Salmon and Sturgeon Compromised in Near-Record Water Year — June 2019

Lower Sacramento River water temperatures exceed water quality standards and lethal levels for newly hatched sturgeon.  In a prior post I discussed compromising water temperatures for sturgeon and salmon under low flows in dry years in the lower Sacramento River (see map, Figure 1).  But I did not expect the Bureau of Reclamation to violate its permit conditions for the Central Valley Project in this record setting wet year.  Flow in the lower river has dropped to 9000 cfs, and water temperature has risen above 20oC (68oF) at Wilkins Slough upstream of the mouth of the Feather River near Grimes (Figure 2; this is downstream of the area shown on the map).  In the week following June 10, Reclamation dropped reservoir release nearly 3000 cfs (Figure 3), leading to the rise in water temperatures.  The water temperature standard of 56oF was also exceeded in the upper river near Red Bluff (Figure 4).  The upper-river standard can be relaxed in drier years, but that would not apply in this near record wet year (Figures 5-8).

Figure 1. Map of the Sacramento River Basin (Princeton Ferry to Keswick Dam)

Figure 2. Water temperature and flow rate of Sacramento River at Wilkins Slough gage near Grimes. Water quality standard for lower river is 20oC (68oF).

Figure 3. Water release from Shasta/Keswick dams in June 2019.

Figure 4. Water temperature of upper Sacramento River near Red Bluff (RDB), Bend (BND), and Balls Ferry (BSF), May-June 2019. Red line is water quality standard for upper river.

Figure 5. Lake Shasta storage in 2019 compared to historical average, wettest, and driest years.

Figure 6. Lake Shasta water level and storage May-June 2019. Lake is at 98% capacity and 118% of average storage on June 15, 2019.

Figure 7. Snowpack in Central Valley December-July. Blue lines are 2019.

Figure 8. Mount Shasta on June 15, 2019.

Improved Yolo Bypass Fish Passage

Some salmon and sturgeon adults migrating up the Sacramento River this spring have had new help in passing upstream via the Yolo Bypass. With roughly half the Sacramento River’s flood waters flowing through the Yolo Bypass at the beginning of March, many salmon and sturgeon returning to the upper river to spawn likely chose entered the lower end of the Bypass at Rio Vista. These fish had a new notch opening to help them get over the Fremont Weir at the upper end of the 40-mile-long Bypass (Figure 1) and back into the Sacramento River to continue their journey.

The new $6-million gated-notch opening in the Fremont Weir is the first of several to be built into the two-mile-wide weir to help fish passage. The notches will allow an easier passage route over the weir, especially for large sturgeon. The notches are especially important in allowing an extended period for adult fish to finish their passage through the Bypass when Sacramento River water levels fall and the river flow ceases spilling over the weir into the Bypass. In the past, these conditions would have trapped any fish that remained in the Bypass. The notches will also help pass downstream-migrating juvenile salmon to enter the Yolo Bypass, where there is potential beneficial tidal and floodplain rearing habitat.

The first year of the new notch’s operation has not been without some glitches.1 Significant numbers of salmon and sturgeon have died and probably continue to die at the weir and in the Bypass.

But the new notch was not the underlying cause of this problem. The problem lies in flood control and reservoir storage management in the Central Valley. Drastic reductions in river flow and water levels led to fish stranding in the Bypass, the draining of the floodplain, and a rapid rise in water temperatures in the Bypass that stressed migrating fish.

  1. Shasta/Keswick reservoir releases were reduced sharply after two major flood releases this winter/spring (Figure 2).
  2. This led to abrupt ends to Fremont Weir overflows into the Yolo Bypass (Figure 3)
  3. The sharp drops in water levels in the river allowed only one week of extended Bypass inflows through the new notch (Figure 4).
  4. That led to a rapid draining of the Bypass (Figures 5 and 6).
  5. This in turn led to excessive water temperatures in the Bypass (Figure 7) for migrating and rearing salmon (>70oF).

