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.

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.)

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.

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.