Category Archives: Smelt

Longfin Smelt – January 2020

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The fall midwater trawl index of spawning adult longfin smelt in 2019 was below expectations for a wet year (Figure 1). In a January 8, 2020 post, I foreshadowed the reduced fall spawner index for 2019, and suggested a grim outlook for the future of the population. In addition, high December 2019 Delta exports forced more spawning upstream into the Delta, increasing the likelihood of larval entrainment into the south Delta export pumps.

January 2020 larval smelt surveys (Figures 2 and 3) indicate that the production of longfin smelt larvae was indeed low. However, modest improvement occurred in both 2018 and 2020 compared to recent drought years (2015 and 2016). Application of the Fall X2 Delta outflow prescriptions in wet years 2017 and 2019 (higher outflow in Figure 4) likely contributed to the higher numbers of longfin larvae in the Bay in January 2018 and January 2020.

The numbers of larvae in 2018 and 2020 were still well below those in January 2012 (Figure 2), when the spawning population (2011) was much higher. Also, December exports in 2011 were much lower than in 2019 (Figures 5 and 6).

In summary, the benefit of the Fall X2 Bay Delta water quality standard has shown up again in the Larval Smelt Survey in January 2020. High December south Delta exports continue to hinder recovery of the longfin smelt population.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. The 2019 brood year index was lower than expected given the potential number of spawners (from the relatively high 2017 index) and 2019 having been a wet year.

Figure 2. Average catch of larval longfin smelt in late January Smelt Larva Survey 2012, 2015, 2016, 2018, 2019, and 2020.

Figure 3. Catch distribution in late January over five years of larval longfin smelt from Smelt Larva Survey.

Figure 4. Fall Delta outflow in years 2016-2019. Note Fall X2 prescription (higher outflows in September and October) was applied in 2017 and 2019.

Figure 5. State exports from Harvey Banks pumping plant in December 2011, 2016-2019.

Figure 6. Federal exports from Tracy pumping plant in December 2011, 2016-2019.

 

NEW FEDERAL BIOLOGICAL OPINIONS IN ACTION

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New federal biological opinions (BO’s) for the long-term operation of the Central Valley Project and the State Water Project in the Delta have been “protecting” salmon and smelt for several months. The record in practice is not good.

The ostensible purpose of the new BO’s is to protect native fishes, including ESA-listed salmon and smelt. A key focus in the new BO’s (as in prior BO’s) is on regulating reverse flows in Old and Middle River channels of the central Delta (Figure 1). Reverse or negative net upstream flows are caused by south Delta federal and state exports. Rules limiting negative OMR flows limit south Delta exports.

The U.S. Fish and Wildlife Service summarizes OMR operation, in part, as follows:1

Old and Middle River Flows

The new BO’s make a commitment to stay within the Delta pumping-related loss experienced under the 2008-09 BO RPA’s. Old and Middle River Reverse flows are to be limited based on timing (no greater than -5,000 cfs Jan-Jun); water quality conditions (short term protections for first flush events); storm event flexibility (can increase beyond -5,000 cfs if there is not a risk to the species); observed annual salvage and loss (specific triggers for loss values similar to those seen under the 2009 RPA); cumulative loss and outcomes from independent review panels.

 

Controlled OMR Flows

The action is consistent with Action 1 of the 2008 RPA by providing for integrated early winter pulse protection which requires reducing exports for 14 consecutive days so that the 14-day averaged OMR index for the period shall not be more negative than -2,000 cfs, in response to “First Flush” conditions in the Delta. In addition, once OMR management begins, Reclamation and DWR will operate to an OMR index no more negative than a 14-day moving average of -5000 cfs, unless a storm event occurs, until that point in which OMR management ends in a season (when temperatures in south Delta become lethal or June 30, whichever is earlier). The Integrated Early Winter Pulse Protection action may occur more frequently than Action 1 in the 2008 RPA, providing equal or greater protection.

To evaluate whether the new BO’s met these new commitments in December 2019 and January 2020, the reader should review Figures 2, 3, and 4 below, and also https://www.usbr.gov/mp/cvo/vungvari/OMR_Jan2020.pdf.

My own review indicates that what looked like, walked like, and quacked like a “first flush” occurred in mid-December. The lack of OMR limit protections and the allowance of maximum exports during and after the first flow pulse under the new BO’s in December 2019 led to what appear to have been grave risks to endangered salmon and smelt.2 The highly negative OMR flows in December were highly unusual and were not the norm under the prior BO’s (Figures 5 and 6). Regardless of the purported commitment to protect Delta native fishes in the new BO’s, Figure 4 shows the real effect of the new BO’s: the export of more water to southern California.

Figure 1. Old and Middle River and direction of negative net OMR flows.

