Author Archives: Tom Cannon

The Twin-Tunnels Project: Effects on Upper Sacramento River Salmon Habitat

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The NOAA 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 the upper Sacramento River salmon, steelhead, and sturgeon in the upper 60 miles of river between Keswick Dam in Redding downstream to Red Bluff.

This is one in a series of posts on the WaterFix. Within that series, it is the first post of the series on the NMFS BO. In this series within a series, I focus on what NMFS determined from its review and the veracity of its conclusions about effects. I pose and respond to the following questions: Will the WaterFix change reservoir storage and release patterns, water temperatures and flow patterns. Will the WaterFix change the rates of survival of Sacramento River salmon, steelhead, and sturgeon? Will changes affect survival and contributions to sport and commercial fisheries?

The Sacramento River between Keswick Dam and Red Bluff is spawning and early juvenile rearing habitat for all four races of salmon, including the listed winter-run and spring-run, and for green sturgeon. All of these species depend on cold-water flows from Shasta reservoir. Winter-run salmon survival was poor in the reach in 2014 and 2015,1 as well as in past droughts when the cold-water supply ran out.

Will conditions improve or get worse with the WaterFix? The NMFS assessment concludes that conditions will worsen with WaterFix only in critically dry years like 2014 and 2015, and possibly in below normal water years. Because such poor survival years are the cause of historic population crashes, it is hard to understand how NMFS concludes that making such years worse is not a worry, or even “jeopardy.”

The NMFS analyses rely on model predictions that NMFS admits are crude, with monthly inputs and outputs. Rules that govern the models are subject to change. In the end, NMFS simply states that adaptive management will protect the salmon in all but critically dry years. The BO makes no attempt to prescribe new rules that would be more protective.

The real concerns about WaterFix are: (1) whether the new Delta export capacity will place new demands on Shasta storage within and among years; (2) whether seasonal flows and water temperatures will change; and (3) whether changes in storage, flows and temperatures will affect salmon, steelhead, and sturgeon.

I really did not get a sense from the BO (or from the EIR/EIS or the Biological Assessment) how WaterFix would be operated. With the extra diversion capacity in the Delta (under the prescribed WaterFix rules for diversions in the Delta), would the Bureau of Reclamation (BOR) or the Department of Water Resources (DWR) release more water from storage in Shasta or Oroville or Folsom to achieve greater south-of-Delta exports under some circumstances? How would they know how much “new” water could be taken, and whether that water would compete with other demands, even from the proposed Sites Reservoir. If they miscalculated the extent of the Shasta cold-water pool in 2014 and 2015, what measures would they take to protect the cold-water pool with the new WaterFix capacity? Would they drain more of Shasta than under present demands? There are lots of questions not posed and not answered.

Excerpts from the NMFS BO, Section 2.5.1.2.

“This preliminary analysis indicated that there is the potential for changes as a result of the PA (WaterFix) in reservoir operations, in stream flows, and water temperatures in the Sacramento River and American River. Therefore, this section assesses potential effects of those changes on listed aquatic species and critical habitat in the American River and Sacramento River upstream of the Delta.” Comment: An example plot from the analyses is shown below. NMFS implies that these are model anomalies and not real. Years 2012 and 2016 were below normal years and represented by the Figure. What did the models assume to create these significant effects? Would WaterFix take more or less water?

PA is WaterFix; NAA is No Action Alternative.

“Existing Biological Opinions on the Long-Term Operations of the CVP and SWP, NMFS and Reclamation are considering modifications to the RPA relating to Shasta Reservoir operations”. Comment: Like many aspects of WaterFix, other regulatory processes could change the rules. Some changes yet to occur could significantly change the amount of water available for WaterFix.

“Under dual conveyance of the Proposed Action (PA), reservoir water releases and, therefore, CWP [Shasta cold-water-pool] availability may be changed from existing conditions for optimization of exports in the north and south Delta. If CWP storage and management is improved or degraded it could have effects on the viability of listed salmonids.” Comment: Ominous uncertainty for a biological opinion.

