April 20, 2015 Smelt Working Group

The Smelt Working Group (SWG) was created as a requirement of biological opinions for the operation of the State Water Project and Central Valley Project under federal and state endangered species acts (ESA/CESA). The SWG is an eclectic mix of federal and state scientists and engineers whose mandate is to provide recommendations to managers on how operate the Delta to protect the ESA/CESA-listed Longfin and Delta smelt. The group holds weekly meetings. Often the meeting notes do not reflect real concerns of group members. One hopes that this is true in this case; the data and the conclusions don’t appear to line up.

At its April 20, 2015 meeting1, the SWG described the following baseline population conditions:

  • The 2014 Fall Midwater Trawl Annual Index for Delta Smelt was 9. This was a record low since the survey began in 1967. With historical indices above 1000 and 600-800 from 2000-2002, an index of 9 is catastrophic.
  • Only three Delta smelt were captured in 20-mm Survey #2 (3/30/15-4/8/15). Only one was captured in Survey #3, although an additional 19 were captured at a previously unsampled site further up the Sacramento Deepwater Shipping Channel (4/13-4/16).
  • Spring Kodiak Trawl Survey #4 was in the field the week of April 6, capturing just one Delta smelt. This is also a record low, as were the February and March survey catches.
    Delta Smelt

Delta Smelt

The SWG “agreed” on April 20 that there was no need to modify exports from their current 1500 cfs level or to modify Old and Middle River (OMR) reverse flows of -2000 cfs to protect Delta smelt. (They were probably thinking there were no smelt left to be concerned about – see Figure 1). In reality, the risk to the few remaining Delta Smelt from these flows moving towards the south Delta pumps is extremely high, even higher than that for Longfin Smelt.

Longfin Smelt

The SWG also concluded there was no concern for Longfin Smelt (CESA listed only), despite multiple indicators to the contrary.

  • Between April 13 and 15, four juvenile Longfin Smelt were salvaged at the CVP pumps and 12 at the SWP pumps; at the same time, a single larva was observed in the larval fish samples at the CVP pumps and four larvae at the SWP pumps. Continued collections in salvage are expected. The SWG concluded that catches in the central and south Delta were not sufficient to reach concern levels based on density or distribution. Note: the odds of a Longfin larvae or juvenile making it all the way to the south Delta, getting through Clifton Court Forebay, and getting salvaged in infrastructure designed to capture much larger fish, are almost infinitesimal. The numbers collected represent a significant take (kill) of Longfin Smelt just from entrainment into the pumping plants. The population’s present distribution and present Delta hydrodynamics support a much higher risk assessment (Figures 2 and 3).
  • Larval densities appeared to increase in the central Delta during 20-mm Survey 2. Nonetheless, the SWG concluded that since exports are very low and most larvae are believed to be outside of the region of entrainment, risk of entrainment remains very low. Note: Larval and juvenile Longfin are obviously not outside the influence of the south Delta exports. Net transport of these planktonic fish from the west, north, and central Delta is toward the south Delta.
  • The SWG concluded that current conditions, particularly the Old and Middle River (OMR) index projected between -1,900 and -2,000 for the week and slightly positive flow at Jersey Point (Qwest), indicate very little risk for fish that do move into or hatch within the central Delta. Thus, they concluded that the overall risk of entrainment remains very low. Note: Figure 3 shows a -2000 cfs Qwest flow at Jersey Pt at Jersey Island. All the indicators show potential for entrainment. The SWG also knew the pulse flow in the San Joaquin River would soon be ending and that conditions (and risk factors) would be worsening in late April.
Figure 1.  Mid April Delta Smelt distribution in 20-MM Survey .

Figure 1. Mid April Delta Smelt distribution in 20-MM Survey2.

Figure 2.  Mid-April Longfin Smelt distribution in 20-MM Survey.  Also shown is approximate location of X2 (2640 EC salinity) at magenta line and head of Low Salinty Zone (500 EC salinity) at green line.  With real Delta outflow near zero, Delta inflow is predominantly from north and passes across the Delta red arrows to south Delta export pumps.  A portion of the inflow passes through the upper Low Salinity Zone (between magenta and green lines).  Net negative flows and tidal pumping (high volume flood tides) move smelt into central and southern Delta.

