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.

WaterFix NMFS Biological Opinion Conclusions on Salmon in the Delta

The National Marine Fisheries Service’s biological opinion (NMFS BO) on the proposed “California WaterFix” (Delta Twin-Tunnels Project) concludes there will be no significant effect on protected salmon, steelhead, and sturgeon in the Central Valley. In this post, I address the conclusions in the NMFS BO on the potential effects of WaterFix on salmon and steelhead in the Delta. This is one in a series of posts on the WaterFix. Within that series, it is the second post of the series on the NMFS BO.

The NMFS BO concludes that WaterFix operations would have significant adverse effects on salmon, steelhead, and sturgeon and their critical habitat in the Central Valley from changes brought about by the WaterFix Twin Tunnels Project. In contrast, the NMFS BO also states that the WaterFix is not likely to jeopardize the species or adversely modify their critical habitat. How such contradictory conclusions are possible, especially for the rather demonstrable Delta effects, is simply beyond reason. Previous drafts of the BO had not made that jump. There is no amount of adaptive management within reason, especially given past poor performance in operating the water projects and managing effects on fish, that can alleviate the potential great risks to Central Valley fishes from the adding the WaterFix Twin Tunnels to the state and federal water projects.

The “new” NMFS BO focuses on changes in flow patterns in the Delta below the three proposed diversion points in the North Delta. The diversions of up to 9,000 cubic feet per second (cfs) would change flow and flow splits downstream in Steamboat, Sutter, and Georgianna sloughs and the Delta Cross Channel, as well as in the main Sacramento River channel. As a consequence, freshwater flows entering the interior Delta from the north Delta would also change, as would Delta outflow to the Bay to the west. Young salmon, steelhead, and sturgeon from the Sacramento River and San Joaquin River basins would be affected by these changes upon entering the Delta on their way to the Bay and ocean.

The NMFS BO concludes that the up-to-9000 cfs diversion of the WaterFix would reduce channel velocities below the intakes in the north Delta. “Under the PA [Proposed Alternative] water velocities in the north Delta would be lower…. This would increase migratory travel time and potentially increase the risk of predation for juvenile salmonids.” (p. 602) In the past, based on my own assessments, survival of hatchery and wild salmon and steelhead to the Bay may have been reduced by 50-to-90 percent based on differential survival of marked hatchery smolts released above and below the Delta under differing flow regimes. The NMFS effects assessment is based on survival of radio tagged, large, late-fall hatchery smolts during the winter; this indicates just a small differential in survival. The real effect is likely somewhere in between and highly variable depending on a wide range of circumstances. No doubt a serious concern remains for the future of the various listed species and success potential of future commercial and recreational fisheries.

The greatest risks are to pre-smolt winter-run salmon in the fall season and to juvenile spring-run and fall-run salmon and steelhead in the spring.

“In the South Delta, median velocities generally increase under the PA…. The positive change in velocity would decrease migratory travel time and reduce predation risk for juvenile salmonids.” (p. 602) The conclusion is that exports from the south Delta will decline from November through June because of WaterFix. That simply is not true, because south Delta exports are already constrained during those months. WaterFix would not change those overall constraints; it would only add to the overall diversion capacity. Export restrictions based on net flows will remain the same; thus there will be no changes in rules governing the south Delta exports. Furthermore, the 9,000 cfs taken by WaterFix will reduce Sacramento River freshwater inflow into the central and south Delta, increasing any effects of south Delta diversions on the interior Delta’s hydrodynamics. The relative effects on San Joaquin River Delta inflows will remain the same or even increase.

“In the Central Delta, there is little difference in magnitude of channel velocities between the NAA [No Action Alternative] and PA.” (p. 602) While it is true there is little difference for channel velocities in this highly tidally driven region, it is not true for freshwater inflow, salinity gradients, and water temperatures, or for relative flow signature differences for the San Joaquin and Sacramento Rivers within the central Delta. The loss of Sacramento River freshwater inflow into the central Delta via Georgianna Slough and the Delta Cross Channel (when open) is significant. Tidal inflows from the west Delta into the central and south Delta in the San Joaquin and False River channels will increase, potentially reducing survival of San Joaquin salmon and steelhead. Sacramento River salmon and steelhead survival, already reduced by lower flows below the tunnel intakes, would be further reduced by lower survival of fish that passed through Georgianna Slough or the Delta Cross Channel, or through cross-Delta movement through Three-Mile Slough.

“In the North Delta, reverse flows would increase in most water years and months…. In the North Delta, the PA had a higher proportion of each day with negative velocities (reverse flow) particularly in Steamboat Slough and Sacramento River downstream of Georgiana Slough”. (p. 602) The loss of freshwater inflow to the WaterFix Twin-Tunnel diversion would decrease the extent in location and timing of unidirectional flow in the tidal Sacramento River (Figure 1). Diversions during times when Freeport flows were in the range of 15,000-35,000 cfs would change the river from virtually non-tidal to tidal.

