June 2020 Delta Outflow – New State Standard Needed

I recommended a new June Delta outflow standard of 10,000 cfs in a post on June 23 2020. This increase from the current standard of 7000 cfs would keep salt and Delta smelt out of the Central Delta and better maintain adequate water temperatures for emigrating Central Valley salmon smolts.

In this post, I consider the recommended 10,000 cfs value in the context of how the California Department of Water Resources (DWR) and the Bureau of Reclamation (Reclamation) estimate Delta outflow as they manage Delta hydrology and federal and state exports from the south Delta. This should further explain why an increase in the June Delta outflow standard is necessary.

It helps to recall my description in a September 2019 post how DWR and Reclamation estimate Delta outflow: “Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay.“ This is different from the US Geological Service’s (USGS) method of calculating real-time outflow. As an example, I overlaid the DWR and USGS for the summer of 2018 (Figure 1).

The State’s D-1641 June water quality standard is: the monthly average of the average outflow for each day must meet or exceed 7000 cfs (monthly average of daily averages). DWR and Reclamation comply with this standard using their own estimation method, not real-time outflow. Figures 2 and 3 below show the differences in the DWR and USGS methods in May-June 2020.

In May-June 2020, DWR and Reclamation maintained Delta outflow (using their own estimation method) near 7000 cfs, except during a mid-May storm when estimated outflow reached a peak of 15,300 cfs (Figure 2). But viewed from a different perspective, there were significant dips in the USGS estimation of outflow during spring tides around June 5 and June 19. The DWR method of estimating didn’t pick up these dips at all. These periods where USGS showed negative net outflow showed up in the monitoring of salinity as well (Figures 4-6). Periods of low or negative outflow were also periods of high salinity at key Delta monitoring stations.

Although net daily Delta flows are relatively small compared to real-time tidal flows (Figures 7 and 8), net flows affect water quality and fish habitat conditions on a daily basis. The salinity data for May-June 2020 at False River (Figure 5) is particularly significant. (Note the spikes in salinity during spring tides around June 5 and June 19). False River is the gateway to Franks Tract. As salinity increases in False River, smelt will move upstream (towards lower salinity conditions) in Franks Tract. As I described in an April 28, 2020 post, Franks Tract is a “smelt trap” where smelt that enter almost invariably perish.

Increasing the standard for June Delta outflow so that the required monthly average of the average outflow for each day is 10,000 cfs, not 7,000 cfs, would not fully offset the effects of spring tides and the use of averaging in DWR’s method of calculating compliance. But it would help protect Delta habitat from salt intrusions during spring tides and keep the low salinity zone and young Delta smelt out of the Delta. Although DWR and Reclamation did a good job in May-June 2020 of staying above 7000 cfs each day using their calculated outflow method, adding an explicit minimum daily flow standard to the monthly flow standard could also help. This would likely have the result of reducing exports during periods of the spring tides in the monthly lunar tidal cycle.

Figure 1: Daily outflow estimated by DWR and USGS in summer 2018.

Figure 2.  DWR’s calculated Delta outflow in May-June 2020.  Note switch to July standard of 5000 cfs

Figure 2. DWR’s calculated Delta outflow in May-June 2020. Note switch to July standard of 5000 cfs outflow on July 1. Source: CDEC.

Figure 3. USGS’s estimate of tidally filtered Delta outflow as estimated in May-June 2020. Spring-tides occurred May 9, May 23 (not measured because of storm inflows), and also on June 5 and June 19. Note dips in outflow on June 5 and 19; these dips do not appear in DWR’s estimate in Figure 2.

Figure 4. Salinity (conductivity) in eastern Suisun Bay at Collinsville in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 5. Salinity (conductivity) in False River in west Delta in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 6. Salinity (conductivity) in eastern Suisun Bay at Pittsburg in May-June 2020. Note peaks in salinity during net negative outflow with spring tides on June 5 and 19 (see Figure 3).

Figure 7. Hourly river flow and tidally filtered flow in lower San Joaquin River channel in western Delta at Jersey Point in June 2020. Note highly negative peak flows with spring tides on June 5 and June 19.

Figure 8. Hourly river flow and tidally filtered flow in lower Sacramento River channel in western Delta at Rio Vista in June 2020. Note spring tides on June 5 and June 19.

Delta Smelt Sanctuary – Deepwater Ship Channel

In a March 2020 post, I described where the remnants of the endangered Delta smelt population spawn and rear in the Sacramento Deepwater Ship Channel (Ship Channel) in the north Delta (Figure 1). In this post, I describe how the rearing conditions in the Ship Channel are poor. This can be seen by comparing habitat conditions in the Ship Channel with those in the lower Sacramento River channel at Freeport several miles to the east in late spring 2020.

Net Flow

Net flow (cfs) in the Ship Channel remains near zero, since the gate at the north end of the channel near Sacramento remains stuck in the closed position as it has been for several decades (Figure 2).

Water Temperature

Water temperature (oC) is significantly higher in the stagnant flows of the Ship Channel than at Freeport, often reaching into the lethal range 23-25°C for Delta smelt (Figure 3).

Salinity

Salinity (conductivity) is much higher in the Ship Channel because of discharges from urban sewage treatment plants and agricultural operations (Figure 4).

Turbidity

Turbidity is much higher in the Ship Channel due to higher plankton production and port-bound ship traffic in the relatively shallow and narrow Ship Channel (Figure 5).

Dissolved Oxygen

Dissolved oxygen levels are much lower in the Ship Channel because of warmer water, high concentrations of suspended organic sediments, and higher plankton production (Figure 6).

Interpretations and Conclusions

Delta smelt are attracted to the Sacramento Deepwater Ship Channel in winter and early spring to spawn in the relatively warm, low salinity, turbid, and more productive water. The adult smelt can also easily tidal-surf up the ship channel without having to content with strong downstream currents of the Sacramento River channel. Their eggs hatch early to an awaiting abundant plankton food supply. However, in spring the Ship Channel lacks net downstream flows to carry the young smelt to the Bay. By late spring, water temperatures in the Ship Channel reach lethal levels for the young smelt.

Opening the gate at the north end of the Ship Channel would help to alleviate the problems by providing net flow with cooler water temperatures, and by flushing and diluting the stagnant waste waters in the Ship Channel. An operable gate at the head of the Ship Channel would allow adaptive management of the habitat conditions for smelt.

Figure 1. Locations where Delta smelt young were captured in EDSM surveys in July 2019. Circles represent regions. Numbers are total July catch in region. The 94 represents the young smelt captured in the Deepwater Ship Channel.

Figure 2. Net daily flow (cfs) in the Ship Channel and in the Sacramento River at Freeport in June 2020. The green line shows flow in the Ship Channel.

Figure 3. Water temperature in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows the water temperature in the Ship Channel.

Figure 4. Conductivity (salinity) in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows salinity in the Ship Channel.

Figure 5. Turbidity in the Ship Channel and Sacramento River at Freeport in June 2020. The blue/purple line shows turbidity in the Ship Channel.

Figure 6. Dissolved oxygen in the Ship Channel and Sacramento River at Freeport in June 2020. The green line shows dissolved oxygen in the Ship Channel.

 

 

The 18 May Storm Brought Water and Fish to the Bay

A mid-May storm in the northern Central Valley brought approximately 250,000 acre-ft of new water to the Sacramento River watershed. A rough conservative estimate indicates approximately 150,000 acre-ft of the storm’s water was put into storage in northern Valley reservoirs, while roughly 100,000 acre-ft of the storm’s water reached the Delta and Bay. No noticeable effect from the storm was observable in the southern Valley or San Joaquin River.

Shasta Reservoir storage at the northern end of the Valley increased 80,000-100,000 acre-ft from the storm (Figure 1). About 50,000 acre-ft of runoff was stored directly in Shasta Reservoir. Another 50,000 acre-ft was added to Shasta storage by reducing downstream releases because downstream irrigation demands were being met by tributary inputs from the storm (Figure 2).

Local runoff and tributary inputs from the storm in the Redding and Red Bluff area increased streamflow in the lower Sacramento River. Sacramento River flow in the area as measured at the Bend Bridge Gage (BND) increased 3000-4000 cfs (about 30%) on May 18-19 (Figure 3). The lower river flow pulse passed downstream by Colusa (RM 144) and Wilkins Slough (RM 120) on May 20-22, and Verona (RM 70) and Freeport (RM 35) on May 21-23 (Figure 3). Most of the storm’s runoff that did enter the lower Sacramento River, other than the 3000-5000 cfs diverted for irrigation, eventually reached the Bay, doubling Delta outflow to the Bay (Figure 4). This significant flow pulse helped young salmon and steelhead passing through the Delta to reach the Bay (Figure 5) and reduced the loss of the young salmon and steelhead at the Delta export pumps (Figure 6). The flow pulse helped keep water temperature down to safe limits (<68°F) (Figure 7). However, after the pulse passed and flows dropped, water temperatures reached 74-77°F, near or at the lethal level for salmon, prompting what appears to be an “emergency” increase in reservoir releases in late May to alleviate water quality and permit violations of water temperature standards.

Most of the lower river flow pulse reached the Bay because Delta exports were not increased as would have been allowed by the latest National Marine Fisheries Service’s (NMFS) 2019 Biological Opinion (BO) for the long-term operations of the Central Valley Project (CVP) and State Water Project (SWP). On May 11, 2020, Judge Dale A. Drozd of the U.S. District Court for Eastern California issued a preliminary injunction sought by the state of California and several environmental and fishing groups. The injunction prevented the Bureau of Reclamation from implementing the new BO until at least June 1, 2020. One immediate result of the injunction was that NMFS’s 2009 BO was put back into effect, with restrictions on May exports.

If there had been no 2009 BO restrictions on Delta exports (the 2009 BO limited exports to 100% of San Joaquin River inflow to the Delta), south Delta exports could have been 6000 cfs (under a State Water Board limit of 35% of total Delta inflow) instead of 1000-2000 cfs (Figure 8). Such higher exports would have greatly reduced the added beneficial Delta outflow from the storm and would have had a greater impact to emigrating salmon and steelhead smolts from the Sacramento River and the San Joaquin River. Less Delta outflow would also have limited benefits to endangered longfin and Delta smelt in the Bay.

In conclusion, the total amount of water from the northern California storm was near 75,000 acre-ft in the Redding-Shasta watershed, with about a third captured in Shasta Reservoir, a third going to irrigation deliveries instead in lieu of deliveries from Shasta storage, and a third passing downstream to the Delta and Bay. The judge’s decision to allow approximately 40% of the stormwater to reach the Bay, at least temporarily, has helped sustain salmon and smelt in this otherwise dry year. After the flow pulse, slow-to-react water managers allowed water temperatures to spike, threatening the listed salmon and smelt that remained in the rivers and the Delta.

Figure 1. Shasta Reservoir storage May 2020. Red line indicates projected storage before the mid-May storm. The difference between the two lines is a rough estimate of added new storage.

Figure 2. Shasta/Keswick dam releases in May 2020. The cuts in Shasta/Keswick releases in mid-May correspond to increase in downstream stormwater inputs that reduced demands on Shasta storage.

Figure 3. Sacramento River streamflow in May 2020 as measured at Bend (RM 259), Hamilton City (RM 200), Colusa (RM 144), Wilkins Slough (RM 120), Verona (RM 70), and Freeport (RM 35). The difference in flows at Bend and flows at Hamilton City, Colusa, and Wilkins Slough in early May is due to irrigation diversions downstream of Bend. Increased flows at Freeport and Verona compared to flows at Wilkins Slough are due to Feather River and American River inputs. Source: http://www.cbr.washington.edu/sacramento/data/ .

Figure 4. Delta outflow (DTO), and Sacramento River flow at Freeport (FPT, RM-35), Verona (VON, RM-70), and Wilkins Slough (WLK, RM-120) in May 2020.

Figure 5. Unmarked salmon smolts captured in trawls leaving the Delta at Chipps Island in eastern San Francisco Bay, 8/1/2019 to 5/15/2020. Note increase in smolts escaping to the Bay after May 11.

Figure 6. Unmarked juvenile salmon salvage at south Delta export facilities 10/1/2019-5/18/2020. Delta exports are shown in acre-ft in center panel. Note reduced salvage when exports were at minimum levels (about 3000 acre-ft per day, or about 1500 cfs) after mid-May.

Figure 7. Sacramento River flow and water temperature at Freeport (FPT, RM-35), Verona (VON, RM-70), and Wilkins Slough (WLK, RM-120) in May 2020. Note the excessively high water temperatures (lethal for salmon at Verona, otherwise highly stressful) at Verona and Wilkins Slough in late May.

Figure 8. May 2020 Delta exports from federal Tracy Pumping Plant (TRP) and state Harvey Banks Plant (HRO).

 

“Improbable Comeback” Not Looking Probable

In an April 19, 2020 blog post entitled Science of an underdog: the improbable comeback of spring-run Chinook salmon in the San Joaquin River, a UC Davis team describes the efforts over the past five years to recover spring-run Chinook salmon in the San Joaquin as a “good comeback story.” It is a great story – as far as it goes.  Eighteen years of litigation and fifteen years of restoration work have put water back in a river that Friant Dam completely dried up in 1950.  There are also some spring-run salmon in the river, and a few made it from near Fresno to the ocean and back in the last few years.

The goal of the reintroduction program is the long-term maintenance of a population of 30,000 spawning adults with negligible hatchery influence.  The count for the 2019 run was 23.  Reaching the goal is highly improbable in the present scheme of things.

Why?  As the UC Davis team stated:  “Most of the tagged fish that enter the interior Delta simply don’t make it out.”  Juvenile salmon from natural spawning areas and hatcheries do not survive downstream passage downstream to and through the Delta in necessary numbers to make the goal achievable.  There are simply too many “obstacles.”

The UC Davis team also stated:  “It is notably sad and ironic perhaps, that the quality of habitat in the lower river is so poor that the best migration path for salmon appears to be as a salvaged fish, trucked around the Delta by DWR or BOR staff.”  The word “best” is just the wrong word to describe a path and procedure that is founded on a dysfunctional fish salvage system that at its best saves a tiny fraction of the fish that the Delta pumps pull off course and ultimately decimate.  Returns of adult salmon to the San Joaquin River are extremely low (Figure 1).  Department of Water Resources and Bureau of Reclamation “staff” collect and truck these totally misdirected, stressed, and abused fish, and dump them into the waiting mouths of predators in the west Delta, not even bothering to truck salvaged fish to the Bay.  Compared to Sacramento River hatchery smolts, the odds of San Joaquin hatchery smolts being “salvaged” are one to two orders of magnitude higher (Table 1).

What could help recover San Joaquin River spring-run salmon?

  1. Reduce exports from the south Delta, especially from March through May.
  2. Increase San Joaquin River and tributary flows during adult and juvenile migration seasons.
  3. Improve habitat in spawning, rearing, and migration corridors from spawning reaches to the Bay.
  4. Capture wild juvenile spring-run below spawning reaches and transport them to the Bay.
  5. Transport hatchery and wild smolts via barge or floating net pens from lower rivers to the Bay.

So far minimal progress has been made on measures 1-3.  As yet, there has been no attempt to address measures 4 and 5 other than pilot studies (encouraging) by the Mokelumne River Fish Hatchery.

“Ironic” is also the wrong word to describe how Delta salvage operations are the least impossible longshot for San Joaquin smolts: it is absolutely infuriating that thirty years of dedicated and talented legal, biological and in-river effort can be undone by the Delta operations that DWR and BOR have just made more efficient at fish killing.

TABLE 1.  Comparison of “loss” in Delta salvage facilities between San Joaquin hatchery spring-run smolts and other Central Valley salmon hatchery smolts 2016-2020.  Note the word “loss” is used instead of “salvaged” in these tallies.  Source:  http://www.cbr.washington.edu/sacramento/tmp/deltacwttable_1587318641_393.htmlTABLE 1. Comparison of “loss” in Delta salvage facilities between San Joaquin hatchery spring-run smolts and other Central Valley salmon hatchery smolts 2016-2020. Note the word “loss” is used instead of “salvaged” in these tallies Table 1. Continued. Table 1. Continued.

Figure 1. Hatchery tag adult returns from San Joaquin releases in 2016 (dry San Joaquin water year). Green dots are San Joaquin hatchery spring run released above Merced River in San Joaquin. Blue dots are releases from Merced hatchery fall run released to the Delta near Sherman Island. Orange dots are Mokelumne hatchery fall run released to the Delta near Sherman Island unless specified: GGB = Golden Gate Bridge, HMB = Half Moon Bay on coast, R = Mokelumne River. Data source: https://www.rmpc.org

Follow-up on Spring 2020 Sacramento River Conditions

In a recent post (May 6, 2020), I discussed the need to increase flows in the lower Sacramento River to reduce water temperatures for emigrating juvenile spring-run and fall-run hatchery and wild Chinook salmon. I recommended maintaining water temperatures below 65°F/18°C per the scientific literature. Water managers increased flows (or reduced diversions) on about May 11 (Figure 1), and with the help of cooler weather (Figure 2), water temperatures came down significantly through the lower Sacramento River (Figures 1, 3, and 4).

The National Marine Fisheries Service (NMFS), California Department of Fish and Wildlife (CDFW), and US Bureau of Reclamation (BOR) have begun a multi-year study to evaluate the potential survival benefits for juvenile spring-run and fall-run Chinook salmon of managed spring flow pulses in the Sacramento River.1 Such action is prescribed in the NMFS 2019 biological opinion for the federal Central Valley Project. The problem with the prescription is that it applies only in wetter years when there is high Shasta Reservoir storage (4 million acre-ft end-of-April), while the need is greatest in drier years when reservoirs capture most if not all the water from limited precipitation events.

But why study the concept with 50 years or more of data available? Just looking at this spring’s data shows the role flow can play in keeping temperature below levels that are known to increase salmon mortality. In this blog I have shown over and over the order-of-magnitude benefits to population recruitment that comes from maintaining flows and water temperature. The scientific literature is replete with analyses of the effects of water temperature on salmon. We know that temperatures in the lower Sacramento River on May 9-10 were bad for immigrating adult salmon and emigrating juvenile salmon, so why not acknowledge the problem and correct it?

And why just study the benefit of a single flow pulse? Results would depend on so many factors. In Figure 1, weather forecasts indicated the May 7-9 heat wave days ahead, so why wasn’t the flow pulse applied earlier? Or were water managers simply responding to water demands or violations in water quality standards that occurred May 8-10 at Verona?

In any case, the May 2020 example shows that flows and water temperatures in the lower Sacramento River need to be actively managed to protect salmon.

Figure 1. Water temperature and streamflow in the Sacramento River at Wilkins Slough and Verona May 1-15, 2020. See Figure 4 for gage location.

Figure 2. Air temperature at Hood near Freeport May 1-15, 2020.

Figure 3. Freeport gage water temperature and daily average flow (tidally filtered) May 1-15, 2020. Figure 4 for gage location.

Figure 4. Gage stations in lower Sacramento River

 

  1. A link to the draft study plan: https://1drv.ms/b/s!ArkjAKW4WdKRwCWsW3cnyJdS5Zac