Category Archives: Smelt

Spring Actions to Save Delta Smelt

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The Smelt Working Group in its April 13 meeting notes1 confirmed that the Spring Kodiak Trawl Survey has recorded record low numbers of adult Delta Smelt in both its March and April surveys. The record lows are consistent with the record low 2014 Fall Midwater Trawl Index. The Group also noted few young Delta Smelt have been collected in the April Smelt Larval and 20-mm surveys. No fisheries agency has objected to State Water Board’s April 6 Order in which the Board reduced the spring Delta outflow standard to 4000 cfs, reduced San Joaquin flow to 200-300 cfs, and moved the salinity standard location for X2 upstream to Threemile Slough provided South Delta exports are held to 1500 cfs.

Given the present state of the smelt populations, the expected habitat conditions this spring and summer will be extremely stressful to the minimal population of this year’s brood of young smelt. As was the case last year, young smelt will be confined to western, central, and northern Delta portions of the lower Sacramento River, lower San Joaquin River, Cache Slough, and Threemile Slough. Exports of 1500 cfs may be insignificant when Delta inflows are 20,000 cfs, but they are not insignificant when inflows are only 6000 cfs. In low inflow conditions, exports pull warm water into the Low Salinity Zone (LSZ), which along with its upstream position leads to lethal or near lethal water temperature (>23C) by the end of spring. Already, May water temperatures will reach or exceed 20°C. The exports also reduce the food productivity of the LSZ through the export of nutrients and plankton.

Mid-April conditions were not extreme (Figure 1) because a mandated San Joaquin River pulse flow kept flows moving in a general downstream direction. However, as the pulse flow ended in late April and the State Board Order took full effect, conditions for Delta Smelt deteriorated quickly (Figure 2). There were three primary negative effects:

  1. Reduced Delta outflow, which results in X2 and LSZ moving upstream. (Magenta arrow in Figure 2.)
  2. Negative net flow in Threemile Slough, which pulls Delta Smelt into the central Delta from the north Delta. (Red arrow located just south of Rio Vista in Figure 2.)
  3. Net flow from the north and central Delta toward south Delta export pumps (Figure 3).

Spring Actions

The following actions would reduce the negative effects on Delta Smelt:

  1. Increase Delta outflow by 1000-2000 cfs, at least during “spring tides”.
  2. Open the Delta Cross Channel during the daytime to increase inflow into the central Delta from northeast by 1000 cfs. (This would reduce net negative flows from north Delta to central Delta via Threemile Slough). Any effect on migrating Sacramento River salmonids can be largely mitigated by keeping the DCC open only in daytime.
    Install Head-of-Old-River Barrier near Vernalis to limit movement of San Joaquin River salmonids into the south Delta.
  3. Install False River Barrier to eliminate tidal pumping of LSZ and young Delta Smelt from Jersey Point into Franks Tract/Old River via False River (slough just north of Bethel Island).
Figure 1. Mid-April 2015 approximate hydrology conditions in Delta. Blue arrows depict flow (cfs) in positive downstream direction. Red arrows depict OMR and export flows. Green line depicts location of head of Low Salinity Zone (500 EC) at low tide. Magenta line depicts average daily location of X2 (2700 EC). Delta Smelt young generally concentrate between the magenta and green lines in spring. (Map source: USGS with monitoring stations)

Figure 1. Mid-April 2015 approximate hydrology conditions in Delta. Blue arrows depict flow (cfs) in positive downstream direction. Red arrows depict OMR and export flows. Green line depicts location of head of Low Salinity Zone (500 EC) at low tide. Magenta line depicts average daily location of X2 (2700 EC). Delta Smelt young generally concentrate between the magenta and green lines in spring. (Map source: USGS with monitoring stations)

igure 2. Expected late-April through May 2015 approximate hydrology conditions in Delta. Blue arrows depict flow (cfs) in positive net downstream direction. Red arrows depict OMR and export flows. Green line depicts location of head of Low Salinity Zone (500 EC) at low tide. Magenta line depicts average daily location of X2 (2700 EC). Delta Smelt young generally concentrate between the magenta and green lines in spring.