“ [T]he extent of habitat cold enough for spawning and early life stage survival changes every year in relation to where in the Sacramento River the upper temperature threshold of 56°F (13.3°C) can be maintained from May to October.” Comment: This is one of the rules that has so easily been changed without adequate review or process. It is one rule that can change to benefit WaterFix water supply.

“Under dual conveyance of the Proposed Action (PA), reservoir water releases and, therefore, CWP availability may be changed from existing conditions for optimization of exports in the north and south Delta. If CWP storage and management is improved or degraded it could have effects on the viability of listed salmonids.” Comment: Incredible uncertainty. There are minimal constraints built into the WaterFix. The conflict between fish and water exports will be more extreme than ever before.

“Recently, a succession of dry years with low precipitation highlighted how difficult the upper river spawning area is to manage for successful spawning and embryo incubation. High mortality (greater than 95%) in the youngest life-stages (eggs, yolk-sac fry) resulted when temperature compliance points were not maintained under 56°F (13.3°C) for the spawning and embryo incubation season (Swart 2016).” Comment: The risks are obvious. Difficulty cannot be an excuse for poor management.

“Green sturgeon have different temperature requirements than salmonids in the upper Sacramento River. The majority of green sturgeon spawn above Red Bluff Diversion Dam. Suitable spawning temperatures must remain below 63°F (17.5°C) to reduce sub-lethal and lethal effects. Temperatures in the range of 57° to 62°F (14 to 17°C) appear to be optimal for embryonic development (Van Eenennaam et al. 2005).” Comment: The assessment on green sturgeon is almost non-existent. The optimal conditions are already exceeded upstream and downstream of Red Bluff in the spring season when sturgeon spawn.

Salmon Conclusions from the NMFS BO

“A high proportion of developing embryos are expected to perish from exposure to lethal water temperatures in critically dry water years.” (p. 279) Comment: This can be reasonably avoided and should not be “expected” or accepted.

“Mean annual temperature-dependent survival would decrease under the PA by 1% in wet years and 3% in below normal years.” (p. 281) Comment: Such predictions from the models are meaningless. Risks to salmon remain serious and are readily avoidable with effective controls.

“All differences in mean annual temperature-dependent survival are likely within the margin of error of the model and are not significant.” (p. 281) Comment: This is true only for the crude model predictions, but not for real risks from WaterFix.

“The SWFSC model results suggest that winter-run Chinook salmon egg survival will largely be the same under the NAA and PA operations.” (p. 282) Comment: Again, this applies to crude model predictions, not to real risks, which are significant given past management, operational rules, and regulatory constraints.

“Overall, the certainty of the three biological tools’ respective ability to accurately estimate thermal impacts to eggs and alevins in the Sacramento River under the PA is low because all three models utilize daily (thresholds analysis and the SWFSC’ egg/alevin mortality model) or weekly (SALMOD) water temperatures downscaled from the same modeled monthly values. Eggs and alevins developing in the Sacramento River spawning gravels experience a thermal regime that varies between day and night and from one day to the next. The downscaled water temperature modeling utilized in all the biological models does not capture that level of thermal variation. Nevertheless, the biological models are useful qualitative indicators of potential thermal impacts under the PA.” (p. 282) Comment: This says it all. The potential risks to salmon and sturgeon from WaterFix are real, unlike the model predictions.

“Adverse thermal effects on these life stages resulting from changes to upstream operations as a result of the PA are not expected. However, for purposes of the analysis in Section 2.7 Integration and Synthesis, the combined effect of PA implementation when added to the environmental baseline and modeled climate change impacts is expected to result in substantial water temperature-related mortality in critically dry years.” (p. 282) Comment: Again, the worst problems for salmon and sturgeon for decades have been in the critical dry years in drought sequences. WaterFix will do little to alleviate the problem, and will likely make it worse.