For the new notches to be effective, an extended period of flow through the new notches will be needed to allow time for migrating and rearing salmon and sturgeon to safely exit the Yolo Bypass without being subjected to a sudden draining of warm water from the shallow margins of the Bypass. With a near record snowpack and filling reservoirs, there were sufficient river flows and reservoir storage this year to extend the duration of river flows into the Yolo Bypass.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 1. New Fremont Weir gated notch to help fish passage between Yolo Bypass and Sacramento River.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 2. Reservoir releases from Shasta/Keswick dams in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 3. Flow into Yolo Bypass from Sacramento River at Fremont Weir in winter-spring 2019.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 4. Water elevation of Sacramento River at Fremont Weir in winter-spring 2019. Top of weir is at 32-ft elevation. Bottom of new notch is at 25-ft elevation. Extended operation of new notch would have occurred from April 22-28.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 5. Flow in upper Yolo Bypass in winter-spring 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 6. Water elevation in mid Yolo Bypass during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.

Figure 7. Water temperature in mid Yolo Bypass at Lisbon Weir during Bypass draining in last week of April 2019.


Would WaterFix Tunnel Intakes be Protective of North Delta Fish? You Judge!

The Department of Water Resources’ consultant on in the WaterFix tunnels hearing testified:

“But for those Smelts that are occurring in that area, the North Delta diversions will be designed to fish agency protective standards”… “That opening, based on analyses, would prevent entrainment of Smelts that are greater than about 21 to 22 millimeters.”1

“In the EIR/EIS, the only significant and unavoidable impact that we found was for Striped Bass and American Shad. This is because of entrainment of early life stages at the North Delta diversions. These are species that spawn upstream of the North Delta diversions, in large part…..2

For American Shad, studies suggest that many American Shad were upstream of the Delta and, therefore, when they’re coming down into the Delta, they would be sufficiently large to be screened by the North Delta diversions.”

Delta Smelt

Delta smelt spawn in the north Delta in late winter and early spring. Their juveniles occur through summer. Their young would be highly susceptible to entrainment throughout spring (Figure 1).

White Sturgeon

Sturgeon, both green and white, spawn above the Delta in the lower Sacramento River in early spring. Their larvae and early juvenile stages reach the Delta in spring at a size highly vulnerable to entrainment (Figure 2).

American Shad

American shad spawn in the lower Sacramento River and tributaries in late spring and summer. Their larvae and early juveniles are prevalent in the north Delta in late spring and would be highly vulnerable to entrainment (Figure 3).

Striped Bass

Striped bass spawn predominantly in the lower Sacramento River in spring. Their larvae reach the north Delta in May and June, and would be highly vulnerable to entrainment (Figure 4).


Splittail spawn in the lower Sacramento River floodplain in spring. Their early juveniles reach the north Delta usually in May and would be highly vulnerable to entrainment (Figure 5).

Prickly Sculpin

Prickly sculpin, an abundant native Delta fish, spawn in the lower Sacramento River in late winter and their larvae are found in the north Delta in early spring and would be highly vulnerable to entrainment (Figure 6).

Sacramento Sucker

Sacramento sucker spawn in Valley rivers in spring. Their larvae and early juveniles are present in the north Delta throughout spring and would be highly vulnerable to entrainment (Figure 7).

Threadfin Shad

Non-native threadfin shad, the most abundant forage fish in the Delta, spawn from late spring into summer throughout the Delta and lower rivers. Their larvae and early juveniles are prevalent in the north Delta in late spring and early summer, and would be highly vulnerable to entrainment (Figure 8).

Summary and Conclusions

Larval and early juvenile lifestages of many Delta fishes would be highly vulnerable to entrainment through the screens of the proposed WaterFix north Delta intakes. Juvenile/fry of these and other species (salmon3) would be highly vulnerable to impingement and predation at the screens.

Figure 1. Length frequency of Delta smelt captured in the California Department Fish and Wildlife’s annual Delta-wide 20-mm Survey. For each sub-graph within this figure and each of the following figures, the x-axis shows the length in millimeters of captured fish, and y-axis shows the number of captured fish of each length. Note that most of the early spring post-spawn larvae and juveniles are of a size highly vulnerable to entrainment (<20 mm).