Figure 2. Mid-April Longfin Smelt distribution in 20-MM Survey. Also shown is approximate location of X2 (2640 EC salinity) at magenta line and head of Low Salinty Zone (500 EC salinity) at green line. With real Delta outflow near zero, Delta inflow is predominantly from north and passes across the Delta red arrows to south Delta export pumps. A portion of the inflow passes through the upper Low Salinity Zone (between magenta and green lines). Net negative flows and tidal pumping (high volume flood tides) move smelt into central and southern Delta.

gure 3.  Net hydrodynamic conditions during mid-April “spring” tides (highest elevation of flood tide in April lunar cycle).  Magenta line is high tide location of X2 (2640 EC salinity).  Light green line is high tide location of head of Low Salinity Zone (500 EC salinity).  Longfin and Delta smelt larvae generally concentrate in waters whose salinity is between these two values.  Net flow direction is shown with arrows, red being negative.  Dark green highlight area is approximate location of mid-April central Delta plankton bloom (chlorophyll levels above 10 micrograms per liter).  (Data sources: CDEC and USGS.)

Figure 3. Net hydrodynamic conditions during mid-April “spring” tides (highest elevation of flood tide in April lunar cycle). Magenta line is high tide location of X2 (2640 EC salinity). Light green line is high tide location of head of Low Salinity Zone (500 EC salinity). Longfin and Delta smelt larvae generally concentrate in waters whose salinity is between these two values. Net flow direction is shown with arrows, red being negative. Dark green highlight area is approximate location of mid-April central Delta plankton bloom (chlorophyll levels above 10 micrograms per liter). (Data sources: CDEC and USGS.)

April 2015 Framework of Actions for Managing the Sacramento River

In an April 13 post1 I discussed what happened in 2014 that led to the catastrophic loss of much of the Winter Run Chinook Salmon production in the Sacramento River when Shasta Reservoir’s cold-water pool was depleted by the end of August.  With a better temperature model, more knowledge of how to manage Shasta’s cold-water pool, and more volume in the cold-water pool this year, the agencies believe they can make it through the summer of 2015 while supplying the same amount of water to the Sacramento River Settlement Contractors (SRSC) with the same end of September storage as last year.

On April 20, 2015, the Bureau of Reclamation released a “Framework” for managing Shasta storage and the Sacramento River in 20152.  The problem with the Framework is that there are no details as to how the state goals of protecting Winter Run while delivering the same amount of water to SRSC in 2015 as last year will be accomplished.

“Agreement on Sacramento River and SRSC operations is the cornerstone to the overall operations of our water management system, and is a key piece needed before other decisions about volume and timing of transfers to junior water rights holders can be negotiated…. This type of creative, cooperative approach among project operators, regulators, and water users is fundamental to getting the most out of our limited water resources….  We must continue close coordination as we implement the plan, reacting to real-time conditions and balancing the inevitable tradeoffs.”  The problem with this statement is that it was also true for last year.  Despite these same efforts, over 95% of the endangered Winter Run salmon production below Shasta was lost last summer to failed efforts.

“Last year, endangered winter-run Chinook salmon redds in the upper Sacramento River were severely impacted by the lack of cool water,” said Maria Rea, Assistant Regional Administrator for NOAA Fisheries Central Valley Office. “This year we will continue to monitor the temperatures and operations of the Sacramento River throughout the summer.”  Part of the cause of widespread mortality of the 2014 Sacramento River cohort of Winter Run salmon was lack of cold water, but only part.  In addition, salmon redds were physically dewatered and eggs and fry were stranded.  This could occur again this summer.  When monitoring indicated there was a problem last summer, it was too late to take action.

