Category Archives: Water Quality

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 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.

Can Winter Run Chinook Salmon be Saved in 2015?

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Various resource agencies are scrambling to protect Winter Run Chinook Salmon this year after last year’s debacle, in which water “saved” in Shasta Reservoir wasn’t cold enough to keep Winter Run eggs and fry alive1. Higher, colder flows are necessary to keep the eggs and fry alive in their spawning and early rearing areas near Redding, but were unavailable last summer because Shasta’s cold-water pool was depleted by the end of August.

The five charts included below tell the story of what happened last year. In summary, these are the main reasons why the Bureau of Reclamation ran out of cold water in Shasta Reservoir…

  • First, approximately 200,000 acre-feet (AF) of cold-water pool storage was released to senior water rights contractors in May. (Amount calculated from Figure 1 and Table 1).
  • Second, approximately 500,000 AF of cold-water pool storage was released in June and July that could be argued was needed for maintaining river temperature control below Redding. However, I would argue that given the precarious state of the Shasta cold-water pool in June and July, federal and state agencies should have released less (to maintain 58°F at Clear Creek instead of the chosen target temperature of 56°F) to sustain Shasta’s cold-water pool. My guess is they could have saved 2000 cfs or about 240,000 AF of total storage in June and July. This water would have come out of the Sacramento River Settlement Contractors’ 560 TAF deliveries for June-July (Table 1).
  • Third, somewhat less cold-water pool water could have been saved in early weeks of August.

If the Bureau of Reclamation had saved this 440,000 AF from May-July (about a third of deliveries), there would have been no extreme mortalities of Winter Run Chinook Salmon in the late August-October period from low flows and high water temperatures. Contractors could have made up some of their loss in the late August-October period when higher colder flows would have been released from Shasta for fish. If Sacramento River contractors were unable to use this water late in season, the water could have been used to maintain Delta water quality standards or left as carryover storage in Shasta Reservoir.

In summary, cold-water pool releases from Shasta Reservoir from May through August of 2014 were too great to support the cold water resource, resulting in the loss of much of the year’s production of Winter Run eggs and fry to low flow, warm water conditions. In similar conditions in 2015, releases for contractor irrigation deliveries should be reduced in order to sustain Shasta’s cold-water pool through the summer. Such protections should be the cornerstone of the Drought Operations Plan being developed by the agencies. NMFS and DFW should not approve the Plan without this element to protect Winter Run.

Figure 1

Figure 1. Mainstem flow of the Sacramento River below Redding, May-Sept 2014. Flows generally reflect releases from Shasta Reservoir. (Source: USGS Mobile Data Site)

Figure 2

Figure 2. Mainstem Sacramento River flows at Wilkins Slough gage below most of the contractor diversions. (Source: USGS Mobile Data Site)

Figure 3

Figure 3. Power-Point slide of risk to Winter Run adults, eggs, and fry as a function of water temperature in Shasta Reservoir releases (as measured Keswick Reservoir releases – KWK).2

Figure 3

Figure 4. Power-Point slide of risk to Winter Run eggs as a function of water temperature in Shasta Reservoir releases (as measured Keswick Reservoir releases – KWK) and temperature in the river below the mouth of Clear Creek near Redding.3

Table 1

Table 1. Water deliveries from Reclamation to Sacramento River contractors in 2014.
(Source: http://www.usbr.gov/mp/cvo/vungvari/table_28_2014.pdf)

  1. See, for instance, https://cdfgnews.wordpress.com/2015/01/26/agencies-taking-measures-to-protect-winter-run-chinook-preparing-to-release-approximately-600000-fish/ ↩
  2. Source: NOAA’s National Marine Fisheries Service’s (NMFS) Update to the State Water Resources Control Board by Garwin Yip, February 18, 2015 ↩
  3. Source: NOAA’s National Marine Fisheries Service’s (NMFS) Update to the State Water Resources Control Board by Garwin Yip, February 18, 2015 ↩

The Delta Plan – where is the water habitat?

