Category Archives: Bay-Delta

Early May Prognosis for Smelt

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How are Delta and Longfin smelt doing after my earlier March and April poor prognoses? As predicted, late April – early May surveys indicated extremely low numbers (Figures 1 and 2), far fewer than the record low numbers of 2013-2014 (Figures 3-6).

In the May 4, 2015 Smelt Working Group meeting1, “Members did make a note of the single Delta Smelt larva from April 23, as well as the three Delta Smelt observed during the primary channel CO2 treatment [at Tracy Fish Salvage Facilities], providing that this is evidence of entrainment. These collections occurred despite at or below minimum exports levels, as defined in the Biological Opinion; OMR flows were also at or close to the most positive flows indicated in the Biological Opinion….Salvage of juvenile Longfin Smelt increased to 52 for the week of April 27 through May 3. Some increase was expected as south Delta water warmed. Between April 13 and 15, four juvenile Longfin Smelt were salvaged at the CVP and 12 at the SWP, at the same time, a single larva was observed in the larval fish samples at the CVP and four larvae at the SWP. During the period of April 17 through 23, seven Longfin Smelt larvae were observed at the SWP and one larva at the CVP in larval fish collections. Continued collections in salvage are expected. Overall, catches in the central and south Delta were not sufficient to reach concern levels based on density or distribution… Longfin Smelt larvae and small juveniles will continue to be detected at the salvage facilities until water temperatures surpass 22 deg C.” The fact that any smelt were collected at the two south Delta export facilities should be a grave warning of a larger and very significant “take” of smelt. As stated many times before, the odds of any young smelt reaching the south Delta export facilities without succumbing along the way are infinitesimal. In addition, no smelt will survive in any part of the Delta where water temperature reaches 25°C.

With the prescribed Net Delta Outflow Index at only 4000 cfs and measured outflow nearer to zero, the low salinity zone critical habitat of smelt is in the central Delta. Remaining smelt are being drawn across the Delta from north to south to the export pumps. Under these conditions the first heat wave of late spring will heat the central Delta to lethal 23-25°C levels for smelt. Unless these conditions are changed by increasing outflow and reducing exports, both smelt species may go virtually extinct2 this spring.

Figure 1. Delta Smelt density distribution in late April 20-mm Survey. Only three were captured in Sacramento Deep-Water Ship Channel, compared to 20 in previous week’s survey.

Figure 1. Delta Smelt density distribution in late April 20-mm Survey. Only three were captured in Sacramento Deep-Water Ship Channel, compared to 20 in previous week’s survey.

Figure 2. Longfin Smelt density distribution in late April 20-mm Survey

Figure 2. Longfin Smelt density distribution in late April 20-mm Survey

Figure 3. Delta Smelt density distribution in late April, 2014 20-mm Survey.

Figure 3. Delta Smelt density distribution in late April, 2014 20-mm Survey.

Figure 4. Longfin Smelt density distribution in late April, 2014 20-mm Survey

Figure 4. Longfin Smelt density distribution in late April, 2014 20-mm Survey

Figure 5. Delta Smelt density distribution in late April, 2013 20-mm Survey.

Figure 5. Delta Smelt density distribution in late April, 2013 20-mm Survey.

Figure 6. Longfin Smelt density distribution in late April, 2013 20-mm Survey.

Figure 6. Longfin Smelt density distribution in late April, 2013 20-mm Survey.

  1. http://www.fws.gov/sfbaydelta/documents/smelt_working_group/swg_notes_5_4_2015.pdf ↩
  2. Virtually extinct means we should not expect to see any next year. ↩

April Delta Bloom Dissipates

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The central Delta plankton bloom described in my April 23 post has dissipated (Figures 1 and 2). The bloom was a consequence of long residence time of water in the lower San Joaquin River channel in the central Delta. The increased residence time resulted from a combination of low south Delta exports during April (1500 cfs), low net flows in the lower San Joaquin River (Figure 3), and a prescribed San Joaquin River “pulse flow” (Figure 4). A high “spring” tide period from 4/17-4/25 (Figure 5) likely helped sustain the bloom by restricting Delta outflow (see Figure 3).

The San Joaquin pulse flow had a double benefit: 1) it provided key nutrients to stimulate the bloom, and 2) it reduced south Delta export demand from the bloom area in the central Delta. The pulse flow is indicative of normal San Joaquin April flows, while the extremely low flows subsequent to the April pulse were allowed by the State Water Board in drought-related change orders.