Figure 1. Example period: flows at Freeport March-July 2017. Red arrow denotes 9,000 cfs WaterFix tunnel diversions above the 35,000 cfs inflow. WaterFix diversions would be minimal below 15,000 cfs inflow. Green line denotes point at which flow would become tidally influenced with WaterFix as seen after June 15 when hourly flows varied from 5000 to 15,000 cfs during a tidal cycle. Note: for location of gages, see Figure 4 map.

The effect downstream at the flow splits of the Sacramento River at Georgianna Slough and Steamboat Slough is even more pronounced (Figures 2 and 3). In the Sacramento River below the Georgianna Slough split, flood tides would turn negative earlier in the season with upstream WaterFix diversions (Figure 2). Likewise, Steamboat Slough flood tides would turn negative with WaterFix when Freeport flows fall to 25,000 cfs. In 2017, that would have meant negative flows nearly a month earlier with WaterFix (Figure 3). Not only do WaterFix diversions reduce flows in the northern Delta channels, they would turn migration period conditions poorer (reverse flows and higher water temperatures) nearly a month earlier than under present conditions. “In order to more thoroughly evaluate the impact of reverse flows on migrating salmon, NMFS undertook an additional analysis. The likelihood of juvenile fish entering migratory routes with reduced survival increases with the daily probability of flow reversal, or with increases in the proportion of each day with flow reversals. The probability of juvenile Chinook salmon getting entrained into migratory routes of lower survival like Georgiana Slough and the Delta Cross Channel is highest during reverse-flow flood tides (Perry et al. 2015). In addition, the proportion of fish entrained into Georgiana Slough on a daily basis increases with the proportion of a day that the Sacramento River downstream of Georgiana Slough flows in reverse (Perry et al. 2010). Consequently, diverting water from the Sacramento River could increase the frequency and duration of reverse-flow conditions, thereby increasing travel time as well as the proportion of fish entrained into the interior Delta where survival probabilities are lower than in the Sacramento River (Perry et al., 2010 and 2015)…. In the north Delta, increase in flow reversals downstream of Georgiana Slough are of concern for migrating salmonids…. Increases in flow reversals would likely reduce the survival probability of outmigrating smolts by moving them back upstream, increasing their exposure to junctions that lead to migratory routes of lower survival, such as in Georgiana Slough.” (p. 603)

Figure 2. Example period: flows at Georgianna Slough flow split March-July 2017. Red line notes when condition in Sacramento River below Georgianna Sough at which flood tides reverse river flow – when Freeport flow is below 25,000 cfs. In contrast, flows in Georgianna Slough would not become negative.

Figure 3. Example period: flow in Steamboat Slough below split March-July 2017. Flow in Steamboat Slough becomes negative when Freeport Sacramento River flow falls below 25,000 cfs. Under WaterFix, Steamboat Slough flows could become negative at Freeport flows below 34,000 cfs.

“The proposed NDD bypass rules include a commitment to an operational constraint that the amount of flow withdrawn at the NDD cannot exacerbate reverse flows (i.e., increase the frequency, magnitude, or duration of negative velocities) at the Georgiana Slough junction from December through June beyond what would occur in NAA. However, the BA does not describe the methods or the modeling that would show how this would be achieved. Specifically, the BA does not describe: 1. The extent that the proposed NDD bypass rules may affect the frequency, magnitude and duration of reverse flows in the lower Sacramento River; 2. The description of how real-time monitoring could be implemented to meet the criteria of not increasing reverse flows; 3. The modeling simulations that would show how this criteria is being met and therefore provide reasonably accurate bypass flow levels.” (p. 603).

In the example shown in Figures 2 and 3 above, WaterFix diversions would exacerbate reverse flows unless no diversion was allowed below a 35,000 cfs Freeport flow, a commitment not made in WaterFix proposal.

This is a major flaw in the NMFS BO assessment. Even NMFS acknowledges this fact: “The probability of a flow reversal in the Sacramento River downstream of Georgiana Slough occurring at some time during a 24-hour period is one hundred percent when Sacramento River flows at Freeport are less than 13,000 cfs (Figure 2-118 top panel). Likewise, when flows are greater than 23,000 cfs, flow reversals are not expected to occur at the Georgiana Slough junction.” (p. 606) A flow of 23,000 cfs would occur below the tunnel diversions when Freeport flow is 32,000 cfs.

“The following assumptions were used: 1) the NDD bypass rules are applied based on mean daily Sacramento River discharge at Freeport, and 2) water is diverted at a constant rate over an entire day such that the bypass flow is constant over the day. The analysis adheres to a strict interpretation of the NDD bypass rules and does not include flow variations at sub-daily timescales.” (p. 606) Note that diverting 9000 cfs on a flood tide with Freeport flow at 30,000 cfs would cause a flow reversal in Steamboat Slough and in the Sacramento River below the split at Georgiana Slough (Figures 2 and 3).

