Delta Smelt Sanctuary – Deepwater Ship Channel

In a March 2020 post, I described where the remnants of the endangered Delta smelt population spawn and rear in the Sacramento Deepwater Ship Channel (Ship Channel) in the north Delta (Figure 1). In this post, I describe how the rearing conditions in the Ship Channel are poor. This can be seen by comparing habitat conditions in the Ship Channel with those in the lower Sacramento River channel at Freeport several miles to the east in late spring 2020.

Net Flow

Net flow (cfs) in the Ship Channel remains near zero, since the gate at the north end of the channel near Sacramento remains stuck in the closed position as it has been for several decades (Figure 2).

Water Temperature

Water temperature (oC) is significantly higher in the stagnant flows of the Ship Channel than at Freeport, often reaching into the lethal range 23-25°C for Delta smelt (Figure 3).


Salinity (conductivity) is much higher in the Ship Channel because of discharges from urban sewage treatment plants and agricultural operations (Figure 4).


Turbidity is much higher in the Ship Channel due to higher plankton production and port-bound ship traffic in the relatively shallow and narrow Ship Channel (Figure 5).

Dissolved Oxygen

Dissolved oxygen levels are much lower in the Ship Channel because of warmer water, high concentrations of suspended organic sediments, and higher plankton production (Figure 6).

Interpretations and Conclusions

Delta smelt are attracted to the Sacramento Deepwater Ship Channel in winter and early spring to spawn in the relatively warm, low salinity, turbid, and more productive water. The adult smelt can also easily tidal-surf up the ship channel without having to content with strong downstream currents of the Sacramento River channel. Their eggs hatch early to an awaiting abundant plankton food supply. However, in spring the Ship Channel lacks net downstream flows to carry the young smelt to the Bay. By late spring, water temperatures in the Ship Channel reach lethal levels for the young smelt.

Opening the gate at the north end of the Ship Channel would help to alleviate the problems by providing net flow with cooler water temperatures, and by flushing and diluting the stagnant waste waters in the Ship Channel. An operable gate at the head of the Ship Channel would allow adaptive management of the habitat conditions for smelt.

Figure 1. Locations where Delta smelt young were captured in EDSM surveys in July 2019. Circles represent regions. Numbers are total July catch in region. The 94 represents the young smelt captured in the Deepwater Ship Channel.

Figure 2. Net daily flow (cfs) in the Ship Channel and in the Sacramento River at Freeport in June 2020. The green line shows flow in the Ship Channel.

Figure 3. Water temperature in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows the water temperature in the Ship Channel.

Figure 4. Conductivity (salinity) in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows salinity in the Ship Channel.

Figure 5. Turbidity in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows turbidity in the Ship Channel.

Figure 6. Dissolved oxygen in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows dissolved oxygen in the Ship Channel.



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.

Delta Smelt Recovery Strategies – Winter 2020 Update

The Delta smelt are in trouble. The state and federal programs to help smelt recover are failing to meet their goals. The Delta Smelt Resilience Strategy adopted in 2016 is the State’s program to save Delta smelt. The State Strategy is not working, and has perhaps even made things worse in the four below normal and wet years that the state strategy has been applied since the 2013-2015 drought. This failure may explain why the strategy document is stored as a “legacy” file on the California Natural Resources Agency’s website.

The State’s Strategy consists of a number of action programs to help smelt:

  • Aquatic Weed Control
  • North Delta Food Web Adaptive Management Projects
  • Delta Outflow Augmentation
  • Reoperation of the Suisun Marsh Salinity Control Gates
  • Sediment Supplementation in the Low Salinity Zone
  • Spawning Habitat Augmentation
  • Roaring River Distribution System Food Production
  • Coordinate Managed Wetland Flood and Drain Operations in Suisun Marsh
  • Adjust Fish Salvage Operations during Summer and Fall
  • Stormwater Discharge Management
  • Rio Vista Research Station and Fish Technology Center
  • Near-term Delta Smelt Habitat Restoration
  • Franks Tract Restoration Feasibility Study

When the Delta Stewardship Council last took a close look on progress of the State Strategy in 2019 it found little that was encouraging. It identified two actions that showed promise: hatchery supplementation of Delta smelt and the operation of the Suisun Marsh Salinity Control Gates (SMSCG). More recently, the State has stated in its February 20, 2020 lawsuit against the Bureau of Reclamation that the Delta smelt hatchery program is not reasonably certain to have positive benefits.

