Franks Tract – Smelt Trap

In a May 2019 post, I described the central Delta as a salmon trap for juvenile salmon. This post describes the “smelt trap.”  Franks Tract in the central Delta (Figure 1) is a longfin and Delta smelt trap.  Longfin smelt were vulnerable to the trap in March 2020 (Figures 2 and 3).  Flow was reversed in False River (Figure 4) because of south Delta exports.

It’s not just the net flow that makes Franks Tract a smelt trap.   It is also tidal pumping of 50,000 cfs in-and-out.  What goes into Franks Tract on the flood tide does not come back out the same (Figures 5-9).  It is different water, warmer, clearer, with less plankton, and probably less smelt larvae and juveniles.  Smelt are simply tidally-pumped into the central Delta where they are susceptible to warmer, less turbid, predator-laden waters of Franks Tract and the central and south Delta.  Most young smelt probably succumb before reaching the south Delta export pumps.

This is another reason why winter Delta exports need restrictions and why the Franks Tract restoration project with its tide gate on False River needs to proceed as part of the state’s program to recover longfin and Delta smelt.  For more detail on the proposed project see: .

Figure 1. Franks Tract and False River gage location in west Delta.

Figure 1. Franks Tract and False River gage location in west Delta.

Figure 2. Longfin smelt distribution in March 2020 20-mm Survey #1.

Figure 2. Longfin smelt distribution in March 2020 20-mm Survey #1.

Figure 3. Longfin smelt distribution in March 2020 Larval Smelt Survey #6. Station 901 is in Franks Tract.

Figure 4. False River net daily tidally filtered flow (cfs) in March 2020.

Figure 5. Hourly flow at False River gage March 29 to April 5, 2020.

Figure 6. Hourly water temperature at False River gage March 29 to April 5, 2020.

Figure 7. Hourly turbidity at False River gage March 29 to April 5, 2020.

Figure 8. Hourly chloropyll at False River gage March 29 to April 5, 2020.

Figure 9. Hourly EC at False River gage March 29 to April 5, 2020. Note slightly brackish water (300-500 EC) moves upstream in False River on flood tides (Figure 5), but returns fresher on ebb tide from mixing in Franks Tract.

A Month of High Exports Pulls Salmon and Smelt to Delta Pumps

Increased Delta exports by the federal Bureau of Reclamation in early April resulted in increased salvage of salmon and longfin smelt at the Central Valley Project’s south Delta Tracy Pumping Plant. Salmon smolts salvaged were predominately from the San Joaquin spring-run salmon recovery program hatchery (Figures 1 and 2). Longfin smelt salvage increased in mid-April (Figure 3) as young longfin reached salvageable size (~25 mm).

Salvage at the State Water Project was much lower in April as the California Department of Water Resources’ (DWR) reduced exports to try to offset the impacts of Reclamation’s increased pumping (Figures 2 and 3).

The state’s Bay-Delta Water Quality Control Plan requires that exports be reduced to be no higher than the San Joaquin River flow at Vernalis from April 15 through May 15. The Bureau of Reclamation and the California Department of Water Resources (DWR) were allowed to move those dates up in 2020, so that the month-long reduction began on April 10 (Figure 4). The average Vernalis flow was about 1500 cfs in mid-April, which is why exports wound down as required (Figure 3).

High exports in early April drew migrating salmon and longfin smelt into the south Delta. Old and Middle River (OMR) flows reached their limit of -5000 cfs (Figure 4). Thus, even after Reclamation and DWR reduced exports on April 10, salvage of both salmon and smelt continued to be high for a week, tapering down to lower levels on April 20.

State and federal exports should not have been ramped up in late March and early April. Had they been given the opportunity, the joint state and federal smelt and salmon science working groups would have recommended a range of -1500 to -2500 cfs OMR limit given the risks to salmon and smelt. However, in the epoch of the 2020 federal Biological Opinions for Delta operations, Reclamation has chosen to export as much as allowed by its view of the letter of the law. California’s view of the law is different: on April 21, 2020, California sought an injunction as part of its ongoing lawsuit against Reclamation’s operations under the new BiOps. See and

If we want to save salmon and smelt, we simply must reduce exports in winter and spring, especially in drier years, as was generally standard procedure over the past decade under the 2008-09 federal Biological Opinions.

Figure 1. Salvage of salmon in water year 2020. The blue dots represent salvage of San Joaquin spring-run hatchery smolts.

Figure 2. Late March and April 2020 daily Delta export rates and salvage of young salmon.

Figure 3. April 2020 daily Delta export rates and salvage of young longfin smelt at south Delta export facilities

Figure 4. Old and Middle River (OMR) flow in the central Delta in 2020.