 “A major component of the overall framework is the temperature management plan for the Sacramento River. With the proposed temperature management plan and anticipated CVP operations assuming conservative inflow estimates, storage in Shasta Lake is projected to be approximately 1.1 million acre-feet at the end of September 2015. Water storage and releases from Shasta Lake will be managed carefully to assure the availability of water for multiple beneficial purposes during this fourth year of drought.”  This is the same end-of-summer storage level as last year.  Water storage, releases, and water temperatures were managed last summer.  What specifically will change to ensure that last year’s problem will not reoccur?  The Bureau’s website offers no clue.

“Reclamation will submit the temperature management plan to the State Water Resources Control Board next week as required by the recent Temporary Urgency Change Order.”  The plan will be based on this year’s conditions and a new temperature model.  What assurances do we have that this year’s plan and model will work better than last year’s?

In order to save salmon in 2015, the Bureau Reclamation proposes: “The following actions are designed to help increase the available cold-water resources, improve habitat for Chinook Salmon, and inform real-time adjustments to the temperature management actions, all of which serve to improve the overall effectiveness of the temperature management plan:  

  • “The State Water Resources Control Board approved (in part) Reclamation’s April-September Temporary Urgency Change Petition on April 6, 2015, which will maintain minimum flows for fish downstream in the Delta. This will help Reclamation preserve as much cold water as possible in Lake Shasta for its operations and temperature management throughout the spring and summer as well as for water supply purposes.” (Note:  minimum required lower Sacramento River flows are adequate to maintain minimum Delta inflow and outflow requirements.  Shasta releases are necessary only for required in-river flows and water temperatures and to meet SRSC irrigation deliveries.)
  • “Biologists from the State and Federal fish agencies will be working in the Sacramento River this summer collecting data to help inform Reclamation operations and temperature management decisions in real time. This work will also provide additional data on salmon spawning and rearing that will be useful in future operations during both dry and wet years.”   (Note: the agencies have been collecting data for many years, including last year, when Winter Run mortality was extremely high.)
  • “For the remainder of 2015, the SRSCs, working with the state and federal fishery agencies and conservation partners, will aggressively implement projects included in the Sacramento Valley salmon recovery program. This includes actions to improve spawning in the upper Sacramento River, protect (against) stranding and increase the survival of salmon smolts.” (Note:  How will the contractors contribute to these actions?)
  • “A significant portion of the anticipated water transfers from the SRSC’s will be released in the late summer and fall on a schedule that will provide beneficial habitat conditions for spawning fall-run salmon.” (Note: this was done last year.  Summer transfers would continue to deplete the cold-water pool and degrade the critical habitat of listed smelt in the Delta by increasing Delta exports.  Fall transfers through the Delta are also detrimental and not normally allowed.)
  • “The federal and state agencies and SRSC’s will have regular meetings to coordinate these actions and will work closely together throughout the year to assure the effective implementation of this plan. We all agree that we stand a better chance of managing limited water supplies with continued communication and cooperation.”  (Note: last year, there was ample communication, yet most of the fish perished.  What will cause the agencies to make better decisions this year?)

Some key facts:

  • Last year Shasta started with 2.4 million acre-ft and ended up with 1.1 million acre-ft (Figure 1). This year the plan is to start with 2.7 million acre-ft and end with 1.1 million acre-ft.  (Note that the benefits of this year’s higher spring storage level is offset by a reduced snowpack)
  • The Bureau states that the Shasta cold-water pool has 0.7 million acre-ft more at the beginning of this year than last year.
  • Last year the Bureau ran out of cold water, resulting in lethal water temperatures and low dissolved oxygen for salmon eggs and fry in spawning reach near Redding, and then dropped flows too low, resulting in dewatered redds.
  • Reservoir releases were too high in spring and too low in late summer and fall for good salmon survival (Figure 2).

In conclusion:

  1. There are no plans to save Shasta storage for carryover for next year despite the 300,000 acre-ft additional storage this year.
  2. There is no explanation for how summer deliveries in 2015 that are functionally equivalent to summer deliveries in 2014 will maintain the cold-water pool in Lake Shasta this year when they caused last year’s disaster.
  3. There are no assurances that late summer and early fall flows will be high enough to avoid dewatering salmon redds near Redding.
  4. There are no assurances that addition summer and fall reservoir releases will not be needed to sustain the Bay-Delta ecosystem.
Figure 1.  Shasta Reservoir storage 2014. Source: CDEC.