Figure 2. Net daily-average OMR flows in the south Delta 11/11/19-1/17/20. Note the extremely negative flows during December that occurred because high south Delta exports are permitted under the new BO’s. Flow remained highly negative even during the period of higher outflow in early December shown in Figure 3. Source: CDEC.

Figure 3. Net Delta outflow 11/11/19-1/17/20. Note pulse of outflow from spate of storms in first half of December. Source: CDEC.

Figure 4. Export rates (cfs) at the federal Tracy (TRP) and state Harvey Banks (HRP) pumping plants in November-December 2019. Rates were near maximum throughout December.

Figure 5. Middle River flow 11/15/2019-1/20/2020 with average for prior 21 years.

Figure 6. Old River flow 11/15/2019-1/20/2020 with average for prior 22 years.

  1. Biological Opinions for the Reinitiation of Consultation on the Long Term Coordinated Operations of the Central Valley Project and State Water Project – Summary (USFWS 10/1/2019).  https://www.fws.gov/sfbaydelta/cvp-swp/documents/ROC_on_LTO_Summary_FINAL.pdf ↩
  2. http://calsport.org/fisheriesblog/?p=2981, http://calsport.org/fisheriesblog/?p=2991, http://calsport.org/fisheriesblog/?p=3006 ↩

Downward Trend in San Francisco Bay Longfin Smelt

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In my last posts on longfin smelt, I expressed some optimism about their recovery from the 2013-2015 drought based on 2017 and 2018 population data (Figure 1).1 I have changed my mind. In this wet water year 2019, the longfin have again crashed.

The long-term trend over four wet-year November adult trawl surveys, including this year (2019), continues downward (Figures 2-5). The trend portrays the underlying strong spawner-recruit relationship: the number of spawners (eggs) is the key factor that determines recruits. On top of that, poor recruitment in drier years (Figure 6) is driving recruitment-per-spawner down. There is 10-100 times higher recruitment from wetter years.

What is it about both dry years and wetter years like 2019 that is so bad? It is low Delta outflow and high exports in the November-December period.

Longfin smelt spawn in November-December in fresh water.2 When their freshwater habitat is in the San Joaquin channel in the central Delta upstream of Jersey Point (See location in Figure 2, Figures 7 and 8), the newly hatched larvae are highly susceptible to unlimited November and December exports. Although 2019 was a wet year, these conditions were present in November and December (Figures 9 and 10).

The prognosis for longfin smelt under current and planned water operations in the Delta is grim. The state and federal water projects need to increase Delta outflow and reduce exports in November and December to reduce spawning of longfin smelt in the central and south Delta.

Figure 1. Fall Midwater Trawl Index for longfin smelt, 1967-2018. Source: http://www.dfg.ca.gov/delta/data/fmwt/indices.asp

Figure 2. Catch distribution of longfin smelt adults in the November 1998 fall midwater trawl survey.

Figure 3. Catch distribution of longfin smelt adults in the November 2011 fall midwater trawl survey.

Figure 4. Catch distribution of longfin smelt adults in the November 2017 fall midwater trawl survey.

Figure 5. Catch distribution of longfin smelt adults in the November 2019 fall midwater trawl survey.

Figure 6. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. The relationship is very strong and highly statistically significant. Adding Delta outflow in winter-spring as a factor makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, lower-outflow years (red years). Spawners in 2017 and 2018 were at record low levels. Recruits in 2011 and 2017 were relatively high because the Fall X2 provision in the 2008 Biological Opinion was implemented. Source: http://calsport.org/fisheriesblog/?p=2513.

Figure 7. Salinity (EC) in November and December 2017 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in fresh water (below 500 EC).

Figure 8. Salinity (EC) in November and December 2018 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in freshwater (below 500 EC), which occurred upstream of Jersey Point.

Figure 9. Salinity (EC) in November and December 2019 at Jersey Point in the lower San Joaquin River channel of the west Delta. Spawning would occur in freshwater (below 500 EC), which occurred upstream of Jersey Point.

Figure 10. Tidally filtered flow in two channels in the lower San Joaquin River upstream of Jersey Point, portraying net flows toward to the south Delta export pumps.

 

The Final Straw for Delta Smelt; Another Dagger for Longfin

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Delta smelt and longfin smelt were not protected in the Delta in November-December 2019. High south Delta exports (Figure 1) and associated highly negative Old and Middle River (OMR) flows (Figure 2) pulled the spawning adult smelt toward the export pumps, likely significantly compromising what is left of the two populations. High exports and negative flows also pulled saltwater from the west Delta into the central Delta (Figures 3 and 4). This forced smelt to spawn further upstream in the fresher water of the central, east, and south Delta, sealing the fate of the numerous larval longfin smelt spawned there to the export pumps this winter. Young Chinook salmon, especially listed winter-run and spring-run entering the Delta in December, were also jeopardized.1

These circumstances were not allowed under the federal 2008 Delta smelt biological opinion (Figure 5) or the state’s longfin smelt incidental take permit (Figure 6). The new October 2019 Biological Opinion (BO) for the operation of the Central Valley Project (issued under the federal Endangered Species Act) does not preclude high exports or highly negative OMR flows. The pending new state Incidental Take Permit (ITP) for the operation of the State Water Project (to be issued under the California Endangered Species Act) follows the requirements of the federal BO for Delta smelt.

Given the December distribution of adult longfin smelt (Figure 7) and the likely distribution of the few remaining adult Delta smelt based on prior year surveys (Figure 8), the Smelt Working Group (SWG), Water Operations Management Team (WOMT), and the Director of the California Department of Fish and Wildlife (CDFW) should have limited south Delta exports in December. They did not.

The Trump administration’s new biological opinions simply do not protect these fish. The pending new state ITP for protection of these fish gives the Director of the California Department of Fish and Wildlife the last word in ordering changes to OMR flows. The CDFW Director’s non-decision in 2019 is a good indication of the level of protection that is likely under the new state ITP.

Figure 1. December 2019 state (HRO) and federal (TRP) south Delta exports. Note the maximum total rate of approximately 11,400 cfs was reached in the latter half of December.

Figure 2. December 2019 Old and Middle River (OMR) net daily flows.

Figure 3. Salinity (EC) in central Delta in December 2019.

Figure 4. Salinity (EC) in Old River in the south Delta in December 2019.

Figure 5. Page 281 of 2008 federal biological opinion for Delta smelt.

Figure 6. Page 10 of 2009 state Incidental Take Permit for longfin smelt.

Figure 7. Distribution of longfin smelt in December 2019 midwater trawl survey. These numbers are very low and show the present depressed level of the population.

Figure 8. Distribution of Delta smelt in December 2011 midwater trawl survey
showing likely distribution of remaining Delta smelt in 2019 (midwater trawl
survey found no Delta smelt in December 2019).

 

Fall X2 should extend through December

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In a recent post, I described the Fall X2 provision in the 2008 Delta Smelt Biological Opinion that protects smelt by requiring a modest Delta outflow from mid-August through October in Above Normal and Wet years.  In the same post, I described how the 2019 Biological Opinion for smelt would move the compliance point for Fall X2 upstream into the Delta, reducing low salinity zone habitat.   In this post, I suggest that the Fall X2 requirement should not only be retained with the old compliance point, but also that the applicable time period should extend through December.

First, if the X2 provision is not extended into December, this is what happens:  (1) Delta outflow drops to zero or even negative, as occurred this past November 2019 (Figure 1); and (2) the low salinity zone moves up into the Delta via the San Joaquin River channel toward the export pumps (Figure 2).

Second, winter-run salmon smolts that pour into the Delta from the Sacramento River in November and December of all but the driest years (Figure 3) will have difficulty surviving and exiting the Delta for the Bay and ocean.

Third, what few Delta smelt that may be surviving will be put at risk of being drawn into the central and south Delta (Figures 4 and 5).

Fourth, longfin smelt will be at risk to being drawn into the Delta (Figures 6 and 7).

Fifth, the primary food of young Delta native fishes, calanoid copepod adults, which concentrate in the low salinity zone, would be drawn into Delta (Figure 8).  Bay-Delta pelagic plankton productivity would suffer.

In conclusion, there are presently few constraints on water project operations in the Delta in November-December.  Freshwater outflow to the Bay can be zero or even negative, as occurred this past month, November 2019.  The updates to the Bay-Delta Water Quality Control Plan and to state permits that regulate Delta exports should extend Fall X2 through December in order to protect Delta native fishes.  Compliance would entail Delta outflows in the 8000-10,000 cfs range and/or Jersey Point salinity of about 500 EC.

Figure 1. Tidally filtered flow in the Sacramento River channel at Rio Vista and Jersey Point in the San Joaquin channel in November 2019.

Figure 2. Salinity (EC) at Jersey Point in the San Joaquin channel of the west Delta in November 2019.

Figure 3. Cumulative catch of winter-run Chinook salmon at Knights Landing rotary screw traps in fall-winter of water year 2017. Source: DOSS 2017.

Figure 4. Trawl catch distribution of Delta smelt fall 2011, the last time Delta smelt were relatively common.

Figure 5. Salvage of Delta smelt pre-spawn adults in fall-winter of water year 2003.

Figure 6. Longfin smelt trawl catch distribution in November 2011.

Figure 7. Longfin smelt trawl catch distribution in December 2011.

Figure 8. Adult calanoid copepod catch distribution in November 2011 zooplankton survey.