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The Delta Stewardship Council’s Jessica Davenport, Program Manager, Ecosystem Restoration and Land Use, released an issue paper in August of last year entitled “Restoring Habitat with Science and Society in Mind”. 1

“The Delta Plan shall include measures that promote all of the following characteristics of a healthy Delta ecosystem:

  1. Viable populations of native resident and migratory species.
  2. Functional corridors for migratory species.
  3. Diverse and biologically appropriate habitats and ecosystem processes.
  4. Reduced threats and stresses on the Delta ecosystem.
  5. Conditions conducive to meeting or exceeding the goals in existing species recovery plans and state and federal goals with respect to doubling salmon populations.”

The Delta Plan,2 much like the Governor’s Bay Delta Conservation Plan (BDCP),3 has no measures that would promote a healthy Bay-Delta ecosystem. The plans virtually ignore water habitat: the characteristics of the water in the hundreds of miles and tens of thousands of acres of open water in the Bay-Delta. The plans fail to even define the components of a healthy ecosystem or how they relate to water habitat:

  • “viable populations” – what constitutes viable?
  • “functional corridors” – what is functional?
  • “appropriate habitats and ecosystem processes” – what is appropriate?
  • “threats and stresses” – what threats and stresses?
  • “conditions conducive to doubling salmon populations” – what conditions?

The plans simply focus on “restoration” of thousands of acres of edge habitat on marginal lands in Suisun Marsh and the Delta, virtually ignoring the “real problem” and its fixes. The “restoration” that is promoted will take decades to implement and will do little to promote a healthy ecosystem, at least in the short term.

The “real problem” is water management in the Central Valley and Bay-Delta. The “real problem” is our insatiable demand for water while virtually ignoring the beneficial uses and public trust requirements of the Central Valley and Bay-Delta ecosystems. There are water quality standards and endangered species biological opinions that provide minimal protections for resident and migratory native fish species. Yet the first thing that regulators do in droughts is relax these protections to provide more water for agriculture. As a consequence, the fish populations and their habitats suffer irreversibly in drier years, and especially in extended periods of drought. The result is fish populations on the verge of extinction, poor Bay-Delta water quality, salt in Delta water diversions, salmon smolts having to be trucked hundreds of miles from hatcheries to the Bay, and no freshwater inflow to the San Francisco Bay estuary.

Water is the ecosystem process ignored in the BDCP and Delta Plan. The characteristics of the water habitat in time and space are the missing element in the plans. The fish habitat that is most important is the water in Delta channels and bays, not the acreage of tidal marsh. Adding tidal marsh habitat will not fix the water habitat or provide a healthy ecosystem

The BDCP justified taking more water via the “tunnels” by offering thousands of habitat acres in return. The Delta Plan promotes these same land acreage solutions.

How can we really restore the Delta as habitat for smelt, salmon, steelhead, sturgeon, and other native fishes? We have to focus on Delta inflows, outflows, tides, and exports: hydrology, salinity, water temperature, and primary productivity patterns in the water habitat. The real habitat of the Delta is the three-dimensional characteristics of water in time and space. What should the water habitat be for Delta smelt when they hatch in the spring to insure good survival? How do we sustain the smelt in summer? Can they actually survive if all the Delta inflow is exported in August under relaxed standards? What happens to all the wild salmon smolts coming out of Central Valley rivers? What kind of water habitat do they need to pass through the Delta? They do not get a truck ride to and around the Delta. What is a “functional migration corridor” for them?

So instead of focusing on acreage, we should focus on the real habitat, water and all of its characteristics in time and space in the Delta, rivers, and the Bay. That way, we can promote the real ecosystem process that provides for a healthy Bay-Delta ecosystem.

The Delta Science Plan4 is just more talk and smoke and mirrors. What the Delta needs is more water and better water habitat. We do not need a new vision.

http://calsport.org/fisheriesblog/wp-content/uploads/2015/04/Box-1.-Delta-Science-Plan.png

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/ )