Figure 2. Length frequency of white sturgeon captured in the 20-mm Survey . Note larval sturgeon were captured soon after their spawning period in spring at a highly vulnerable size to entrainment. Many larvae of the main lower Sacramento River population of white sturgeon would pass the proposed WaterFix intakes.

Figure 3. Length frequency of American shad captured in the 20-mm Survey . Note that most of the shad would have to pass the proposed north Delta intakes in spring at a size highly vulnerable to entrainment (<20 mm).

Figure 4. Length frequency of striped bass captured in the 20-mm Survey . Note that most of these striped bass larvae would have had to pass the area of the proposed north Delta WaterFix intakes at a size would be highly vulnerable to entrainment (<20 mm).

Figure 5. Length frequency of splittail captured in the 20-mm Survey Note that many splittail spawn in the Sacramento Valley floodplain just upstream of the proposed north Delta WaterFix intakes, and that many of the juvenile splittail emigrating back to the Delta would pass the proposed WaterFix intakes at a size vulnerable to entrainment (<20 mm).

Figure 6. Length frequency of prickly sculpin captured in the 20-mm Survey . Note that the larvae of winter-spring spawning sculpin would be highly vulnerable to entrainment (<20 mm).

Figure 7. Length frequency of native Sacramento sucker captured in the 20-mm Survey . Note that the juveniles of late winter-early spring river spawning suckers return to the Delta at a size vulnerable to entrainment (<20 mm).

Figure 8. Length frequency of threadfin shad captured in the 20-mm Survey . Note the late spring-early summer spawning threadfin shad are highly vulnerable to entrainment (<20 mm).

  1. WaterFix hearing transcript, 2/23/18, Page 124, line 2:  Dr. Greenwood testimony at State Board WaterFix hearing.
  2. Id., Page 156, line 6.  Note that many shad and striped bass spawn their buoyant eggs in the area of the proposed intakes and immediately upstream, as well as in the lower Feather, Sacramento, and American rivers.  Nearly all the eggs and newly hatched larvae would pass the proposed CWF intakes.
  3. Much of the wild salmon production from the American and Feather rivers’ fall-run populations comes from fry (30-50 mm) leaving these rivers in winter.  Winter is the peak period of proposed north Delta diversions of the WaterFix project.  These fry would not be protected by the proposed WaterFix screens.

Sites Reservoir —
Potential Benefits for Fish,
Potential to Worsen Conditions for Fish
Working Presumption: Thumbs Down

The proposed Sites Reservoir1 would be a new off-stream storage reservoir covering 12,000 -14,000 surface acres with 1.8 million acre-ft of storage capacity on the west side of the Sacramento Valley (Figure 1). The project would capture and store unregulated Sacramento River winter-spring runoff and some water previously stored in Shasta Reservoir. The diversion capacity to the reservoir would be 5400-6500 cfs, supplied by two existing river diversions (up to 1800 cfs at Red Bluff; up to 2100 cfs at Hamilton City) and a new diversion near Colusa (proponents are evaluating alternative capacities of 1500 and 3000 cfs, in addition to the currently preferred capacity of 2000 cfs). The Sites Authority webpage estimates that it could have diverted over 1 Million acre-ft to storage in Sites in 2018 and 1.8 Million acre-ft to storage in 2017; these figures assume bypass flow requirements at the diversion points and at Freeport, and sufficient storage capacity in the reservoir. The Draft Environmental Impact Report/Environmental Impact Statement (DEIR/DEIS) for the Sites Reservoir Project estimates the average annual diversion to Sites storage at about 500,000 acre-ft; actual diversions would vary depending on hydrology and regulatory constraints.

As an off-stream storage reservoir, Sites would store water behind a dam that is not on a major waterway. Water diverted to the reservoir would be pumped into canals from the Sacramento River, and then pumped into the storage reservoir from small holding reservoirs on the canals. The two existing diversions that would fill Sites have modern fish screening facilities. As currently envisioned, a pump-back hydroelectric operation would allow partial recovery of pumping costs.