“There are extensive real-time operations management processes currently in place for CVP/SWP operations that affect water temperatures upstream of the Delta (see BA Section 3.1.5.1 Ongoing Processes to support Real-Time Decision Making), those processes have minimized such impacts in the past (Swart 2016), and the PA does not propose changing the existing real-time operational processes. Therefore, NMFS concludes that the real-time operations management process would minimize adverse effects indicated in the modeling for the PA to a similar extent as the real-time operations process has minimized such impacts in the past.” (p. 282) Comment: Incredible statement. Past poor real-time management has led to the near extinction of winter-run. Even the extremes of 2014 and 2015 were avoidable if management had been effective. Yet WaterFix proposes no changes in management.

“NMFS expects that climate conditions will follow a trajectory of higher temperatures beyond 2030. Not only are annual air temperatures expected to continue to increase throughout the 21st century, but the rate of increase is projected to increase with time. That is, in the early part of the 21st century, the amount of warming in the Sacramento region is projected to be less than it is in the latter part of the century under both low and high carbon emissions scenarios (Cayan et al. 2009). Because water temperatures are influenced by air temperatures, NMFS expects that climate change will amplify adverse thermal effects of the proposed action combined with the environmental baseline and modeled climate change past 2030.” (p. 283) Comment: With future climate change, operations under WaterFix will likely create significant added risks to salmon, steelhead, and sturgeon.

Some Final Thoughts

While it is possible that the WaterFix would cause few changes in reservoir management upstream of the Delta, WaterFix is likely to increase demands at times on that storage, with many potential ramifications. The NMFS BO does not address any such changes and the rules that might limit them. Rules could even become more stringent to protect salmon and sturgeon, thus potentially reducing the water supply benefits of the WaterFix. But without operational constraints for reservoirs and other aspects of WaterFix, there is no basis for NMFS to state in a BO that it has predicted and mitigated the effects of the WaterFix on salmon, steelhead and sturgeon.

Finally, I have seen no suggestions to use WaterFix to improve upon existing Central Valley water operations to benefit salmon. For instance, WaterFix should make it possible to adjust some water demands to allow better management of Shasta’s cold-water pool. For now, WaterFix would seem to be just another tool to exploit the water resources of the Sacramento River system at the expense of salmon, steelhead, and sturgeon.

WaterFix will devastate more than just Salmon

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Dave Vogel and I are contributing a series of posts on the potential effects of the WaterFix Twin Tunnels Project on Delta fishes. Our focus to date has been on salmon. In this post, I focus on the “other” fishes of the Bay-Delta that will be harmed by WaterFix.

Striped Bass (non-native gamefish)

Striped bass will be devastated by WaterFix tunnel intakes located on the lower Sacramento River. The main spawning run of striped bass is in spring in the lower Sacramento River from near Colusa down to the tidal Delta. Eggs and larvae are buoyant and are carried by currents to the tidal Delta and Bay. Nearly all the eggs and larvae must pass the tunnel intakes. The original Peripheral Canal (circa 1980) had a provision to limit diversions during the striped bass spring spawn. The Vernalis Adaptive Management Program (VAMP) from the late 1990s to the late 2000s protected striped bass in spring with higher Delta inflows and reduced exports (generally a limit of 1500 cfs from mid-April to mid-May). The D-1485 Delta standards had a limit on exports through June (6000 cfs). The proposed WaterFix would have spring exports up to 15,000 cfs (9000 from tunnels and 6000 from existing South Delta pumps). Those eggs and larvae that pass the tunnel intakes would be subject to the pull of south Delta exports without the benefit of the extra flow taken at the tunnel intakes.

Longfin Smelt (native)

Longfin smelt will suffer from reduced flows in the winters of drier years. The WaterFix will take a quarter to a third of sporadic uncontrolled winter flow pulses that support the spawn of longfin smelt in drier years. The lower flows will force longfin to spawn further upstream in the Delta where they are vulnerable to central and south Delta exports. The longfin population declines in drier year sequences; the WaterFix will add to downward population pressure.

