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.

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.

 

Delta Smelt – Spring 2019 Status

Late April and early May 20-mm Surveys provide an excellent picture of the status of Delta smelt population in the estuary. Since 2017, some surveys collected no Delta smelt (Figures 1-3) in the San Francisco Bay-Delta estuary. The 2018 and 2019 survey catches (Figures 1 and 2) are a new low for Delta smelt, lower even than the 2017 survey catch (Figure 3), and the lowest in the 1995-2019 survey period.

The outlook for the Delta smelt population remains grim after these lows. Despite good conditions in spring 2018 and 2019, the severely depressed number of adult spawners indicates a continuing weak potential for recovery.

Figure 1. Catch and lengths of Delta collected in the 20-mm Survey in spring 2019. None were collected in survey 3.

Figure 2. Catch and lengths of Delta collected in the 20-mm Survey in spring 2018. None were collected in surveys 4 and 5.

Figure 3. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2017.

Napa River Smelt Sanctuary

The Napa River and its estuary are an important spawning and rearing area for longfin and Delta smelt, especially in wet years. Wet years, with their high Delta outflows (Figure 1) and modest Napa River flows (Figure 2) provide spawning habitat for the smelt in the Napa River and its estuary (Figures 3-6).

Wet year 2019 shows use by longfin (Figure 3), but little use by Delta smelt (Figure 7), which likely reflects their low population abundance.

Because the smelt populations have strongest recruitment in wet years,1 the Napa River estuary likely is an important contributor to their overall population health and abundance. The Napa River estuary deserves more attention in smelt recovery strategies. However, that should not take away from improving upper Bay-Delta estuary habitat conditions in all water year types.

Figure 1. Delta outflow in recent wet years 2011, 2017, and 2019.

Figure 2. Napa River flows 2009-2019.

Figure 3. 20-mm Survey results for Longfin smelt March 2019. Source

Figure 4. 20-mm Survey results for Longfin smelt March 2017.

Figure 5. 20-mm Survey results for Delta smelt April 2011.

Figure 6. 20-mm Survey results for Delta smelt April 2017.

Figure 7. 20-mm Survey results for Delta smelt April 2019.

 

 

Winter Trawl Survey – Delta Smelt 2019 Adult Spawning Run Update

A January 2, 2019 California Department of Fish and Wildlife (CDFW) memo relates that the fall midwater trawl index for Delta smelt was zero (none collected), though an attachment from the U.S. Fish and Wildlife Service (USFWS) shows that some Delta smelt were captured in late 2018 in non-index locations, as was the case in other recent years. The CDFW memo also relates that 5 smelt were captured in the December Kodiak Trawl Survey.

In an effort to update my last winter trawl post, April 2018, I present the winter survey results from 2002 through 2019 in the figure below. The 2018 and 2019 winter indices are consistent with the fall and summer surveys.

The fact that some Delta smelt remain in the Bay-Delta indicates that it might not be too late to save them from extinction, especially with hatchery supplementation. However, there has been no public description of CDFW’s or USFWS’s plan for Delta smelt recovery in 2019-2020. The present recovery plan for Delta smelt is dated 1996. USFWS should update the Delta smelt recovery plan immediately, and USFWS and CDFW should implement it. The State Water Resources Control Board’s effort to update Delta water quality standards should also include measures to recover smelt.

Chart of winter smelt survey results from 2002 through 2019