The Sites project has potential benefits for fish, but also the potential to worsen conditions for fish.

Potential Benefits for Fish

  1. Under current operations, existing irrigation diversions on the Sacramento River draw water primarily in spring and summer via several major canal systems on the west side of the Sacramento Valley. These diversions draw mainly on water that was previously stored in Shasta Reservoir and released to the Sacramento River in part to keep river water temperatures cool. Shasta Reservoir’s cold-water pool varies in volume depending on storage and other factors, and can run out if it is not managed carefully. If the cold-water pool is depleted at the end of the summer, this threatens the viability of winter-run salmon. Under current operations, spring and summer irrigation diversions from the Sacramento River also cut flow and raise water temperatures in the lower river, which harms salmon, steelhead and sturgeon. Water diverted to storage in Sites in the winter could substitute for some of the spring and summer irrigation deliveries that currently come from Shasta. A greater percentage of water released from Shasta in spring and summer could then flow all the way to the Delta. More water could also be retained in Shasta Reservoir to protect the Shasta cold-water pool into the fall and as carryover for the following year.
  2. If more water were delivered to the Delta from Shasta Reservoir in the spring and summer, less water would theoretically be needed from Folsom and Oroville reservoirs to meet Delta water quality, outflow and other requirements. This could allow more targeted releases of water into the lower American and lower Feather rivers to protect fish in those waters. It could also allow better maintenance of cold-water pools and greater carryover storage in Folsom and Oroville, also very important for the respective fisheries downstream.
  3. Water stored in Sites could be delivered directly to the Delta via the Colusa Basin Drain (CBD) system and Yolo Bypass, reducing outflow demands from other Valley reservoirs. Water delivered directly to the Delta from Sites would be of higher potential productivity and could stimulate winter-spring Bay-Delta plankton blooms that would benefit Delta native fishes.

Potential to Worsen Conditions for Fish

  1. The proposal includes a new point of diversion on the Sacramento River with a capacity to divert 2000 cfs. This would give the project higher diversion capacity and the capability of diverting tributary runoff that would otherwise be unavailable to the two upper river diversions that now enters the Delta. This diversion would also affect flows and water temperatures in the lower Sacramento River, and subject migrating juvenile salmon, sturgeon, and steelhead to a third large screening facility. The new point of diversion would be particularly problematic if it diverted water outside the peak runoff season (late fall through spring).
  2. The new diversion and the reoperation of canal intakes at Red Bluff and Hamilton City to divert water in winter would compete for water with Delta diversions and would affect Delta outflow to the Bay.
  3. Water deliveries and hydropower releases from Sites Reservoir to the lower river at the new diversion site could affect water quality in the lower Sacramento River.
  4. With available winter off-stream storage, the existing diversions at Red Bluff and Hamilton City would be capable of diverting uncontrolled flows from tributaries that have otherwise remained relatively untouched down to the Delta.
  5. The greater diversion capacity may increase demands on Shasta storage and will increase diversion of uncontrolled tributary flows, further compromising fishes in the Sacramento River and the Bay-Delta.
  6. A small but potentially significant amount of water supply stored in Sites Reservoir would be lost to evaporation and groundwater seepage.

Above all, there is too much unknown to evaluate how Sites would affect fish.

As is the case for most proposed water supply projects, the project description in the draft DEIR/DEIS for Sites describes several potential configurations of project infrastructure and a description of proposed constraints. The DEIR/DEIS does not evaluate different constraints, such as different bypass flow requirements past each point of diversion; the DEIR/DEIS only evaluates one value for each point. In spite of numerous requests that the DEIR/DEIS evaluate project diversions with more stringent Delta flow and water quality requirements than the existing inadequate ones, the DEIR/DEIS only evaluates project yield with existing Delta constraints.

The benefit side is even more vague and conceptual. The entire construct of hypothetical Sites benefits would in fact require a new type of proscriptive rules and enforcement mechanisms that would be unprecedented for California water projects. There is simply no clue in any of the Sites literature what those rules would be or even could be.

