May 2 Spring Tide Affects Delta

Posted on May 10, 2015 by Tom Cannon

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 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.

http://www.fws.gov/sfbaydelta/documents/smelt_working_group/swg_notes_5_4_2015.pdf ↩

Spring Actions to Save Delta Smelt

Posted on May 8, 2015 by Tom Cannon

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:

Reduced Delta outflow, which results in X2 and LSZ moving upstream. (Magenta arrow in Figure 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.)
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:

Increase Delta outflow by 1000-2000 cfs, at least during “spring tides”.
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.
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)

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.

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

Open the Delta Cross Channel

Posted on May 7, 2015 by Tom Cannon

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 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

Posted on April 24, 2015 by Tom Cannon

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 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.

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.)

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

Posted on April 23, 2015 by Tom Cannon

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 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 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 6. Blind Point chlorophyll levels April 2015.

Figure 7. Old River chlorophyll levels April 2015.

Figure 8. Prisoners Point chlorophyll levels April 2015.

Figure 9. Middle River chlorophyll levels April 2015.

Figure 10. Turner Cut chlorophyll levels April 2015.

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 ↩
Jassby, A., J. Cloern, and A. Muller-Solger. 2003. Phytoplankton fuels Delta food web. California Agriculture 57(4): 104-109. ↩

California Fisheries Blog

Science, Management, Issues, Problems, and Solutions

Category Archives: Bay-Delta