Category Archives: Water Quality

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)

April 2015 Framework of Actions for Managing the Sacramento River

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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.