The project description places no numbers on how much water stored in Sites the project’s operators would dedicate to actions designed to benefit fish. The project description defines no decision-making process for dedicating water to fish, other than to say that on an overarching basis fish agencies will decide. The project description defines no way in which project operators will apportion water for fish against water for water supply. For all the offsets that seem to comprise the lion’s share of fish benefits, the project description does not say how water from Sites will generate improvements in operation of state or federal reservoirs, or whether it will be Sites operators or state and federal operators who make the calls.

Then there is the question of whether there would be any offsets at all. There is no assurance that there will be any decreases at all in water use from Shasta or from other state and federal reservoirs. Water freed up by using Sites to meet Sacramento Valley water supply could simply allow Sac Valley water users to irrigate more land or sell more water for export at the Delta pumps. The DEIR/DEIS proposes no mechanism of enforcing offsets: who would regulate the project’s use of water, who would manage the interaction between Sites water and water from Shasta, Oroville, Folsom and perhaps Trinity reservoirs, and how and against whom any requirements would be enforced.

There are other problems. A shift to winter-spring diversions and use of canal systems would potentially change groundwater recharge and use patterns in the Sacramento Valley. The project would compete for water available to the proposed WaterFix Twin Tunnels project in the Delta. Sites and WaterFix have their “sights” on the heretofore untouched tributary inflows that are also protected by Delta export OMR limits so the flows reach the Bay. There will be a big fight over this uncontrolled water that now makes up a significant portion of the Bay’s freshwater input in drier years. Both projects have claimed future benefits of the same pot of water.


There are potential benefits from Sites project’s main features to Central Valley fishes, including salmon, steelhead, sturgeon, smelt, and striped bass. Most of the benefits would result from switching the diversion time period of the two existing upper river diversions and Shasta reservoir releases to these diversions. The added new diversion and increase in winter diversions will at important times reduce Sacramento River flow and Bay-Delta inflow and outflow, harming fish in certain but sometimes hard to quantify amounts.

Past water developments in the Central Valley have overwhelmingly made conditions for fish worse. The Sites project proponents claim that their project will be different. These proponents have not done themselves, the public, or public policy any favors by relying on generalities and politics as the centerpieces of their efforts to advance their project. At this time, there are too many unknowns to meaningfully evaluate the possibility that benefits might outweigh the harm and justify the costs. In the meantime, it is a reasonable working presumption that the Sites project will worsen conditions for fish as well.

Figure 1. Proposed Sites Reservoir and associated infrastructure on west side of the Sacramento Valley.

Sacramento River Salmon and Water Right Order 90-5

Operation of the Central Valley Project’s Shasta-Trinity Division is governed in part by the State Water Board’s Water Right Order (WRO) 90-5. Issued in 1990, this Order prescribes reasonable protection for Sacramento River salmon, steelhead, and sturgeon even under today’s conditions. The problem in recent years is that “requirements” are not being met by the Bureau of Reclamation.

Even in the past three non-drought years, including record wet 2017 and this year’s normal classification, Reclamation has not met requirements. This has caused significant impacts to salmon, steelhead, and sturgeon, which I have documented in prior posts. In the past three years, Reclamation has used its poor performance during the 2013-2015 drought and global warming as excuses to prioritize preserving water storage in Lake Shasta over meeting water temperature requirements for the Sacramento River under WRO 90-5. But while Reclamation has argued it must preserve Shasta Reservoir’s cold-water pool, Reclamation has maintained full deliveries to its Sacramento Valley contractors.

The State Board has a whole website dealing with the issue and problems dealing with Reclamation on the issue: ( ).

