Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Delta Outflow Measurement

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Delta outflow has been estimated by state and federal agencies for over 50 years.  The Department of Water Resource’s Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay.  The federal Bureau of Reclamation’s Delta Outflow estimate is calculated similarly and presented as a daily average flow in cubic feet per second on Reclamation’s website.

Now a third estimate of Delta Outflow is available from the federal US Geological Survey on one of its websites (https://waterdata.usgs.gov/nwis/inventory?agency_code=USGS&site_no=380245121532301).  This site has daily average estimates for a “gage” near Chipps Island since summer of 2016.  The estimate is from tidally filtered flow/stage data.

A comparison of the DWR and USGS estimates is shown below in Figures 1 and 2.  The two estimates are very similar.  A closer comparison during the low-flow summer periods of 2018 (Figure 3) and 2019 (Figure 4) indicates significant differences, or at a minimum a modicum of uncertainty in one or both of the estimates.  The average flow in the DWR data for 2018 data is about 10% higher over the period than the USGS data.  The role of tides or tidal filtering in the USGS estimate is a likely factor in the difference.  Under high seasonal tide periods (termed spring tides), outflows can fall to near zero, with major ramifications to salinity and water over the entire Bay-Delta, especially in the high export summer season.

The state’s current water quality control plan for the Delta includes objectives for Delta outflow (Figure 5).  The objectives are stated as a monthly average.  The low level of the objectives 3000-8000 cfs should give one pause as to the level of protection that these objectives provide to public trust resources like fish.  The Water Resources Control Board is in the process of updating its plan and water quality objectives.

In past posts, I have advocated for daily salinity standards for the Delta rather than bi-weekly or monthly objectives for outflow, flow, export, and salinity.  Such daily standards could be readily planned for, managed, monitored, and assessed for effectiveness.

Figure 1. USGS estimate daily Delta outflow Sep 2016 to Sep 2019.

Figure 2. DWR estimated daily Delta outflow Sep 2016 to Sep 2019.

Figure 3. Estimated daily outflow by DWR and USGS summer 2018.

Figure 4. Estimated daily outflow by DWR and USGS summer 2019.

Figure 5. Delta outflow objectives in state’s water quality control plan.

It is Fall X2 Time Again

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The 2008 Delta Smelt Biological Opinion for Central Valley Project (CVP) and State Water Project (SWP) includes the Fall X2 provision to keep brackish water west of the Delta through October in wet years to protect Delta smelt.  X2 or the low salinity zone is defined as the location where salinity is 2 parts per thousand (about 4000 EC). Keeping X2 at Chipps Island (km 71 from the Golden Gate) benefits the longfin smelt and Delta smelt populations.  In wet years, the smelt are protected by Delta agriculture salinity standards through August 15.  The Fall X2 provision keeps X2 and the smelt west of the Delta through October.

This is the third wet year since 2008 (the others were 2011 and  2017) in which the provision for X2 in the Biological Opinion has applied.  When I last posted about the 2017 implementation, I remarked that the US Bureau of Reclamation had requested not to apply the provision because of the high cost of water and minimal benefit to the smelt populations.  In the end, the provision was applied, but in an unusual way that likely had some new negative consequences on smelt and their Bay-Delta critical habitats.

Reclamation has again requested exemption from the provision in wet year 2019.  Again, Reclamation referenced the high cost of water and minimal benefits to smelt, despite unequivocal evidence that smelt benefit (Figures 1 and 2).

The Fall X2 flows are being applied with extra releases from Shasta, Oroville, Folsom, and New Melones reservoirs (Figure 3).  Without the X2 requirement that is creating inflows to the Delta of about 25,000 cfs, Delta inflow would only need to be 15,000 cfs to meet 65% export-to-inflow requirement.  With lower reservoir releases, river flows and Delta outflows would be lower at the discretion of Reclamation.  In the past, Reclamation has also failed on many occasions to meet water temperature standards in the lower Sacramento River and the American River, as well as south Delta salinity standards.

Application of the Fall X2 provision benefits smelt and the fall upstream migration of salmon in the Sacramento and San Joaquin rivers and their tributaries.  In Suisun Bay and the western Delta, salinities and water temperatures would be higher without Fall X2 (Figures 4-6).  Fall X2 application also helps maintain the water temperature requirements in Reclamation’s water right permits and the water quality standards in the lower Sacramento River between Red Bluff and the Delta.

Figure 1. Delta smelt spawner-recruit relationship. Note strong recovery in 2011. Source: http://calsport.org/fisheriesblog/?p=1966

Figure 3. Bay-Delta hydrodynamics in late August 2019 under Fall X2 operations. Flows are average daily cfs. South Delta exports are in red. Red circle is location of X2.

Figure 2. Longfin smelt spawner-recruit relationship. Source: http://calsport.org/fisheriesblog/?p=2513

Figure 4. Water temperature and salinity (EC) in eastern Suisun Bay, August 1, 2017 through November 1, 2018. Fall X2 was applied in 2017 (red outlined box). Note lower salinity and lower water temperature in 2017 compared to 2018.

Figure 5. Water temperature and salinity (EC) in the lower Sacramento River channel of the west Delta near Decker Island August 1, 2016 through November 1, 2018. Fall X2 was applied in August-September 2017 (red outlined box). Note lower salinity and slightly lower water temperature in 2017 during Fall X2 application compared to 2016 and 2018 without Fall X2.

Figure 6. Water temperature and salinity (EC) in the lower San Joaquin River channels near Jersey Point in the western Delta from August 1, 2016 through November 1, 2018. Fall X2 was applied in August-September 2017 (red outlined box). Note lower salinity and slightly lower water temperature in 2017 during Fall X2 application compared to 2016 and 2018 without Fall X2.

 

Striped Bass Status – Summer 2019

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I last reported the status of striped bass in 2016.  The prognosis was not good after four years of drought (2012-2015).  Today, after a sequence of water years (2016-2019) that were below normal, wet, below normal and wet, the prognosis has not improved, notwithstanding the remarkable resilience of striped bass.

After improving in below-normal 2016 and wet year 2017, the below-normal 2018 fall index equaled that of below-normal 2010, the lowest since 2000 (Figure 1).  A similar pattern occurred in the 2018 summer index (Figure 2).

The summer-to-fall recruitment relationship (Figure 3) shows a continuing strong relationship between the summer index and fall recruitment.  Furthermore, the relationship continues to show a positive response in wet years (2011 and 2017), but a poor response in the below normal years (2010, 2016, and 2018).  This indicates that summer conditions in these below-normal water years is depressing  the fall recruitment of striped bass.

Early indicators for wet year 2019 give me pause and further concern for striped bass recruitment this fall.  First, numbers and densities in the 2019 late spring 20-mm survey were way down as compared to 2017.  Second, despite high south Delta exports in July 2019, juvenile striped bass salvage is also lower compared to July 2017 (Figure 4), consistent with the lower 20-mm survey results.  The summer and fall indices for 2019 will help complete the story.

Figure 1. Striped bass fall index 2000-2018.

Figure 2. Striped bass summer index 1959-2018.

Figure 3. Striped bass Fall Midwater Trawl Survey Index (log10[index+1]) versus prior Summer Townet Index (log10). Select years labeled, with color of number showing year type: blue=wet, green=normal, and red=critically dry.

Figure 3. Striped bass Fall Midwater Trawl Survey Index (log10[index+1]) versus prior Summer Townet Index (log10). Select years labeled, with color of number showing year type: blue=wet, green=normal, and red=critically dry.

Figure 4. Striped bass salvage at south Delta export facilities with export levels (acre-feet) summer 2017-summer 2019. Note near maximum export levels in July 2017 and 2019.

Delta August Adjustment

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The State of California has markedly increased inflows to the Delta and reduced exports in early August 2019 (Figure 1). There is no announced reason for this major hydrologic adjustment that has had a major effect on Bay-Delta habitat. The likely reason was to maintain the 14-day average salinity standard of 450 EC at Jersey Point,1 which was exceeded on a daily basis beginning on August 10 (Figure 2).

“Adjustments” to Delta inflow and exports began at the end of July as daily Jersey Point salinity began to exceed the 450 EC standard. The federal Central Valley Project made little or no contribution to this correction.

These recent changes are a textbook example of why the 14-day salinity standard needs to change to a daily standard. State water managers gamed easily controlled parameters, using the 14-day average to squeeze out more exports through July. This operation caused a major system reaction with far-reaching consequences to the State Water Project system and to the Bay and Delta.

The state could have maintained a daily 450 EC limit with gradual small system adjustments and support from the CVP.

Further discussion of the effects follows below.

Figure 1. Sacramento River Delta inflow at Freeport (FPT flow), Delta outflow (DTO resflow), state exports (HRO pumping), and federal exports (TRP pumping), 7/1-8/9, 2019. Note only state exports were affected.

Figure 2. Salinity (EC) at Jersey Point near mouth of San Joaquin River in the Delta 7/14-8/10, 2019.

Delta Inflow
Sacramento River inflow to the Delta at Freeport increased about 3000 cfs to just over 20,000 cfs (Figure 3).  The extra flow came from the Feather River (Oroville Reservoir of the SWP).  The higher inflow coincided with a drop in water temperature at Freeport from 23oC to 21oC.

Delta Outflow
Delta outflow rose about 9000 cfs from near 7000 cfs to 16,000 cfs (3000 from inflow and 6000 from reduced exports, Figure 1).  Outflows rose in the Sacramento channel at Rio Vista (Figure 4) and San Joaquin channel (Figure 5).  Water temperatures also fell about 1oC.

Interior Delta
Flow also increased and water temperature fell in Georgianna Slough (Figure 6).