These events are important because they highlight the importance of San Joaquin River inflows and monthly tidal cycles in the Delta for Delta Smelt and Longfin Smelt rearing in the Delta. Smelt are significantly affected by their plankton food supply and the potential entrainment of that food supply into the south Delta export pumps. The pulse flow, like other management actions, should be considered an adaptive management experiment from which valuable insight might be learned for managing the Delta. The bloom was a very rare event, and the circumstances behind it could be important in the future management of the Delta.

Figure 1. Chlorophyll levels at Blind Point in the western Delta in the San Joaquin River channel during April 2015. (Source: CDEC)

Figure 1. Chlorophyll levels at Blind Point in the western Delta in the San Joaquin River channel during April 2015. (Source: CDEC)

Figure 2. Chlorophyll levels in Old River adjacent to Franks Tract in the central Delta during April 2015. (Source: CDEC)

Figure 2. Chlorophyll levels in Old River adjacent to Franks Tract in the central Delta during April 2015. (Source: CDEC)

Figure 3. Net flow in the lower San Joaquin River near Jersey Point. (Source: USGS).

Figure 3. Net flow in the lower San Joaquin River near Jersey Point. (Source: USGS).

Figure 4. Net inflow of the San Joaquin River at Stockton in April 2015. (Source: USGS)

Figure 4. Net inflow of the San Joaquin River at Stockton in April 2015. (Source: USGS)

Figure 5. Tidal effect on water surface elevation at Jersey Point in the lower San Joaquin River in April 2015. A “spring” tide occurred from 4/17-4/25. (Source: USGS)

Figure 5. Tidal effect on water surface elevation at Jersey Point in the lower San Joaquin River in April 2015. A “spring” tide occurred from 4/17-4/25. (Source: USGS)

May 2 Spring Tide Affects Delta

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The State Board’s weakened standards require a Net Delta Outflow Index of 4000 cfs and limit south Delta exports to 1500 cfs. 4000 NDOI was achieved during the first three days of the month, but a spring tide pushed into the Delta, resulting in actual negative net Delta outflows (NDOs) that were -6000 cfs on May 2. So much salt pushed into the central Delta (see charts below) that South Delta exports had to be reduced from the allowed 1500 cfs to less than 700 cfs. Export reductions were necessary to stop the salt intrusion and to offset the fact that the exported water was becoming too salty. The Smelt Working Group, at its meeting on May 4,1 expressed no apparent concern about the disappearance of the Low Salinity Zone, or about the fact that the population remnants of Delta and Longfin Smelt were pulled into the south Delta.

Meanwhile, the state and federal water project operators dropped Sacramento River Delta inflow from 6900 cfs on April 30 to 5600 cfs on May 2 (oops). They raised Shasta/Keswick releases on May 2 from 7000 to 7500 cfs after lower river flows near Yuba City dropped to 3500 cfs on May 1, as a result of watering up rice fields in the Sacramento Valley. American River (Folsom Reservoir) releases remained settled in at 1000 cfs.

There is simply no excuse for this poor Delta water management. The moon has been around for billions of years and tides are totally predictable. Export water need not have been 600 EC salinity (barely safe for humans and many crops). The several thousand cfs demands for rice fields in the Sacramento Valley could have been restricted for a few days to allow inflow to offset the spring tides in the Delta. Folsom releases could have been bumped up 500 cfs at least for the weekend rafters.

The salt will take a few days to be flushed out by neap tides, but spring tides and salt will soon return. Will Delta water managers be ready?

Salinity (EC) from 4/27-5/7 at Holland Cut in the South Delta on Old River – a primary source of South Delta exports.

Salinity (EC) from 4/27-5/7 at Holland Cut in the South Delta on Old River – a primary source of South Delta exports.

Salinity (EC) from 4/27-5/7 at Threemile Slough - the connection between the Sacramento and San Joaquin rivers near Rio Vista. It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at Threemile Slough – the connection between the Sacramento and San Joaquin rivers near Rio Vista. It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at False River - the major connection between the western and central Delta at Franks Tract and Old River. It is a major channel for incoming tides into the central Delta.

Salinity (EC) from 4/27-5/7 at False River – the major connection between the western and central Delta at Franks Tract and Old River. It is a major channel for incoming tides into the central Delta.

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)