Phantom Predator – Striped Bass?

In a recent 2020 essay in SAN FRANCISCO ESTUARY & WATERSHED SCIENCE, authors Nobriga and Smith describe striped bass as a “phantom predator” that for a century has been secretly driving down their “naïve prey,” the Delta smelt. The authors hypothesize that Delta smelt were much more abundant that the earliest regular monitoring data would indicate, and that striped bass did most of this damage to the Delta smelt population before there was widespread monitoring of either Delta smelt or striped bass.

The authors’ analyses, interpretations, and conclusions have a major omission. They fail to include the potential role of other native and non-native predatory fish in driving down the population of Delta smelt, regardless of the actual abundance of Delta smelt in the eighty years after stripers were introduced to the Bay-Delta in 1879 and 1882. Dozens of other predatory species also proliferated in the Delta over that past century, especially over the past several decades. Today, those other predatory species are far more abundant than the striped bass, and many are equal if not greater potential predators on young smelt than striped bass. In fact, striped bass are more likely to prey on juveniles and adults of other predator species than on smelt.

The authors are from the US Fish and Wildlife Service, the federal agency bound to protect the Delta smelt under the Endangered Species Act. The authors used “California Department of Fish and Wildlife fish monitoring data to provide evidence for a ‘phantom predator’ hypothesis: that ephemeral but persistent predation by Striped Bass helped to marginalize Delta Smelt before the estuary was routinely biologically monitored.”, The authors argue against “a misinterpretation that Striped Bass had little contemporary effect on Delta Smelt,” and “contend that the Delta Smelt population has declined steadily since Striped Bass were introduced to the estuary, and that has masked a substantial predatory effect of Striped Bass on Delta Smelt.” The article describes and supports a hypothesis that striped bass remain a problem for Delta smelt, despite the precipitous decline in the production of juvenile striped bass over the past century or so.

To partially address the hypothesis myself, I analyzed some Interagency Environment Program (IEP) data1 collected over the decade of 2009-2018 from one of the remaining Delta smelt strongholds – the lower Yolo Bypass portion of the Cache Slough Complex of the north Delta (Figure 1). Delta smelt were a common seasonal resident of the area (Figure 2). Striped bass, as expected, were very abundant in all age groups over much of the survey periods (Figure 3). But so were many species of invasive non-native catfish, sunfish, crappie, gobies, minnows, tule perch, black bass, and shad, most of which have been present in the Delta as long as striped bass.

Black crappie alone make up an equivalent or greater predator force on Delta smelt (Figure 4). In addition, black crappie as well as many of the other abundant predators compete with Delta smelt for their common zooplankton food supply. Not one of these potential other sources of predation or competition is mentioned in the essay.

Nobriga and Smith do acknowledge: “A generalist predator like Striped Bass, however, could suppress Delta Smelt competitors in addition to Delta Smelt, leading to non-linear and counter-intuitive community dynamics” – a theory that once-abundant striped bass have been suppressing other non-native predators and competitors of Delta smelt. So how long has that dynamic been functioning? Was it functioning in the hypothesized epoch of “phantom” predation? Did striped bass accelerate the decline of Delta smelt or, by eating and consuming other predators, slow it down? And assuming that Delta smelt really were much more abundant than previously believed prior to widespread monitoring in the Delta, to what degree was predation a factor in that decline?

Figure 2. Lengths of Delta smelt collected in fish surveys in lower Yolo Bypass 2009-2018. Note that up to 70% of the smaller young 20-60 mm smelt were later genetically identified as Wakasagi.

Figure 3. Lengths of striped bass collected in fish surveys in lower Yolo Bypass 2009-2018.

Figure 3. Lengths of black crappie collected in fish surveys in lower Yolo Bypass 2009-2018.

Increasing Salmon Production in the Central Valley

The state of California has a comprehensive Water Plan to provide a guide for the state’s future water supply.  Why is there no state Salmon Plan?  California also has a plan to restore Bay-Delta habitat called California EcoRestore.  Why not a SalmonRestore, or at least a comprehensive salmon plan as a part of EcoRestore?

Much of the key to increasing salmon production in the Central Valley is to increase flows in rivers and Delta inflow and outflow.  Another key element is to improve reservoir management for water temperatures and the protection of spawning habitat downstream of dams.  Water in sufficient quantity and of sufficient quality is indispensable.

In addition to better water management, the state needs a plan to implement five basic physical approaches to increasing salmon production in the Central Valley.