In a March 14, 2018 letter to Reclamation, the State Board’s Deputy Director for Water Rights wrote to Reclamation on compliance with WRO 90-5,1 stating:

As you know, Order 90-5 requires Reclamation to maintain a daily average temperature (DAT) of 56 degrees Fahrenheit (F) in the Sacramento River at Red Bluff Diversion Dam during times when higher temperatures will be detrimental to fish, unless factors beyond Reclamation’s reasonable control prevent it from maintaining such temperatures. If Reclamation is unable to meet the temperature requirement at Red Bluff Diversion Dam throughout the temperature control season, Reclamation must develop an operations plan for approval by the Chief of the State Water Board’s Division of Water Rights (Deputy Director). The plan, which is required to be developed in consultation with the California Department of Fish and Wildlife, U.S. Fish and Wildlife Service, National Marine Fisheries Service (NMFS) (collectively fisheries agencies), and the U.S. Western Area Power Administration (WAPA), must designate a location upstream of Red Bluff Diversion Dam where the temperature requirement will be met. Order 90-5 includes specific monitoring and reporting requirements in addition to a general requirement (Condition 3) that Reclamation conduct such monitoring and reporting as is required by the Deputy Director to ensure compliance with the terms and conditions of Order 90-5.

Given potential concerns with temperature management this year and the degraded status of the winter-run Chinook salmon population following the drought, Reclamation should be aware that operational changes may be needed beyond those proposed by Reclamation in their TMP to minimize impacts to winter-run Chinook salmon and avoid redirected impacts to other native species. Reclamation should acknowledge those needs in its TMP and provide for a process for continually evaluating conditions and operations to ensure that needed adjustments to temperature control operations are considered in a timely manner.

On April 2, 2018, Reclamation responded2:

This response not only states that Reclamation will not meet WRO 90-5 water temperature requirements at Red Bluff (river mile 243), but also that it will not meet these requirements at Balls Ferry (river mile 276), 30 miles upstream and half way to Keswick Dam. In fact, Reclamation to date has blatantly kept the promise of not meeting requirements (Figure 1), despite the fact that Shasta Reservoir is full of cold water. It is not even May yet!

The Coleman Fish Hatchery just stocked 4 million fall-run salmon hatchery smolts at Battle Creek upstream of Red Bluff, with another 2 million soon to follow.3 The recently released hatchery fish (and their wild counterparts) are being subjected to highly stressful conditions in their 200-mile journey to San Francisco Bay (Figures 2 and 3).

There is plenty of cold water in Shasta Reservoir (Figures 4 and 5) to meet the flow and temperature needs of salmon in the lower Sacramento River through the summer, as required by WRO 90-5. It would take a total release of about 6000 cfs from Shasta to meet WRO 90-5 requirements at this time just at Balls Ferry. Reclamation increased releases in the past several days to 5300 cfs to meet water contractor demands. The problem remains that this water is not reaching the lower river, where water temperatures now hit 70°F and exceed the WRO 90-5 limits of 68°F (Figure 3). It will take an added 2000-3000 cfs at Wilkins Slough to keep the lower river below its 68°F limit This added release would represent about one foot of Shasta Reservoir water-surface elevation per week (Figure 4).

Sacramento Valley contractors have been given a 100% water allocation. South of Delta San Joaquin CVP contractors have been allocated only 40%. Reclamation is fully capable of meeting WRO 90-5 requirements, as it did historically. It is up to the State Board to enforce the CVP permit requirements. Given the state of the salmon populations, there should be no compromise on the permit requirements.

Figure 1. Reclamation report on Sacramento River temperatures through 24 April, 2018. Source:

Figure 2. Water temperature at Red Bluff (RM 243), April 2018. Red line is limit requirement in WRO 90-5. Source: cdec.

Figure 3. Water temperature at Wilkins Slough (RM 118) April 2018. WRO 90-5 limit is 68°F. Water temperatures in excess of 65°F are highly stressful to juvenile salmon. Source: cdec.

Figure 4. Shasta storage characterization for water at the dam’s temperature control device (TCD), March 23 – April 22, 2018. Source: (See link for updates.)

Figure 5. Shasta Reservoir storage as of April 24, 2018.

  3. Note that Coleman Fish Hatchery on Battle Creek normally stocks 12 million fall-run smolts, but brood year 2014 salmon did not provide sufficient spawners (eggs for hatchery), and the hatchery thus produced only 6 million smolts in 2017. Hopefully, the 2 million smolts that have not yet been released will be trucked to the Bay.