Figure 2. Expected late-April through May 2015 approximate hydrology conditions in Delta. Blue arrows depict flow (cfs) in positive net downstream direction. Red arrows depict OMR and export flows. Green line depicts location of head of Low Salinity Zone (500 EC) at low tide. Magenta line depicts average daily location of X2 (2700 EC). Delta Smelt young generally concentrate between the magenta and green lines in spring.

Figure 3. Location of Delta Smelt larvae in late April – early May 2014 from Smelt Larvae Survey. Arrows indicate primary net flow routes of larval smelt from North and Central Delta to South Delta.

Figure 3. Location of Delta Smelt larvae in late April – early May 2014 from Smelt Larvae Survey. Arrows indicate primary net flow routes of larval smelt from North and Central Delta to South Delta.

  1. http://www.fws.gov/sfbaydelta/documents/smelt_working_group/swg_notes_4_13_2015.pdf ↩

Open the Delta Cross Channel

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The Delta Cross Channel (DCC) (Figure 1) is closed in spring to minimize the diversion of juvenile salmon from the Sacramento River into the central Delta. However, opening the DCC in May and June will help reduce the detrimental effects of drought on Delta Smelt and Delta water quality.

With San Joaquin River inflows to the Delta at extreme lows and the DCC closed, fresh water flow to the south Delta export pumps comes primarily from the Sacramento River via Threemile Slough (TSL) and Georgiana Slough (GGS) (Figure 2). Net flows from both these sloughs are south toward the state and federal pumping plants via Old and Middle Rivers. Delta Smelt enter the central Delta via Threemile Slough. Salmon, sturgeon, steelhead, and striped bass young enter the central Delta via Georgiana Slough as well as Threemile Slough. Opening the DCC will change Delta net flow patterns and contribute to net downstream flows in the lower San Joaquin River in the central Delta (Figure 2), thus benefitting all the fish entering the central Delta including those migrating downstream from the San Joaquin and its tributaries. With the DCC open, less salt will intrude into the central Delta with the more positive net flows of the lower San Joaquin River. Less of the Low Salinity Zone and its concentrations of pelagic fishes including smelt will flow or be tidally pumped upstream into the central Delta. More of south Delta exports will come directly from the Sacramento River via the DCC, rather than through Threemile Slough or Georgiana Slough, or fromthe Low Salinity Zone.

Yes, the late spring migrations of young wild salmon and steelhead, as well as larval Striped Bass and sturgeon from their spring spawns will enter the Central Delta via the DCC, but fewer will enter via Threemile and Georgiana sloughs. Those that do enter the central Delta will benefit from higher net positive downstream flows in the lower San Joaquin River channel to the Bay. Opening the gates only in daytime may provide many of the above benefits while minimizing impacts (Perry et. Al. 2013, 2015).

Perry, R. W., P. L. Brandes, J. R. Burau, P. T. Sandstrom & J. R. Skalski. 2015.
Effect of Tides, River Flow, and Gate Operations on Entrainment of Juvenile Salmon into the Interior Sacramento–San Joaquin River Delta
Transactions of the American Fisheries Society. Volume 144, Issue 3, 2015, pages 445- 455.

Perry, R. W., P. L. Brandes, J. R. Burau, A. P. Klimley, B. MacFarlane, C. Michel, and J. R. Skalski. 2013. Sensitivity of survival to migration routes used by juvenile Chinook Salmon to negotiate the Sacramento–San Joaquin River Delta. Environmental Biology of Fishes 96:381–392.

Figure 1. Location of Delta Cross Channel gate.

Figure 1. Location of Delta Cross Channel gate.

Central Delta net flow changes from opening Delta Cross Channel

Figure 2. Central Delta net flow changes from opening Delta Cross Channel (DLC in map). Blue arrows are increased net flows. Red arrows signify decrease in net flows. Blue dots indicate CDWR CDEC flow gages. (Base Map Source: CDEC)

April 20, 2015 Smelt Working Group

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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 Delta Smelt Update

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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

What is wrong with summer water transfers?