Figure 1. Shasta Reservoir storage 2014. Source: CDEC.

Figure 2. Shasta Reservoir releases 2014. Source: CDEC.

Delta April Bloom Related to Low Exports and San Joaquin Pulse Flow

A San Joaquin River pulse flow and low Delta exports in April have led to a plankton bloom in the Central Delta. The pulse flow (Figure 1) and low exports (1500 cfs) were the result of two drought-related actions of the State Water Resources Control Board in its April 6, 2015 Temporary Urgency Change Order. The bloom is a consequence of low net transport flows in central Delta channels toward the south Delta export pumps and of the water habitat thus being allowed to “stew” with nutrients from the San Joaquin River. Chlorophyll levels rose with the onset of the pulse flow and recently have begun to decline with the end of the pulse flow (Figures 4-10). Chlorophyll levels were much lower in the west, north, east, and south parts of the Delta and in Suisun Bay, when compared to the central Delta. This process was described by Arthur and Ball (1977)1

“During spring through fall, export pumping from the southern Delta caused a net flow reversal in the lower San Joaquin River, drawing Sacramento River water across the central Delta to the export pumps. The relatively deep channels and short water residence time apparently resulted in the chlorophyll concentrations remaining low from the northern Delta and in the cross-Delta flow to the pumps.”

Such a spring bloom is important because it stimulates Delta productivity that is key to native Delta fish survival and production. Lack of Delta productivity over the past several decades (Figure 2) has been related to the Pelagic Organism Decline and near extinction of Delta Smelt (Jassby et al 2003)2. Low chlorophyll levels are also related to poor zooplankton growth rates (Figure 3).

Figure 1.  San Joaquin River inflows into the Delta at Vernalis during April 2015.

Figure 1. San Joaquin River inflows into the Delta at Vernalis during April 2015.

Figure 2. Spring Delta chlorophyll levels below 10 micrograms per liter are considered low primary productivity. (Source: Jassby et al. 2003)

Figure 2. Spring Delta chlorophyll levels below 10 micrograms per liter are considered low primary productivity. (Source: Jassby et al. 2003)

Figure 3.  Zooplankton growth rates peak above chlorophyll levels above 10 micrograms per liter.  (Source: Jassby et al. 2003)

Figure 3. Zooplankton growth rates peak above chlorophyll levels above 10 micrograms per liter. (Source: Jassby et al. 2003)

Figure 4.  The six stations with chlorophyll data presented in the following charts from west to east are: •ANH – Antioch •BLP – Blind Point •OSJ – Old River at Franks Tract • PPT – San Joaquin River at Prisoners Point •HLT – Middle River at Holt •TRN – Turner Cut

Figure 4. The six stations with chlorophyll data presented in the following charts from west to east are:
• ANH – Antioch
• BLP – Blind Point
• OSJ – Old River at Franks Tract
• PPT – San Joaquin River at Prisoners Point
• HLT – Middle River at Holt
• TRN – Turner Cut

Figure 5.  Antioch chlorophyll levels April 2015.

Figure 5. Antioch chlorophyll levels April 2015.

Figure 6.  Blind Point chlorophyll levels April 2015.

Figure 6. Blind Point chlorophyll levels April 2015.

Figure 7.  Old River chlorophyll levels April 2015.

Figure 7. Old River chlorophyll levels April 2015.

Figure 8.  Prisoners Point chlorophyll levels April 2015.

Figure 8. Prisoners Point chlorophyll levels April 2015.

Figure 9.  Middle River chlorophyll levels April 2015.

Figure 9. Middle River chlorophyll levels April 2015.

Figure 10.  Turner Cut chlorophyll levels April 2015.

Figure 10. Turner Cut chlorophyll levels April 2015.

  1.   Arthur, J, and M. Ball. 1977. Planktonic Chlorophyll Dynamics in the Northern San Francisco Bay and Delta. Fifty-eighth Annual Meeting of the Pacific Division of the American Association for the Advancement of Science, San Francisco State University, San Francisco, California, June 12-16, 1977.  http://downloads.ice.ucdavis.edu/sfestuary/conomos_1979/archive1029.PDF 
  2. Jassby, A., J. Cloern, and A. Muller-Solger. 2003.  Phytoplankton fuels Delta food web.  California Agriculture 57(4): 104-109.