Suisun Bay
Salinity and water temperature fell in Suisun Bay west of the Delta (Figure 7).

Figure 3. Flow and water temperature in Sacramento River at Freeport 7/1-8/10, 2019.

Figure 4. Flow and water temperature in Sacramento River at Rio Vista, 7/1-8/10, 2019.

Figure 5. Flow and water temperature in San Joaquin River at Jersey Pt, 7/1-8/10, 2019.

Figure 6. Flow and water temperature in Georgianna Slough in the central Delta, 7/1-8/10, 2019.

Figure 7. Salinity and water temperature in Suisun Bay near Pittsburg, 7/1-8/10, 2019.

 

  1. The standard applies for wet years through August 15. ↩

Mokelumne Hatchery 2016-2018 Releases

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In a post last year I remarked on the progressive management of the Mokelumne River hatchery. The hatchery is a mitigation hatchery operated by the California Department of Fish and Wildlife in partnership with the East Bay Municipal Utility District. Its activities over the past several decades have led to the recovery of Mokelumne River salmon.

The hatchery’s 6 million smolt releases continue to survive well under present management practices (Figures 1 and 2). Escapement of adults to the river and hatchery below Camanche Dam have numbered from 10,000 to 20,000 in recent years,1 a remarkable improvement given that they were produced during the 2012-2016 drought period.

The hatchery is still learning under its adaptive management program. The program has a diversity of release strategies that provide valuable information about the program and what works and what does not. Table 1 shows a summary of their smolt releases from 2016.

Table 1.  Summary of Mokelumne Hatchery smolt releases in spring 2016.  Source:  https://www.rmpc.org

Release Date Release Location Smolts Released
4/20/16 Sherman West Delta 902,000
4/27/16 Sherman West Delta 470,000
5/05/16 Sherman West Delta 450,000
5/09/16 Mokelumne River 102,000
5/10/16 Golden Gate Bridge 202,000
5/12/16 Sherman West Delta 902,000
5/20/16 Sherman West Delta 920,000
5/25/16 Half Moon Bay (coast) 485,000
5/26/16 Mokelumne River 402,000
5/28/16 Sherman West Delta 915,000
6/03/16 Sherman West Delta 771,000
2016 Total 6,521,000

Returns from the 2015 spawn year (brood year 2015) from code-wire-tagged smolt groups released in below-normal/dry water year 2016 ranged from near zero to two percent (Figure 3). The half-million smolts released to the river had near zero returns to fisheries and river/hatchery, while the half-million releases to Half Moon Bay on the coast south of San Francisco had a good return of 2.2 percent. Returns from the remaining 5.5 million smolts released at Sherman Island in the west Delta ranged from 0.1 to 1.4 percent.

The wide-ranging survival rates provide clear guidance for future hatchery smolt-release management.

  • April releases do not fare as well as May releases, suggesting that the larger size of May smolts provides a survival advantage.
  • River releases in a below normal or dry year like 2016 have poor survival, especially with below average freshwater flows in the lower San Joaquin River (Figure 4) and low Delta outflow (Figure 5).
  • Releases at Sherman Island in the west Delta in early June had poor survival compared to May releases, coincident with rapidly falling flows (Figures 4 and 5) and rising water temperatures (Figure 6).

2017 and 2018 release strategies were similar, but weighted more heavily toward Bay and ocean releases.

  • Over one million smolts were released on the coast and at the Golden Gate in 2017; 730,000 in 2018.
  • Most of the 4 million smolts released at Sherman Island in 2017 were released in May.
  • Over 4 million smolts were released at Sherman Island in 2018 from mid-April to early June over a broad range of conditions.
  • Nearly 500,000 smolts were released in the Mokelumne River in 2017 and 2018. The 2017 smolts were released in June of a wet cool year, while the 2018 releases were in May of a drier, warmer year.2

If and when information on the tag returns from 2017 and 2018 releases becomes available, it may be possible to move toward a still more effective release strategy that increases smolt survival and contributions to fisheries and river escapement.

Figure 1. Escapement estimates to the Mokelumne Hatchery 1964-2018

Figure 2. Escapement estimates to the Mokelumne River 1952-2018.

Figure 3. Percent return of 2016 Mokelumne Hatchery tagged smolt releases. Source: https://www.rmpc.org

Figure 4. Inflow of San Joaquin River to the Delta in May 2016 along with long-term median flow.

Figure 5. Delta outflow in spring 2016.

Figure 6. Water temperature in lower San Joaquin River at Jersey Point in spring 2016.

  1. The American and Feather River escapement has been 20,000-30,000 and 40,000-60,000, respectively, for similar numbers of smolt releases. ↩
  2. Note that San Joaquin River flows and Delta outflows are most important to Mokelumne Hatchery smolts, as the closure of the Delta Cross Channel results in the Mokelumne River being a tributary of the lower San Joaquin River. ↩