Delta Smelt (native)

A recent post by Moyle and Hobbs at UC Davis suggests Delta smelt will be better off under WaterFix:

“The status quo is not sustainable; managing the Delta to optimize freshwater exports for agricultural and urban use while minimizing entrainment of delta smelt in diversions has not been an effective policy for either water users or fish.” Comment: So allowing the water projects to take more water will help? Delta inflow and outflow are the key factors in Delta smelt population dynamics – both will be negatively affected by WaterFix.

Moyle and Hobbes point out “reasons to be optimistic about Waterfix,” as follows:

  • “Entrainment of smelt into the export pumps in the south Delta should be reduced because intakes for the tunnels would be upstream (of) current habitat for delta smelt and would be screened if smelt should occur there.” Comment: The existing south Delta intakes will continue to take spring-summer water (and smelt) from the Delta in similar amounts as in the past. However, smelt in the south Delta will not have the benefit of the inflow taken by the proposed tunnels. Smelt will also be more likely to spawn near or upstream of the tunnel intakes. Screens on the tunnel intakes would not help save larval smelt and would be minimally effective for adult smelt.

  • “Flows should be managed to reduce the North-South cross-Delta movement of water to create a more East-West estuarine-like gradient of habitat, especially in the north Delta.” Comment: If outflow remains low or becomes even lower, the low salinity zone will more frequently move further into the Delta. The north Delta already has a strong gradient – allowing the gradient to move further upstream into the Delta will have adverse effects. Circulation in the south Delta will remain poor, and the south Delta will continue to experience reverse flows, because south Delta exports will continue. The south Delta will lose the benefit of inflow taken by the tunnels.

  • “Large investments should be made in habitat restoration projects (EcoRestore) to benefit native fishes, including delta smelt.” Comment: Delta smelt are totally dependent on pelagic (open-water) habitats, but few EcoRestore projects will improve such habitats. Salinity, water temperature, turbidity, tidal-flow dynamics, water quality, and nutrients are by far the most important factors controlling smelt population dynamics.

Steelhead (native)

Steelhead, much like salmon, are affected by ancillary changes in reservoir storage and releases, river flows, Delta inflow and outflow, water temperatures, and turbidities. But the greatest threat to steelhead, as for salmon, is from the three large intakes and their screen systems, which will adversely affect young steelhead passing on their way to the ocean.

Splittail (native)

Splittail were once on the endangered species list. Today, splittail numbers, especially for recruitment of juveniles, are way down, well below the numbers occurring at the time of their listing. Splittail from the Bay-Delta migrate upstream into river floodplains upstream of the Delta to spawn in spring. The three largest floodplain areas are in the Yolo Bypass, Sutter Bypass, and the lower San Joaquin River wildlife areas. The Sutter group will be at high risk to fry-stage entrainment/impingement at the tunnel intakes. The San Joaquin group will have a continued risk to south Delta exports, a risk made worse by the diversion of inflow from the Sacramento River into the tunnels.

American shad (non-native gamefish)

American shad migrate from the ocean to Valley rivers to spawn in the spring. Eggs, larvae, and fry from the major spawning rivers of the Sacramento Valley must pass the tunnel intakes in the north Delta. Like the striped bass, these lifestages of American shad will be devastated by entrainment and impingement at the tunnel intakes.

Pacific Lamprey

Like salmon and steelhead, Pacific lamprey migrate from the ocean to spawn in Valley rivers during the spring. Young larval lamprey would pass the tunnel intakes on their migration back to the ocean. Because they are weak swimmers they would be highly vulnerable to impingement or predation at the screens.

Native Minnows and Suckers

Many species of native minnows and suckers migrate upstream from the Delta to Valley rivers to spawn in spring and summer. Their young must pass the tunnel intakes on their return to the Delta, and thus will be at risk to entrainment/impingement at the tunnel screens.

The Delta smelt Summer Townet Index is at record low numbers in recent years including the wet year 2017 index.

The striped bass Summer Townet Index remains near record low in 2017.

