Category Archives: Water Quality

Franks Tract – Smelt Trap

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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: https://mavensnotebook.com/2019/02/07/bay-delta-science-conference-franks-tract-feasibility-study-applying-the-guidance-of-a-delta-renewed/ .

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.

Increasing Salmon Production in the Central Valley

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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

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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.

 

Delta Smelt Recovery Strategies – Winter 2020 Update

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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.

No Miracle March for Delta Fish

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A nice spurt of Delta inflow and outflow occurred during mid-March 2020 (Figure 1). In past dry winters, this would have been a life saver for many juvenile salmon and smelt in the Delta. But this March brought no miracles for Delta fish. Without new rules for the State Water Project (SWP), the Project’s Banks pumping plant in the south Delta maxed out exports (Figure 2), just like the SWP did after last December’s storms.1  March exports have been just below the maximum export-to-inflow (E/I) ratio allowed by the State Water Board (35%). From 2009 through 2019, the state’s incidental take permit (ITP)2 limited exports by restricting negative flows in Old River and Middle River (OMR restrictions) to protect the state-listed longfin smelt and Delta smelt. Not so in the winter of 2020.

Longfin smelt need more protection. See Figures 3-7. In the past, March 2020 conditions would have been termed high risk by the Smelt Working Group. But the Smelt Working Group disappeared while the new federal Biological Opinions for Delta operations were making their entrance in late 2019. Although managers often ignored the recommendations of the Smelt Working Group, there was at least some outside technical documentation and accountability.

Meanwhile, the state’s soon-to-be-released new ITP looks like it will divert the discussions that the Smelt Working Group used to have to an in-house colloquy between the Department of Water Resources and the Department of Fish and Wildlife. The ITP also has provisions to allow more negative OMR’s and thus higher levels of exports during storm events. This will make fish in the Delta more dependent on miracles even as miracles become harder to come by.

Figure 1. March 2020 calculated Delta outflow. Source: CDWR.

Figure 2. March 2020 Delta exports. TRP = Federal Tracy Plant. HRO = state Harvey Banks Plant.

Figure 3. Early March 2020 Larval Survey for Longfin Smelt. Yellow denotes X2 location. Blue arrow denotes positive downstream Sacramento River channel flow. Red arrows denote interior Delta net flow direction. Pattern indicates risk to Longfin Smelt.

Figure 4. Mid March 2020 CDFW Larval Survey – partial survey results for longfin smelt.

Figure 5. Mid March 2020 CDFW 20-MM Survey – partial survey results for longfin smelt.

Figure 6. March 2020 Old and Middle River combined daily average flows in Central Delta. Source: USBR.

Figure 7. March 2020 tidally-filtered flows at three Delta locations that represent net Delta outflow. Note mid-March outflow (sum of three) was negative for several days. Source: USGS.