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Summer water transfers are predominantly made with water released from Shasta and Oroville reservoirs.  Instead of being used by Sacramento Valley CVP and SWP contractors, water is sold to South of Delta contractors who take the water via the South Delta CVP and SWP export pumps.  Non-project water transfers are also facilitated by CDWR.  Transfers usually occur in drought years when allocations to South of Delta contractors are low and excess export capacity exists at the South Delta pumping plants.  Purchasers must also pay for an additional 15-25% of “carriage” water to limit salinity intrusion into the Delta that would occur with export of transfer water.

Under existing “rules”, up to 600,000 AF of water may be transferred through the Delta during the allowed summer transfer “window”.  In 2014, 110,000 AF of CVP water from Shasta Reservoir was transferred from July through November (Reclamation was granted a temporary change to transfer water in the Oct-Nov period in 2014).  In 2014, approximately 300,000 AF of transfers were conducted by CDWR during the summer.  In 2015 CVP transfers of Shasta water are expected to be 240,000 AF, while SWP transfers are expected to be less than they were in 2014.

So what are the problems with water transfers from an ecological perspective1?

  1.  Transfer water is released from reservoirs in summer where during drought years there may be a limited cold-water pool to sustain downstream fish populations through the summer and fall. In 2014, the brood year for Winter Run Chinook Salmon was lost when the Shasta cold-water pool was exhausted at the end of August (Figure 1).  Some would argue that the water would have been released in any case to downstream ag contractors.  However, there are other options that would keep the water in the reservoir (e.g., fallowing programs, water purchase, deferring transfers).
  2. The water is released from multi-year storage, thus limiting the amount of carry-over storage in the coming years that is needed to sustain fish and their habitat, as well as water supplies for public health and safety.
  3. Transfer water exported from the Delta is not the same water released from the reservoirs. Water exported is a combination of Sacramento River inflow, San Joaquin River inflow, and Delta low-salinity (brackish) water from the North, Central, and West Delta.  Sacramento River inflow includes flows from the Feather, Yuba, and American rivers, as well as many smaller rivers.
  4. The already inadequate protections that apply to “normal” export water don’t apply to transfer water. Transfers increase the flow towards the Delta pumps, pulling fish with them.  But the ratio of inflow to outflow that generally limits exports doesn’t count transfer water; there are no restrictions in moving transfer water through the Delta other than carriage water requirements.  Transfer water can make up 25% or more of Delta inflow.
  5. Transfer water exported thus takes water with fish from many Central Valley habitats. Most prominently is the taking of Delta Smelt from the brackish and freshwater zones of the North, Central, and West Delta. Transfer water essentially must pass through the Delta’s designated critical habitats to get to the South Delta export facilities (Figure 2).
  6. When water quality standards for inflow, outflow, and salinity are relaxed, the process is further aggravated. Adding transfers during drought conditions with barriers, DCC open, low exports, low inflows, and low outflows worsens the effects of transfers by bringing in added warm, fresh, low turbidity water to the Low Salinity Zone from the north, while exporting turbid, brackish, higher turbidity, more biologically productive water from the south (Figure 2).
  7. Delta Smelt are highly vulnerable in the summer of drought years because the entire population is within the Delta (figure 3), where water temperatures are near or above lethal levels.
Figure 1. Water temperature of Keswick Dam releases in summer 2014. Chart depicts rapid rise in water temperature in early September as Shasta cold-water pool was exhausted. (Chart Source: NMFS)

Figure 1. Water temperature of Keswick Dam releases in summer 2014. Chart depicts rapid rise in water temperature in early September as Shasta cold-water pool was exhausted. (Chart Source: NMFS)

Figure 2. Freshwater inflows to the Delta (blue arrows) including transfer water must mix first with many other source waters including brackish waters (green lines) from San Francisco Bay. South Delta exports draw water across the Delta (red arrows).

Figure 2. Freshwater inflows to the Delta (blue arrows) including transfer water must mix first with many other source waters including brackish waters (green lines) from San Francisco Bay. South Delta exports draw water across the Delta (red arrows).

igure 3. Catch distribution of Delta Smelt in CDFW Summer Townet Survey, July 2014. (Source: http://www.dfg.ca.gov/delta/data/townet/ )

Figure 3. Catch distribution of Delta Smelt in CDFW Summer Townet Survey, July 2014. (Source: http://www.dfg.ca.gov/delta/data/townet/ )