The Federal Strategy shows even less progress and little future promise. The Federal Strategy consists of a number of action programs to “help” smelt while further reducing water allocated to their recovery:

  • Delta Smelt Outflow Action
  • Operations of the Suisun Marsh Salinity Control Gates
  • Directed Outflow Project (DOP)
  • Mesocosm (Cage) Studies – cultured smelt raised in cages
  • EDSM: Endangered Delta Smelt Monitoring is a year-round weekly sampling program administered by the Service and voluntarily funded by Reclamation.
  • Drivers of Delta Smelt Health Study
  • The Salinity and Growth History of Delta Smelt Study
  • The Delta Outflow Augmentation Modeling Study
  • Roaring River Distribution System Restoration: Experimentally produces food through wetland management in the Suisun Bay and Marsh.
  • Sacramento Deepwater Ship Channel nutrient manipulation involving experimentally seeding nutrients in the Deepwater Ship Channel to enhance productivity in Cache Slough.

It is worth noting that while both the State and federal programs point to the importance of Delta outflow, the latest State and federal operating plans for the Delta both propose to reduce outflow compared to recent past operations. Reducing outflow requirements leads to higher Delta exports.

Below, I summarize results of two experiments to increase north Delta smelt food production in 2019.

In a prior update in October 2018, I opined that the benefits of 2018 north Delta food actions were questionable, despite optimism by the state and federal programs. The actions were applied again in 2019, with results similar to those in 2018. During September 2019, approximately 600-800 cfs of river and ag-return water (Figure 1) was routed down the Colusa Basin Drain and through the Yolo Bypass into the north Delta at Cache Slough near Rio Vista. As in 2018, the Lisbon gage indicated depressed levels of dissolved oxygen (Figure 2), reflecting the high organic load in drain water from the agricultural Colusa and Yolo Basins carried in the Colusa Basin Drain. Though the organic load was higher in 2019, the level of chlorophyll (algae) was lower at the Lisbon gage (Figure 3) and in the north Delta (Figure 4). The organic load was accompanied by an increase in nutrient and mineral components (salts) (Figure 5). Normally, higher dissolved oxygen depressing organic loads and higher salt levels are considered pollution; however, in this case, high levels are designated as “fertilizer” with the ascribed benefit of producing more food for smelt in the Delta.

Reclamation’s attempt to stimulate food production by “fertilizing” the Deepwater Shipping Channel adjacent to the lower Yolo Bypass involved dispersal of 6 tons of nitrate salts via crop dusters (Figure 6) in August 2019. There may have been some limited stimulus of chlorophyll production in the Sacramento channel near Rio Vista (Figure 4) and in the lower Ship Channel (Figure 7). However, the chlorophyll concentrations in the middle (Figure 8) and upper (Figure 9) Ship Channel showed little or no response to the “fertilizing” effort.

In conclusion, the state and federal strategies to help recovery of Delta smelt either lack progress or show little if any benefit in terms of smelt food production and smelt reproduction. The federal Enhanced Delta Smelt Monitoring Program’s (EDSM) intensive survey of adult Delta smelt over the past four winters indicates further declining numbers (see chart immediately below).

Figure 1. Flow in tidal lower Yolo Bypass at Lisbon Weir gage near I-80 causeway in summer 2019.

Figure 2. Dissolved oxygen levels at Lisbon gage in the lower Yolo Bypass in summer 2019.

Figure 3. Chlorophll levels at Lisbon gage in the lower Yolo Bypass in summer 2019.

Figure 4. Chlorophyll concentrations in the north Delta channel of Sacramento below the mouth of Cache Slough near Rio Vista in summer-fall 2019.

Figure 5. Electrical conductivity recorded in the lower Yolo Bypass near Liberty Island in summer 2019.

Figure 6. Crop dusting fertilizing in Ship Channel August 2019. Reclamation photo.

Figure 7. Lower Ship Channel chlorophyll concentrations summer-fall 2019.

Figure 8. Middle Ship Channel chlorophyll concentrations summer-fall 2019.

Figure 9. Upper Ship Channel chlorophyll concentrations summer-fall 2019.