“October-November operations can greatly increase the probability of reverse flow; for example, when flows at Freeport are between 20,000 to 25,000 cfs there would be ~100% increase in flow reversals under the PA (Figure 2-124)… .(p. 606) The months with the largest increases in travel time for both the PA and L1 occur during the off-peak Chinook salmon migratory months of October, November, and June. During the peak Chinook salmon migratory window of December through April, February and March have the largest increases in travel time under the PA.” (p. 615) Such flows may occur in October-November from early storms, and a large influx of winter-run salmon pre-smolts would be expected to enter the north Delta under these circumstances. NMFS expects that restrictions on diversions during early pulses and changes to Delta Cross Channel operations would protect winter-run.

“However, if flow in November becomes sufficient through storm runoff events to trigger winter-run emigration towards the Delta, a pulse protection will apply that will limit diversions to low level pumping for a certain amount of days or until fish presence is not detected based on real-time management criteria. Without this protection, early emigrating winter-run would be subject to some of the more extreme diversion levels allowed, probability of reverse flows would increase, and winter-run Chinook salmon would face greater risk of entrainment into interior Delta and overall lowered survival.” (p. 625) WaterFix does not propose to protect all fall pulses, nor winter flow pulses. There would be no restrictions on south Delta diversions, which would be 11,400 cfs under these conditions. The WaterFix would thus exacerbate the existing level of impacts, which are quite serious in the fall of wetter years.

NMFS also notes potential serious consequence to spring-run and fall-run salmon: “May has a unique set of NDD bypass rules that is slightly less protective than the diversion rules in December through April because Level 2 or 3 could be enacted if bypass flow criteria have been met. 5% to 13% of spring run Chinook salmon smolts are expected to be in the Delta during this month (Table 2-171). They may experience slightly longer travel times than smolts traveling during earlier months given the same inflow at Freeport. This would be due to lower velocities that may result from less restrictive diversions as defined by the NDD bypass rules.” (p. 631) Most Sacramento Valley hatchery fall-run smolts are released into rivers or the Delta in late April and early May – they too are vulnerable to WaterFix-induced reverse flows in the Delta.

  • NMFS eventually concludes that reductions in survival in the north Delta are balanced by increased survival in the south Delta: “Interpretation of these analyses must also consider that small changes in absolute survival could translate to a large effect to a population, especially in years when overall Delta survival is low. The 2-7% increase in Delta survival that would occur if entrainment into the interior Delta were eliminated (Perry et al. 2012) resulted in a 10-35% relative change in survival for five of the six release groups in that study.” (p. 663) First, there is no basis to the assessment findings that Delta exports, already restricted in the December to June period, would be further restricted with WaterFix. Second, the assessment of the south Delta effects did not take into account the added stress of reduced inflow of Sacramento River water into the interior Delta because of WaterFix. NMFS qualifies its own conclusion: “The extent to which management actions such as reduced negative OMR reverse flows, ratio of San Joaquin River inflow to exports, and ratio of exports to Delta inflow affect through-Delta survival is uncertain.” “Uncertainty in the relationships between south Delta hydrodynamics and through-Delta survival may be caused by the concurrent and confounding influence of correlated variables, overall low survival, and low power to detect differences.” (p. 687)

NMFS concludes no adverse effects: “After reviewing and analyzing the current status of the listed species and critical habitat, the environmental baseline within the action area, the effects of the proposed action, any effects of interrelated and interdependent activities, and cumulative effects, it is NMFS’ biological opinion that the proposed action is not likely to jeopardize the continued existence of Sacramento River winter-run Chinook salmon, CV spring-run Chinook salmon, CCV steelhead, Southern DPS of North American green sturgeon or destroy or adversely modify designated critical habitat for these listed species.” (p. 1111) The basis for these conclusions appears to be balancing of north Delta negative effects with south Delta benefits, as well as the adaptive management capability offered by WaterFix.

In summary, then:

  • NMFS has understated the potential effect of the WaterFix on salmon migration survival through the Delta and the potential to minimize tidal effects based on WaterFix’s proposed rules and commitments. “(I)n the May 2016 Revised PA, DWR committed to Delta habitat restoration at a level that RMA Bay-Delta modeling indicates could prevent exacerbation of reverse flows in the north Delta due to the PA by changing the tidal prism in the Delta (see Section NDD Bypass Flows and Smolt Entrainment Analysis).” (p. 623)
  • NMFS has overestimated the potential benefits of changes in the south Delta.
  • Based on past experience, NMFS’s assumption that real-time management of Delta operations by DWR and Reclamation (USBR) can overcome potentially damaging conditions is unfounded.

Figure 4. Map of key north Delta flow measurement locations.
“A” is Sacramento River at Freeport.
“B” is Sutter-Steamboat Slough.
“C” is Sacramento River below outlet to Georgiana Slough.
“D” is Georgianna Slough.