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

Are Delta Smelt in Hot Water? Yes, and water management has been putting them there.

A March 14, 2019 post in Maven’s Notebook summarized a presentation at the 2018 Bay Delta Science Conference on Delta smelt growth factors in the Bay-Delta estuary. The main author, Dr. Hobbs, described UC Davis research on smelt growth rates from analysis of smelt ear-bone cross sections.

The research indicates that growth rate is related to salinity, water temperature, and water clarity (turbidity). Growth rates were depressed when salinity was above 3-4 parts per thousand (ppt),when water temperature exceeded 20-21oC, and when water clarity was relatively high.

Dr Hobbs also addressed the question: HOW WILL FLOW AUGMENTATION AFFECT THE DELTA SMELT?
“The answer generally is that it will have an effect if the flows will actually reduce salinity, increase turbidity or reduce temperature.” They found that flow affects salinity, but temperature and turbidity not so much.

  • “But from 2015-2017, we had an excessive period of time when it was above 22 degrees throughout the estuary.”
  • “The average temperature from 1999 to present shows that 2014 and 2015 were exceptionally warm and the water has been getting clearer throughout the estuary since the early 2000s. How are we going to manage freshwater flows to affect these other two important variables?”
  • “We’ve been thinking about how to manage freshwater flows for Delta smelt for the better part of 20 years, and what we need to be thinking about now is how do we manage temperature for Delta smelt? How do we manage temperature at all? Can we even manage temperature?”

My answer to the question about the effect of flow on Delta smelt is that flow is extremely important to salinity, water temperature, and turbidity, as thus Delta to smelt survival and population abundance.

  1. Dr. Hobbs implied that flow has little effect on water temperature, but he failed to mention that his two warmest years, 2014 and 2015, had the lowest spring-through-fall Delta inflows and outflows. Flow standards were relaxed in both years to save water in depleted reservoirs. He failed to mention that more flow keeps the low salinity nursery area of Delta smelt further west in Suisun Bay, where the air and water are cooler than the Delta.
  2. Dr. Hobbs also implied that flow has little effect on turbidity. But it is a fact that lower flows and higher exports in the 2000’s led to lower turbidities. More reservoir releases to feed south Delta exports lowers Delta turbidity. When the low salinity zone is west of the Delta, it benefits from the increased turbidity provided by higher winds and from more open shallow bays than are afforded by narrow deep Delta channels.
  3. Dr. Hobbs failed to mention that flow affects the transport of adults upstream to spawning areas and the movement of juveniles downstream to the low salinity zone nursery area.

Three additional points:

  1. Higher flows also benefit smelt food production and availability.
  2. Flow does affect the temperature of water entering the north Delta, in addition to affecting salinity and turbidity. In wet year 2017, summer inflows were low and consequently warm, negatively affecting smelt.1
  3. Smelt production is strongly related to the number of adult spawners (or eggs laid), and 2017 also suffered from poor numbers of spawners.2

Revised Delta Smelt Take Permit

The Interior Department’s US Fish and Wildlife Service (USFWS) issued a memo1 on January 30, 2019 that revised the federal take permit for Delta smelt for the combined operation of the Central Valley Project and the State Water Project. The memo stated:

“It has become clear over the past several years that surveys are reaching their detection limits given the declining population of delta smelt, and in 2018, the FMWT [fall midwater trawl] Index was zero, indicating that the FMWT Index may no longer provide an accurate predictor of incidental take.”

The new take criteria are now the old action criteria of limiting Old and Middle River (OMR) reverse flows during the winter and spring under certain conditions. When smelt would normally be expected to be present, OMR flows would be restricted to being no more negative than -2000 or -5000 cfs. The new “surrogate” criteria essentially keep the south Delta pumping plant operations at status quo until such time as the ongoing reinitiated Endangered Species Act (ESA) consultation is completed and new take permits are issued.

The importance of the rule change is diminished by the fact that Interior (combined action of US Bureau of Reclamation and USFWS) has not enforced the rules to protect Delta smelt. The state of California has also failed to protect Delta smelt as well as California ESA-listed longfin smelt. One only has to review recent early winter information to see this is the case. After the first Delta outflow pulse at the beginning of December 2018, outflow fell to only 4000 through mid-December (Figure 1). High exports (Figure 2) contributed to the low outflow and exceptionally low (negative) OMR flows (Figure 3).