  1. Restore River Rearing Habitat – Restore river corridor and side-channel rearing habitat in the mainstem rivers and tributaries
  2. Restore Floodplain Rearing Habitat – Increase volitional access of juvenile salmon to the Valley’s agricultural floodplain through gated weirs; enhance such rearing habitat, and implement strategies to reduce stranding of adult and juvenile salmon in that habitat.
  3. Restore Spawning Habitat – Restore salmon spawning habitat in the mainstem rivers and their tributaries by introducing spawning gravel and improving other physical aspects of channel habitat.
  4. Implement Upstream and Downstream Trap and Haul Capture juvenile salmonids and transport them from existing spawning areas downstream in dry years when low flows and resulting high water temperatures are unsuitable for volitional downstream migration and survival. Capture and transport adult salmon to upper watersheds above impassable dams, and capture and transport their juvenile progeny back downstream of those dams to locations where high survival is likely.
  5. Increase Hatchery Contributions – Increase the number of hatchery smolts that reach the ocean, while minimizing negative effects of hatcheries on wild salmon populations.

Available options in each of the five categories are virtually limitless, as are the potential costs and benefits.

The National Marine Fisheries Service has a Recovery Plan for salmonid species that are listed as threatened or endangered under the Endangered Species Act.  Such recovery is valuable and important.  But fisheries agencies also can and must do better in supporting the commercial and recreational fishing industries that depend largely on fall-run salmon that are not listed under the ESA.  A state Salmon Plan should be part of the strategy, and the sooner the better.







Wild Central Valley Salmon: Managers Missing an Opportunity

This winter and early spring of 2020 have been drier than normal in the Central Valley. However, precipitation in January, March, and now April provided opportunities to greatly enhance this year’s brood of fall and spring run salmon success. Water managers missed these opportunities by capturing all the water in reservoirs. What happened to prescribed spring flow pulses for salmon in state and federal plans? Is holding the promised water back the “best science”?1 No.

Shasta, Oroville, and Folsom reservoirs, the largest in Sacramento Valley, have released no flow pulses since January 1 to the Sacramento, Feather, and American rivers (Figure1). These are the rivers with the state’s biggest runs of fall-run and spring-run salmon. These three reservoirs now hold 6.5 million acre-feet (MAF) of stored water, over 95% of average for this date. Also available is 2 MAF of water now stored in Trinity Reservoir, which is at 109% of average for this date. Local rainfall and un-dammed tributaries have provided three significant flow pulses in lower rivers and the Delta, but these pulses have not touched the spawning and rearing grounds just downstream of the major dams.

Figure 1. Streamflow (cfs) in the upper section of the lower Sacramento River below Shasta (KWK – Keswick), the middle section of the lower Sacramento River (WLK – Wilkins), the lower section of the lower Sacramento River (FPT – Freeport), the lower Feather River (GRL – Gridley), and the lower American River (AFO – Fair Oaks).

The lower San Joaquin River watershed had a similar record this year, with minimal contribution to Delta inflow and outflow or to flow pulses from reservoirs (Figure 2).  The watershed’s largest reservoir, New Melones on the Stanislaus River, has 121% of average for the date with 1.9 MAF of water in storage.  New Melones did provide a small release in early February and appears to be ramping up releases in early April.  But the State Water Board has already written a letter to the Bureau of Reclamation calling Reclamation out for failing to maintain required flows in the lower San Joaquin River.

Figure 2. Streamflow (cfs) in the lower San Joaquin River (VER – Vernalis), the lower Stanislaus River (RIP – Ripon), and Delta outflow (DTO).

The river flow and Delta outflow pulses in early April have spurred the annual exodus of juvenile spring and fall run salmon from the Delta (Figure 3).  It is important to get as much of the river juvenile salmon production into the Delta as soon as possible to take advantage of this critically-timed pulse in Delta outflow.  The tailwaters of the large dams holds tens of millions of wild fry and juvenile salmon (30-50 mm in length) that need to get downstream to grow and to emigrate into and through the Delta.  These young salmon need reservoir releases to encourage their emigration and improve their growth and survival.  Most importantly, pulses will piggy-back on the present April pulse in Delta outflow.  This need is most pronounced in the San Joaquin salmon watersheds, where flows have been low and few salmon have reached the Delta (Figure 4).  The need to support the fall-run and spring-run salmon emigration extends at least through April and into May, including over 20 million hatchery salmon smolts released from tributary hatcheries (Figures 5 and 6).

Figure 3. Catch of juvenile salmon at exit from the Delta at Chipps Island In 2020.

Figure 4. Catch of juvenile salmon in the lower San Joaquin River at Mossdale at entrance to the Delta In 2020. Note catch was only one so far in 2020.

Figure 5. Timing of the fall-run salmon exiting the Delta in brood years 2005-2018 (2006-2019).

Figure 6. Timing of the spring-run salmon exiting the Delta 2006-2019.