April Delta Smelt Update

The chart below shows the recent record low catch of Delta smelt in the recent early April Kodiak Trawl by the California Department of Fish and Wildlife.  Trawls at 40 locations in the estuary collected a single Delta smelt, the fewest ever collected.  This result is consistent with other recent surveys, including the 2014 Fall Midwater Trawl (lowest in the historical record), the late April 2015 Smelt Larva Survey and early April 20 mm Survey.  Delta smelt, once the most numerous species in the estuary, is now hovering on the brink of extinction.  Longfin smelt are not far behind.  Yet the State Water Board continues to weaken already inadequate criteria established to protect these and other species.

Kodiak Trawl Survey

April Spring Tide in Delta

Under Weakened Delta Standards

To save water, the State Water Board’s April 6 Drought Order reduced the Delta outflow standard to 4000 cfs Net Delta Outflow Index (NDOI) and allowed the Delta salinity standard compliance point to move upstream to near Rio Vista. Normally the NDOI would be 7100 cfs, and the salinity compliance would be further downstream toward Collinsville. South Delta exports are limited in the Order to 1500 cubic feet per second (cfs).

I provide the following picture of Delta conditions during a mid-April spring tide (strong incoming tide phase).

(Map source: USGS map of Delta gage locations.)

(Map source: USGS map of Delta gage locations.)

The magenta and light green lines represent, respectively, the high tide upstream salt-intrusion limit of X2 (2640 EC salinity) and upper extent of the Low Salinity Zone (LSZ) (500 EC salinity). The red and blue arrows represent the net tidally filtered (average daily) flows in cfs for their locations. The dark green region represents an area of strong plankton bloom determined from mid-April chlorophyll measurements.

There are a number of important points about this picture and what it depicts:

  1. The Order requires NDOI of 4000 cfs. Reclamation’s calculated NDOI on April 16 was 4966 cfs1. The USGS measured the actual Net Delta Outflow on April 16 as -3741 cfs. Outflow is negative because the high spring tide overcomes the freshwater inflows to the Delta.
  2. The spring tide also moves X2 and the LSZ upstream into the central area of the Delta.
  3. Longfin and Delta smelt young tend to concentrate in the area of X2 and upstream to the head of the LSZ (light green line). One reason for this is that it puts them in the zone of high estuary productivity (high chlorophyll and turbidity), where their potential for higher growth and survival is greater.
  4. Net negative flows draw smelt into the central Delta including Franks Tract, a notorious habitat of predatory fish. The smelt (and the LSZ and its plankton bloom) are also being drawn south in Old and Middle Rivers to the south Delta federal and state export pumps. Water pulled from the central Delta is replaced by water from the Sacramento River near Rio Vista, which becomes poor smelt habitat because it is fresh and warm, and has low turbidity and productivity.

In addition to restoring Delta flow and salinity requirements that were weakened by the State Board’s April 6, 2015 Order, what else should be done to reduce these negative effects on the LSZ and smelt during drought conditions?

  • During spring tides, more real Delta outflow is needed. This can come in two ways: 1) more inflow (reduce upstream Valley diversions); or 2) reduced Delta exports and diversions.
  • Install a False River flow barrier (on north side of Bethel Island), which would stop tidal pumping of X2 water from the Jersey Point area of the west Delta into Franks Tract in the central Delta. (Note that tidal flow would then be forced up the San Joaquin channel on north side of Bradford Island and Webb Tract.)
  • Open the Delta Cross Channel (part of the day) in the north Delta to increase freshwater inflow to lower San Joaquin channel in the central Delta. Since salmon tend to migrate at night, daytime Delta Cross Channel openings draw fewer young salmon from the Sacramento River.
  • Install the Head-of-Old-River flow barrier (location is south and east of the map area) to increase freshwater flow from the San Joaquin River into the central Delta.