These low outflows and high exports created very high risk conditions for the two smelt species. What few Delta smelt remained were observed in the west Delta (Figure 4). Longfin smelt were spawning in Suisun Bay and the west Delta (Figures 5 and 6).

Smelt are not being protected. The Smelt Working Group mandated under the Federal and State take permits has been inactive and has not provided mandatory guidance. New take permits are needed immediately to protect the two listed smelts. The State Water Board, in revisiting water right permits and water quality standards for the Delta, should also adequately protect the listed smelts. To protect the smelts, the OMR limit for December should have been no more negative than -2000 cfs. The export-to-inflow limit criteria for December should be 35%, not the present 65%. December outflow minimums should be 6000-8000 cfs, not the present 3500-4500 cfs.

Figure 1. Delta outflow 11/10/18 to 1/8/19. Note very low outflow in early December after initial rainfall pulse.

Figure 2. State project exports at Clifton Court December 2018 to February 2019. Federal exports were near maximum (3500-4200 cfs) for most of period.

Figure 3. OMR flows November 2018 to January 2019.

Figure 4. December 2018 Kodiak trawl survey catch of Delta smelt.

Figure 5. December 2018 midwater trawl longfin smelt catch.

Figure 6. Smelt Larvae Survey #1 for 2019 catch of newly hatched longfin smelt.

Longfin Smelt February 2019

In my last update on the status of longfin smelt (February 2018), I decried the continuing decline of the Bay-Delta population of longfin, which are listed under the California Endangered Species Act.  The fall index for 2018 indicates continued low population levels (Figures 1 and 2), with 10 to 100 times higher production in wetter years than dry years.  After the very poor recruitment in 2015 and 2016, there was some recovery in wetter years 2017 and 2018.  Despite record low spawner numbers in 2015 and 2016, recruits increased with wetter years 2017 and 2018, which in turn could lead to improvement in 2019 and beyond with indices above 100 (log 2.0 in figure 2) or perhaps even near 1000 (log 3.0 in figure 2).  If drought returns, bets are off.

Figure 1. Fall Midwater Trawl Index for longfin smelt, 1967-2018. Source:

Figure 2. 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). Data source:

Longfin Smelt End of 2018 A Case for Higher Delta Outflow Standards in June

In a February 2018 post I last updated the status of longfin smelt in the Bay-Delta. I showed that longfin smelt have a strong spawner-recruit or stock-recruitment relationship wherein new recruits into the population depend on the abundance of spawning parents (Figure 1). The relationship also indicated a strong influence of water–year type.

What is it in wetter years that improves survival? What is it about wet years that is important to longfin survival? My analysis is it is the spring Delta outflow, with June likely being important. The fall longfin index is significantly correlated with June outflow (Figure 2). It requires Delta outflows in the 8000-10,000 cfs range to keep the low salinity zone and young longfin in the Bay, west of the Delta and away from the south Delta export pumps and warm low-productivity pelagic habitats.

Present standards (see link, pdf pages 26-27) for June require outflow of 7100 cfs on a 30-day running average. This contrasts sharply with previous June standards under Water Rights Decision 1485 (see link, pdf page 43) which required an average monthly flow of 9500 cfs in some below normal years, 10,700 cfs in Above Normal years, and 14,000 cfs in Wet years. In its ongoing update of the Bay-Delta Plan, the State Water Resources Control Board must account for the importance of the outflow standard for June in protecting Bay-Delta ecological resources.

Figure 1. Longfin Recruits (Fall Midwater Trawl Index) vs Spawners (Index from two years prior) in Log10 scale. Wet years in blue. Dry years in red. Note the progressive decline in recruits in the last three wet years (06, 11, 17). The relationship is very strong and highly statistically significant. Taking into account Delta outflow in winter-spring makes the relationship even stronger. Recruits per spawner are dramatically lower in drier, low-outflow years (red years). Source:

Figure 2. Fall midwater trawl index for longfin smelt versus average June outflow (cfs) 2008-2017. Wet years in blue. Normal years in green. Dry years in red. Source of data: