Category Archives: Water Quality

Water Projects’ Temporary Urgent Change Petition 3/18/22 Comment on Provision #1 – Spring (April-June) Delta Outflow and Salinity Intrusion

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The U.S. Bureau of Reclamation and the California Department of Water Resources (Reclamation and DWR) filed a “Temporary Urgency Change Petition” (TUCP) on March 18, 2020.  If granted, the TUCP reduce Delta outflow requirements.  The proposed averaging requirements in the TUCP pose a problem in addition to the problem of too little overall outflow.

The TUCP states:

Reclamation and DWR are requesting to modify certain terms as the Projects’ storage and inflow may not be sufficient to meet D-1641 requirements and additional operational flexibility of the Projects is needed to support Reclamation and DWR’s priorities, which include: operating the Projects to provide for minimum health and safety supplies (defined as minimum demands of water contractors for domestic supply, fire protection, or sanitation during the year); preserve upstream storage for release later in the summer to control saltwater intrusion into the Sacramento-San Joaquin Delta (Delta); preserve cold water in Shasta Lake and other reservoirs to manage river temperatures for various runs of Chinook salmon and steelhead; maintain protections for State and federally endangered and threatened species and other fish and wildlife resources; and meet other critical water supply needs. (3/18/22 TUCP, p. 1)

The TUCP is requesting reduced Delta outflow requirements for the April 1 through June 30, 2022 period, for the stated primary purpose of preserving storage in Oroville and Folsom reservoirs.   What I term Provision #1 is reduction of outflow requirement from 3-day average of 7,6001 to 14-day average of 4,000 cubic feet per second (cfs).

The requirement in Revised Water Rights Decision 1641 of a 3-day average of 7,600 cfs is meant to keep salt water from encroaching upstream from the Bay into the Delta in drought years like 2021 and 2022.   This helps to protect the beneficial uses in the Delta including fish, fish low-salinity habitat, Delta agriculture, and south Delta water export water quality.  The TUCP’s proposed Delta outflow of 4000 cfs is meant to provide minimum protection in the face of low available water supply (reservoir storage and precipitation).

The overriding problem with the TUCP’s proposed flow reduction is that it does not require enough flow.  Yet, even accepting the need to reduce flow to allow storage of more water in Reclamation and DWR’s reservoirs, the requested change could be modified to better protect beneficial uses.

Under past TUCPs, DWR and Reclamation have used the 14-day averaging window to game operations to skate as closely as possible to the edge of compliance.  This has led to erratic outflows, often below 4000 cfs (Figure 1).  More precise estimates taking into account tides show outflow is lower than intended (Figure 2).  In these circumstances, salinity has increasingly moved up from the Bay into the Delta under such minimum freshwater outflow (Figures 3-6).

I recommend the outflow required be more stable, allowing for only minimal salinity increase over the spring.  A 3-day average of 4,000 cfs measured outflow would provide greater protection of beneficial uses.

Salinity criteria are more easily defined and measured, and more directly related to beneficial uses.  Criteria for Collinsville, Emmaton, Jersey Point, and Old River that have a maximum for a 3-day average or a maximum daily level with a minimum increase over the spring would also be more protective.

Figure 1. Daily Delta outflow estimated from measured Delta hydrology conditions in spring 2014, 2015, and 2021, drought years when previous TUCPs were implemented

Figure 2. Measured Delta outflow into Suisun Bay in spring 2021.

Figure 3. Salinity in eastern Suisun Bay in spring 2021.

igure 4. Salinity in lower end of Sacramento River near Rio Vista in late April 2021.

Figure 5. Salinity and net tidal flow in lower San Joaquin River channel at Jersey Point in spring 2021.

Figure 6. Salinity (EC) and net tidal flow in lower Old River channel in south Delta near Byron in spring 2021.

  1. The normal requirements are stated in Revised Water Rights Decision 1641, Table 3, footnote 10, pp. 185-186.  The April-June requirement in a Critically Dry year is also met if either the daily average or 14-day running average EC (measurement of salinity) at the confluence of the Sacramento and the San Joaquin rivers is less than or equal to 2.64 mmhos/cm (Collinsville station C2).  From May 1 through June 30, if the Sacramento River Index is less than 8.1 million acre-feet, the flows requested in the TUCP would be the same as the required flows under Decision 1641. ↩

Salmon Released from Central Valley Hatcheries

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Hundreds of thousands of smolts of endangered salmon are being released to the lower Sacramento River from federal and state hatcheries this winter, the San Francisco Chronicle reported on March 2.1 It is a drought year, and most of the young salmon will likely perish in the jaws of predators on their 300-mile journey to the ocean through the river, Delta, and Bay. Without the protection of adequate river flow, cold water, and turbidity for the journey, there is little hope. Reservoir storage is depleted from the past two years of overzealous water deliveries. What little rain and snowmelt there has been in the Valley is being stored in reservoirs. Warm weather has come early. The 400 thousand smolts released on March 2 could use some help, but they have not received it and are not likely to get it.

River Flow

Flow from Shasta Reservoir to the upper river via Keswick Dam has been minimal (Figure 1, KWK). 40 miles downstream at the Bend (BND) gage near Red Bluff, the river received some snowmelt from tributaries in January, but even that tapered off by the end of January. Flow into the Delta from the Sacramento Valley at Freeport (FPT) reached minimal levels by the end of January. Delta outflow (Figure 2) settled at its minimal prescribed level near 12,000 cfs after some January export taking.

Water Temperature

Warm weather and low flows have allowed water temperatures in the lower Sacramento River and north Delta migration corridor to reach the mid-fifties (Figure 3), temperatures that activate lower river predators like striped bass, resident trout, and pikeminnow.

Turbidity

Turbidities (Figure 4) are now at seasonal lows from the upper river near Red Bluff (RDB) to the Delta near the Rio Vista Bridge (RVB), reflecting clear waters needed by sight-feeding predators like striped bass.

Delta Salmon Salvage

Hatchery salmon smolts released in December at least reached the Delta during the December storms (Figure 5). It remains to be seen if the February and March smolt releases even reach the Delta.

What’s Needed

The article in the Chronicle mentioned that only one of the 140 radio-tagged hatchery smolts released in February has reached the Delta. The March 2 release of 400,000 smolts could use a pulse of cold turbid water from Shasta, Oroville and Folsom reservoirs to help them reach the Bay. So far, only Oroville releases have increased, from 3500 to 5500 cfs in recent days, with the added 2000 cfs showing at Freeport (Figure 1). While this helps near the Delta, it does little for the upper 200 miles of river the smolts have yet to transit.

Figure 1. River flows near Keswick (River Mile-RM 300), Bend (RM 250), and Freeport (RM 50) in winter 2022.

Figure 2. Delta outflow in tidally averaged daily cfs in winter 2022.

Figure 3. Water temperature in Sacramento River near Bend (RM 250), Wilkins Slough (RM 140) and Freeport (RM 50) in winter 2022.

Figure 4. Water turbidity in Sacramento River near Bend (RM 250), Red Bluff (RM 240), Freeport (RM 50), and Rio Vista (RM 30) in winter 2022.

Figure 5. Salmon salvage observed at Delta Fish Facilities in water year 2022.

Yuba River Salmon in 2022

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In a December 2020 post, I described the status of the fall-run salmon population in the Yuba River.  Hatchery salmon predominate, while natural production is minimal.  The population remains in a very poor state – at about 10% of recent historical levels during and subsequent to multiyear droughts such as 2007-2009 and 2013-2015 (Figure 1).

In a January 11, 2022 post, the South Yuba River Citizens League (SYRCL) promotes cleaning the two fish ladders at Daguerre Dam half way up the river to the impassable Englebright Dam, in order to provide better passage for spawning salmon to prime spawning habitat.  Without effective ladders, salmon are delayed or even forced to spawn downstream of Daguerre Dam in marginal habitat.  The ladders must be maintained per the federal NMFS biological opinion and take permit to operate Daguerre Dam as a water diversion dam for the Yuba County Water Agency (YCWA).

SYRCL’s plea to clean the fish ladders is helpful in bringing attention to the problems facing salmon (and steelhead) in the lower Yuba River.  However, the fish ladders at Daguerre are only a small part of the problem for Yuba River salmon.  River flows and habitat in the lower Yuba River need improvement.

River Flows

It is instructive to compare flows in 2020 (Figure 2) to flows in 2021 (Figure 3), particularly at the Marysville gage, where water has passed downstream of all the local agricultural diversions at Daguerre Dam.

2020

From May through mid-August of 2020, flows at Marysville averaged about 1000 cfs (Figure 2).  The vast majority of this water was released through YCWA’s New Colgate Powerhouse upstream of Englebright Dam.  In the fiscal year from July 1, 2020 to June 30, 2021, YCWA had revenues from power sales of over $80 million. 1 Water released during the summer creates more power revenue than flows released in spring.

Better management for fish would release more of the water in the spring, providing more areas in the lower Yuba River for juvenile salmon and steelhead to grow and higher flows to move them downstream when they are ready to leave the system.  SYRCL, CSPA, and other conservation organizations, as well as staff from fisheries agencies, have recommended such a change in release pattern during the ongoing relicensing of YCWA’s hydropower project.

Some of this water released in the summer of 2020 was also sold out of the watershed, generally to entities south of the Delta.  In the fiscal year ending June 30, 2021, YCWA also made $12 million on water sales.2 The large flow increase at the end of August 2020 – likely a water sale – had no benefit for fish.  Its biggest effect on fish was that It drew down storage in New Bullards Bar Reservoir, which created a cascading effect in the very dry year 2021, when flows for all purposes were limited by lack of stored water.

2021

In a very dry year like 2021 that follows a dry year like 2020, river flows in spring and summer (Figure 3) become a major limiting factor.  First, there are no late-winter, early-spring flow pulses to attract adult spring-run salmon.  At a flow of 400 cfs at the bottom end of the lower Yuba River, there is insufficient flow to help adult spring-run salmon move upstream through many shallow riffles and through the Daguerre ladders.  Very low late-summer and fall low flows likewise hinder fall-run salmon.  Second, flows in late winter and early spring are too low to efficiently carry juvenile salmon downstream while avoiding the many predators on their way to the Bay and ocean.  Downstream of Daguerre Dam, over-summering juvenile salmon and steelhead must contend with low flows and associated stressful water temperatures.  Additionally, spawning at 400 cfs flow leads to redd scour if fall rainstorms occur: a late-October storm in 2021 brought Yuba flows up to 15,000 cfs and raised water levels nearly 10 feet (Figure 4).

Habitat

Feeding and cover habitat in the lower Yuba River are virtually nonexistent.  Predatory fish abound below Daguerre Dam.  Floodplain off-channel habitat and woody debris are severely lacking, especially during when winter-spring river flows are relatively low.  Many fall-run salmon spawn in poor spawning habitat below Daguerre.  To its credit, YCWA has contributed on a voluntary basis to several habitat improvement projects in the lower Yuba River, including the ongoing restoration at Hallwood.  However, it has vigorously resisted the establishment of regulatory requirements for additional projects.

Biological Opinion (BO)

Keeping the ladders clean is already a mandate.

  • Measures shall be taken by the Corps to minimize the effects of debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • When Yuba River flows exceed 4,200 cfs, the Corps shall provide notifications to NMFS on the status of debris accumulations and fish passage conditions at the Daguerre Point Dam fish ladders.
  • The Corps shall take action within 24 hours, or as soon as it is safe, to remediate fish passage conditions related to debris maintenance and removal at the Daguerre Point Dam fish ladders.
  • The Corps shall, by January 31 of each year, report to NMFS an update on previous year’s debris maintenance and removal actions, including details on amount of debris removed, the timing of removal and the conditions that triggered debris accumulation.
  • The Corps should consider predator removal at Daguerre Point Dam.

 Summary and Conclusions

Flow regimes and habitat improvements are necessary to save Yuba salmon, in addition to ladder repairs and cleaning at Daguerre Dam.  The Yuba River Accord, which has defined lower Yuba River flows since 2008, leaves too much flow in the summer by shorting flows that salmon and steelhead need in the spring.  The channel of the lower Yuba River also needs extensive physical improvement.

Figure 1. Yuba River salmon escapement 1953-2020.

Figure 2: Yuba River flow (cfs) March 1 – September 15, 2020 above (orange) and below (blue)
Daguerre Dam.

Figure 3. Yuba River flow (cfs) March 15 – September 15, 2021 above (orange) and below (blue) Daguerre Dam.

Figure 4. River flow (cfs) and stage (feet) in lower Yuba River below Daguerre Dam near Marysville in fall 2021.

  1. See YCWA financial report for 2021 and 2020 at https://www.yubawater.org/Archive.aspx?ADID=310, pdf p. 14. ↩
  2. Id. Compare wet year 2019, with likely no out of basin water sales, and water sale revenues of $531 thousand. ↩

Delta Pumps Throttled Back – December 2021

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A January 1 article in the Bee noted federal and state Delta pumping plants were “throttled back” in late December to protect the nearly extinct Delta smelt and other fish.  Exports had reached 9000 cfs from December 17-19, 2021, and then cut to 2000 cfs on December 20, despite high Delta inflows from the Sacramento River (Figure 1).  With the Delta Cross Channel closed in December and the False River Barrier in place, exports were drawing from the interior Delta via the Old and Middle River channels (Figure 2).  Most of that water was replaced via Georgianna Slough from the Sacramento River (7000 cfs) and San Joaquin River (1000 cfs).  The overall pattern from December 19 is shown in the map below.

Map of daily average flow conditions in the Delta, December 19, 2021.

Export cutbacks in December were prompted by the federal ESA biological opinions to protect Delta smelt, as well as winter-run and spring-run salmon from the Sacramento River.  Adult smelt move up into the interior Delta from the Bay with the first late-fall, early-winter runoff events.  Juvenile salmon move downstream to the Delta during these same early storm events and move into the interior Delta via Georgianna Slough.

Historically, exports were maxed-out near 11,000 cfs during December storm flows to refill San Luis Reservoir in the San Joaquin Valley after the irrigation season.  But such high exports resulted in heavy losses of smelt and salmon at the south Delta pumping plants (Figures 3 and 4), prompting the mandates in the biological opinions for export reductions.

San Luis Reservoir at the end of December 2021 was only at 30% of its 2 million acre-feet capacity; when the historical average for December has been 60%.  There is strong pressure to refill the reservoir.  On the other hand, the smelt and salmon are endangered species on the verge of extinction after several multi-year droughts in the past 15 years.  The smelt and salmon are in the Delta now, and need protection, whereas San Luis still has a chance of filling this winter under the allowed exports if 2022 continues normal or wet.  Because Federal and state laws mandate protecting the endangered fish and the biological opinions specify priority be given to the fish under these specific circumstances, export restrictions are the appropriate prescription.

Figure 1. Delta inflow from the Sacramento River at Freeport (FPT) and San Joaquin River at Mossdale (MSD) November-December 2021.

Figure 2. Internal Delta tidally-filtered flows in Old and Middle River en route to south Delta export pumps in December 2021.

Figure 3. Exports and salvage of winter-run salmon at export pumps from December 1, 2002 to February 1, 2003.

Figure 4. Exports and salvage of Delta smelt at export pumps from December 1, 2002 to February 1, 2003.

Fall Shasta Reservoir Pulse Flow Release – needed for winter run salmon in 2021

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Flow pulses released from Shasta Reservoir are badly needed in fall to match up with downstream tributary flow events.  Such flow pulses are needed to support the emigration of young winter-run salmon from the spawning reach near Redding.  The Redding reach receives no flow pulses because fall-precipitation inflows to Shasta are retained as storage in the reservoir, even in wet years.  In a December 2018 post, I described the lack of these badly needed and widely recommended fall flow pulses.

The problem occurred in fall 2021.  Because water year 2021 was a critically dry year with near record low end-of-September Shasta storage, there was understandably a common interest in retaining inflows to the reservoir.  But since water year 2022 began on October 1, there were major Valley-wide storm events, including significant inputs into Shasta Reservoir (Figure 1).

Despite these inflows, there were only reduced releases from Shasta this fall as irrigation demands and water transfers ebbed (Figure 2).  When the flow rates in the Redding reach dropped, water levels also fell 3 to 4 feet, reducing available rearing habitat as well as flows that might stimulate emigration.  The minimal Shasta-Keswick flow releases were high in turbidity (Figure 4), due to the storm-caused erosion in the severely storage-depleted reservoir.  The stage drop and higher turbidity also hurt the fall-run spawners during the peak of their fall spawning in the river near Redding.  None of Mother Nature’s late October flow gift to Shasta Reservoir was shared with beneficial uses immediately downstream.

Further downstream, the Sacramento River received its own gifts (Figure 4), but only from downstream (20-60 miles) tributary inputs.  The young winter-run salmon in the Redding spawning reach should have been given a boost to get them to where they could have benefitted from tributary inputs to the main lower river.  Higher flows in the mainstem provide quicker and safer trips to the Delta, Bay, and ocean.

It is apparent that many of the young salmon left the spawning reach earlier, during the higher September-October flows (Figure 5).  Many of these fish spent the early fall rearing in the upper 60 miles of river in less-than-optimal water temperatures, greater than 58ºF (Figure 6).  This is another reason a flow pulse to stimulate the emigration of those juvenile salmon that remained in the uppermost and coolest reach near Redding was important.

The reason that flow rate is important is that it speeds young salmon emigration.  How fast they move to the Bay-Delta greatly influences their survival (Figure 7).  In low-flow drought years like water year 2014, the fall emigration takes longer (Figure 8). Tag data also indicate flows near 10,000 cfs improve survival over lower fall flows (Figure 9).

So what should the prescription for the fall of 2021 have been?  First, Shasta Reservoir should not have been drawn down so far as to provide release of only warm muddy water.  Second, a pulse flow of at least 7000 cfs was needed coincident with the first lower river flow-pulse event with the reservoir release sometime between October 23 and November 1.  This would have added 2000 cfs to the already existing 5000 cfs reservoir releases (see Figure 2), and 2000 cfs to the already existing 8000 cfs Red Bluff flow (see Bend flow in Figure 4).  Third, a second flow pulse of about 5000 cfs Keswick release was needed on or about December 13 coincident with the second precipitation event and Red Bluff pulse.  This would have added 2000 cfs to the already existing 3000 cfs reservoir release.  Such one-day pulse releases should be short enough in duration to make them unlikely to stimulate substantial spawning of fall-run salmon in areas where the eggs would be subject to stranding.

In conclusion, the two days with an added release of 2000 cfs to create two separate pulse flows would have amounted to 8000 acre-feet of Shasta or Whiskeytown/Keswick storage.  Whiskeytown held 200,000 acre-feet of storage of cooler, lower turbidity Lewiston Reservoir/Trinity River water that could have provided the 8000 acre-feet needed for the Keswick flow pulses.  These two flow pulses would have provided significant benefit in improving the survival of emigrating young winter-run salmon in the Sacramento River near Redding.  A December pulse would also have created benefits for the fall-run spawn.

A one-day flow pulse with an added release from Keswick of 2000 cfs in early January would still provide benefits for outmigrating fall-run salmon.

Figure 1. Four significant precipitation events produced 5000 to 13,000 cfs daily inflow to Shasta Reservoir in fall 2021.

Figure 2. Flow and stage in the Sacramento River below Keswick Dam near Redding in fall 2021.

Figure 3. Water temperature and turbidity in the Sacramento River below Keswick Dam (KWK, RM 300) and above mouth of Clear Creek (CCR, RM 290) near Redding in fall 2021. Red line is 7 NTU turbidity above which eggs and embryo salmon in spawning redds are adversely affected.

Figure 4. Daily flow average (cfs) of Sacramento River below Keswick Dam (KWK, RM 300), at Bend Bridge (BND, RM 240), and at Wilkins Slough (WLK, RM 140) in fall 2021.

Figure 5. Passage rate of juvenile winter run salmon at Red Bluff screw traps and nearby Bend Bridge gage flow summer-fall 2021. Note increased catch rate during pulse flow events.

Figure 6. Water temperature (F) in the Sacramento River below Keswick Dam (KWK, RM 300) and at Red Bluff (RDB, RM 240) in fall 2021.

Figure 7. Estimated survival rate from Redding to Delta for juvenile salmon per the number of days spent upstream. Source: NMFS presentation.

Figure 8. Cumulative passage of winter-run at Red Bluff screw traps 2007-2013. Note longer period of passage in fall 2013 for Brood Year 2013. Source: USFWS Red Bluff.

Figure 9. Survival of juvenile salmon (acoustic-tagged wild and hatchery spring-run and fall-run salmon) as a function of flow in upper Sacramento River from Red Bluff (RM 240) to the Delta (RM 100). NMFS, Santa Cruz: “Nonlinear survival of imperiled fish informs managed flows in a highly modified river”. Cyril J. Michel $, Jeremy J. Notch, Flora Cordoleani, Arnold J. Ammann, Eric M. Danne. First published: 19 May 2021 doi.org/10.1002/ecs2.3498. Ecosphere / Volume 12, Issue 5 / e03498