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.

Reclamation’s Proposed Delta Smelt Fall Habitat Action In 2019

The US Bureau of Reclamation (Reclamation) is proposing a “Delta Smelt Fall Habitat Action” that would eliminate the requirement to increase outflow from the Delta in the late summer of this wet water year.1 The “Fall X2” flow increase that Reclamation has placed on the chopping block is a major provision in the 2008 Delta smelt biological opinion (BiOp). Reclamation describes the substitute proposed Action in a summary its webpage:

The Proposed Fall Habitat Action (Proposed Action) for Delta Smelt habitat in Water Year (WY) 2019 will achieve the Action 4 objective. Action 4 of the 2008 BO requires adaptive management to ensure that the implementation addresses the uncertainties about the efficiency of the action. Action 4 also states that as new information is developed and as circumstances warrant, changes by the Service to the Fall X2 action itself may be necessary. The Proposed Action is a plan to adaptively manage and modify its operation of the CVP/SWP under RPA Action 4.2

In brief, the “circumstances” that “warrant” this “adaptive management” are that getting rid of Fall X2 will allow Reclamation to export more water from the Delta this fall.

In August 2019, Reclamation issued an Environmental Assessment (EA) of the Proposed Fall Habitat Action. Though the Action will unravel a major component of the 2008 Biological Opinion for smelt, the comment period was 15 days. CSPA submitted comments; some of them are restated below, in response to citations from the “Effects Analysis,”3 an appendix to the Environmental Assessment.

The Effects Analysis quotes the BiOp to portray the Proposed Action as a scientific investigation, stating:

“[T]here is a high degree of uncertainty about the quantitative relationship between the size of the Action described above and the expected increment in Delta Smelt recruitment or production.” (p. 1).

Comment: After 2011, it has been nearly impossible to measure population response to changes in management because the smelt population has become so low. Likewise, a negative response cannot be detected at the present population level. The only certainty to be gained from harming a nearly extinct population even more is that Reclamation will increase exports from the south Delta.

The Effects Analysis selectively calls out results of the first implementation of the Fall X2 requirement in 2011:

“Abiotic habitat did increase in 2011 as predicted from the AMP, but other variables such as zooplankton abundance were too variable to draw a conclusion, and Delta Smelt growth rate comparisons remain incomplete as of 2019.”  (p.2)

Comment:  Following implementation of Fall X2 flows, smelt abundance increased sharply in the fall 2011 index. A quick look at zooplankton 2011 vs 2010 (Figure 1) also indicates an increase in zooplankton (key smelt food source) in Suisun Bay/Marsh in 2011.

Figure 1. Zooplankton (key Delta smelt food source) in September 2011 and 2010.
Note increased abundance downstream in 2011.

The Effects Analysis tries to explain the lack of response of Delta smelt to the 2017 Fall X2 action as a function of water temperature, concluding that the action was just futile:

In 2017, a Fall X2 adaptive management action was implemented. The results of the 2017 monitoring program were evaluated in the IEP’s 2019 draft FLOAT-MAST, which concluded that summer water temperatures were a major factor in the condition of Delta Smelt in 2017, stating at p.102: Given the long periods in July and August >22C we are confident that water temperature had a major negative effect on Delta Smelt in 2017 and is likely a primary factor in the lack of response of the Delta Smelt population to the high flows.  And at p. 104: Dynamic biotic components were somewhat better in 2017; however, the lack of response of the Delta Smelt population suggests that any benefits of changes in the habitat were minimal. (p. 3)

Comment:  It is true that recruitment of Delta smelt in 2017 was exceptionally low, despite the Fall X2 action.  This is because the number of adult spawners in 2017 was at a record low (Figure 2).

Fall 2017 water temperatures were slightly higher in the west Delta at Jersey Point compared to 2011 (Figure 3).  However, fall 2017 water temperatures were not unusually high compared to fall 2011 for Freeport or for Rio Vista in the Sacramento River channel of the Delta (Figure 4).  June and July Sacramento River water temperatures were substantially higher in 2017 than in 2011, because June and July Sacramento River flows were much lower in 2017 compared to 2011 (Figure 5). 

In general, spring habitat conditions were poorer in 2017 than in 2011:  2017 had lower spring Delta outflows (Figure 6) and much higher south Delta exports (Figure 7).

In sum, the 2017 fall index for Delta smelt was unusually poor because of poor conditions for Delta smelt in the spring and summer.  However, the response of longfin smelt to the implementation of Fall X2 in 2017 had a better outcome (Figure 8).  Despite poor number of spawners, the 2017 recruitment of longfin smelt per spawner was high. 

These data undermine Reclamation’s conclusion that the 2017 Fall X2 action had no benefit. 

Figure 2. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet years. Red years are dry and critical water years. Year types are determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Figure 3. Comparison of Jersey Pt habitat conditions in 2017 versus 2011. Tidally filtered flow data were not available for 2011.

Figure 3. Comparison of Jersey Pt habitat conditions in 2017 versus 2011. Tidally filtered flow data were not available for 2011.

Figure 4. Freeport and Rio Vista water temperatures 2013-2019.

Figure 5. Freeport flow and water temperature summer 2011 and 2017.

Figure 6. Summer Delta outflows in 2011 and 2017.

Figure 7. South Delta federal exports (TRP) and state exports (HRO) in 2011 and 2017.

Figure 8. Longfin smelt spawner-recruit relationship, with improved recruitment in 2011 and 2017. Wet year blue, dry year red. Source: http://calsport.org/fisheriesblog/?p=2513

So, after stating inaccurate and misleading reasons why the Fall X2 action is not effective, the Effects Analysis offers inaccurate and misleading reasons why not implementing Fall X2 and instead fussing with the Suisun Marsh Salinity Control Gates (SMSCG) will be a positive switch.

“Forecast of salinity conditions in the Delta indicate that operating to an X2 of 80 km along with SMSCG operations in September and October would result in suitable salinity conditions (< 11,000 uS/cm) in the western Delta including Suisun Marsh, Grizzly Bay, and Honker Bay during these two months.”  (p. 17)

Comment:  Operating the SMSCG tide gates, while not implementing Fall X2, will push more Delta outflow into Suisun Marsh, with less outflow reaching eastern Suisun Bay.  Both actions would potentially negatively affect Delta smelt compared to implementing the Fall X2 Action per the existing BiOp.

“However, as explained above, this estimate of abiotic habitat index does not account for the habitat created in Suisun Marsh through the operation of the SMSGC, which would increase the index.” (p. 31)

Comment:  moving outflow through SMSGC reduces habitat in eastern Suisun Bay, and subsequently traps any Delta smelt in Suisun Marsh once the gates are again closed.

Conclusion:  Stock-recruitment models show a strong positive population response for Delta smelt in 2011 (see Figure 2) and longfin smelt in 2017 (see Figure 8).  The strong population responses in 2011 and 2017 offer a strong case for implementing the Fall X2 action in 2019.  Reclamation’s only justification for eliminating the Fall X2 action in 2019 is to increase water available for export.  Biology has nothing to do with it.

Delta Outflow Measurement

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

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

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

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.