mention that more flow keeps the low salinity nursery area of Delta smelt further west in Suisun Bay, where the air and water are cooler than the Delta.
  2. Dr. Hobbs also implied that flow has little effect on turbidity. But it is a fact that lower flows and higher exports in the 2000’s led to lower turbidities. More reservoir releases to feed south Delta exports lowers Delta turbidity. When the low salinity zone is west of the Delta, it benefits from the increased turbidity provided by higher winds and from more open shallow bays than are afforded by narrow deep Delta channels.
  3. Dr. Hobbs failed to mention that flow affects the transport of adults upstream to spawning areas and the movement of juveniles downstream to the low salinity zone nursery area.

Three additional points:

  1. Higher flows also benefit smelt food production and availability.
  2. Flow does affect the temperature of water entering the north Delta, in addition to affecting salinity and turbidity. In wet year 2017, summer inflows were low and consequently warm, negatively affecting smelt.1
  3. Smelt production is strongly related to the number of adult spawners (or eggs laid), and 2017 also suffered from poor numbers of spawners.2

Revised Delta Smelt Take Permit

The Interior Department’s US Fish and Wildlife Service (USFWS) issued a memo1 on January 30, 2019 that revised the federal take permit for Delta smelt for the combined operation of the Central Valley Project and the State Water Project. The memo stated:

“It has become clear over the past several years that surveys are reaching their detection limits given the declining population of delta smelt, and in 2018, the FMWT [fall midwater trawl] Index was zero, indicating that the FMWT Index may no longer provide an accurate predictor of incidental take.”

The new take criteria are now the old action criteria of limiting Old and Middle River (OMR) reverse flows during the winter and spring under certain conditions. When smelt would normally be expected to be present, OMR flows would be restricted to being no more negative than -2000 or -5000 cfs. The new “surrogate” criteria essentially keep the south Delta pumping plant operations at status quo until such time as the ongoing reinitiated Endangered Species Act (ESA) consultation is completed and new take permits are issued.

The importance of the rule change is diminished by the fact that Interior (combined action of US Bureau of Reclamation and USFWS) has not enforced the rules to protect Delta smelt. The state of California has also failed to protect Delta smelt as well as California ESA-listed longfin smelt. One only has to review recent early winter information to see this is the case. After the first Delta outflow pulse at the beginning of December 2018, outflow fell to only 4000 through mid-December (Figure 1). High exports (Figure 2) contributed to the low outflow and exceptionally low (negative) OMR flows (Figure 3).

These low outflows and high exports created very high risk conditions for the two smelt species. What few Delta smelt remained were observed in the west Delta (Figure 4). Longfin smelt were spawning in Suisun Bay and the west Delta (Figures 5 and 6).

Smelt are not being protected. The Smelt Working Group mandated under the Federal and State take permits has been inactive and has not provided mandatory guidance. New take permits are needed immediately to protect the two listed smelts. The State Water Board, in revisiting water right permits and water quality standards for the Delta, should also adequately protect the listed smelts. To protect the smelts, the OMR limit for December should have been no more negative than -2000 cfs. The export-to-inflow limit criteria for December should be 35%, not the present 65%. December outflow minimums should be 6000-8000 cfs, not the present 3500-4500 cfs.

Figure 1. Delta outflow 11/10/18 to 1/8/19. Note very low outflow in early December after initial rainfall pulse.

Figure 2. State project exports at Clifton Court December 2018 to February 2019. Federal exports were near maximum (3500-4200 cfs) for most of period.

Figure 3. OMR flows November 2018 to January 2019.

Figure 4. December 2018 Kodiak trawl survey catch of Delta smelt.

Figure 5. December 2018 midwater trawl longfin smelt catch.

Figure 6. Smelt Larvae Survey #1 for 2019 catch of newly hatched longfin smelt.

Winter-Run Salmon Update – March 2019

This post updates a 7/25/18 post on the status of the endangered winter-run Chinook salmon population of the Sacramento River. Figure 1 is an updated figure showing the influence of water supply conditions on the spawner-recruit relationship of winter-run during the recruits’ first year of life in the Sacramento River. The relationship is also influenced by hatchery contributions that began in 1998 and continue today.1 Other factors, including water temperature control improvement at Shasta Dam and changes to permits and water quality plans (not depicted), are also likely unaccounted-for factors. Figure 2 depicts raw run numbers by spawning year.

What the relationship shows is that there is a strong positive spawner-recruit relationship heavily influenced by water supply conditions and hatchery contributions. The recent estimates of >70% contribution from the hatchery to the population recruits1 reflects the importance of the hatchery role and the underlying problem of declining “wild” spawner contribution. Note that the spawner numbers for 2018 (recruits from critical year 2015 spawners) are as yet unpublished. Hatchery smolt production and releases were doubled in 2015, the third critical year of the 2013-2015 drought.

Figure 1. Spawners versus recruits (spawners three years later) transformed (logx minus 2). Year is spawner year. For example, 2014 is spawning year with 2017 recruits. Color denotes water-year type in spawning year: bold red is critical year, non-bold red is dry year, green is normal year, and blue is wet year. For example, red 13 represents critical water year 2013. Squares around numbers indicate the presence of hatchery contributions (begun in 1998).

Figure 2. Spawning population estimates of adult winter-run salmon in the upper Sacramento River from 1974 to 2017. Source: CDFW.