Category Archives: Bay-Delta

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.)

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

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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

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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

April Spring Tide in Delta

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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.