 

American River Chinook Salmon – Status and Future

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The American River is one of the larger tributaries of the Sacramento River (Figure 1). Its watershed runs from the central Sierra Nevada range, from which it runs through the city of Sacramento to join the Sacramento River. The American River’s lower 20 miles are a tailwater of the Central Valley Project’s Folsom Dam. This tailwater supports a major run of fall-run Chinook salmon that produces 15-20% of the total Central Valley fall-run Chinook salmon population.

American river run size (adult escapement) has ranged from 6,000 in 2008 to 178,000 in 2003 (Figure 2). The CVPIA long-term average goal for the American River fall-run is a contribution of 160,000 adult fish to the overall goal of 750,000 for the Central Valley. Many of the American River spawners are from the American’s Nimbus hatchery, or are strays from other Valley hatcheries. However, a large part of the run spawns naturally in the upper ten miles of the lower American River below Nimbus dam within Sacramento County’s urban parkway. The hatched fry of natural spawners rear by the millions in the lower river and in the Delta. Each spring, about 5 million Nimbus hatchery smolts are trucked to the Delta or Bay and released.

The American River fall run is often considered a hatchery run, with the 20 miles of river described as a mere conduit to the hatchery. The hatchery smolts are nearly always trucked to the Bay or lower Delta because of the high potential risk from water diversions or predation in the river or the upper Delta. Trucked and Bay pen-acclimated hatchery smolts generally have a relatively high survival-contribution rate and low straying rate compared to other Central Valley hatchery tagged fish.1

Brown 2006 reviewed the status of the American River population during its peak 2000-2005 runs. He attributed the strong runs to a variety of improvements at the hatchery:

  1. Changes in fish ladder operations to bring fish into the hatchery later in the fall to minimize temperature problems.
  2. Change in egg incubation and size at release (to all smolts).
  3. Elimination or control of early disease problems with the help of DFG pathologists.
  4. Elimination of most bird depredation within the hatchery through deployment of exclusion nets over the raceways.
  5. Change in the DFG approach to hatchery operations since 1999 when the National Marine Fisheries Service (NOAA Fisheries) urged DFG to adopt standard operating procedures.
  6. Change in release location to San Pablo Bay and change in the method of release to net pens in place of direct releases from the transport trucks to the Bay.

Others offered additional reasons for the improvement in the fall Chinook runs in the Central Valley, including the following:

  • Gravel and rearing enhancement (enhancements to spawning and rearing habitat had occurred under the CVPIA Program).
  • Better hatchery practices (mentioned above)
  • Good ocean conditions
  • Reduced ocean fisheries
  • Better instream conditions (1995-2000 were wet years)
  • Some combination of the above

Subsequent to the good runs from 2000-2005, runs declined sharply to record lows during the 2007-2009 drought (see Figure 2). The general decline across the Central Valley was attributed mostly to poor ocean conditions.2 This seems reasonable since 2006 was a wet year with good river-Delta rearing conditions that should have produced a strong 2008 run rather than a record low run. The decline is also related to high late summer and early fall water temperatures in the lower American River that led to poor adult and egg survival (Figure 3). Such conditions occurred in the drier period of 2001-2005. I describe this specific problem in detail in a prior post.

I took a closer look at the spawner-recruit relationship of the American fall-run salmon (Figure 4). There was a significant underlying positive relationship between spawners and recruits three years later. That relationship was modified by water year conditions during the rearing year (most likely the winter-spring rearing conditions) and by the fall spawning conditions in both the spawning year (from poor egg-embryo viability) and the return year (pre-spawn mortality of adults). Poor recruits-per-spawners stand out in the two drought periods 1990-1992 and 2007-2009. Years 90, 92, and 09 especially stand out with (1) poor initial spawning conditions in the fall of 87, 89, and 06, (2) poor rearing conditions in drought years (red numbers), and (3) poor spawning conditions in drought years (red circles).

Year 2008 recruits stand out in Figure 4 as the lowest recruit year despite a wet rearing year in 2006. There are at least several possible contributing factors for this particular outlier:

  1. Winter 2006 (Dec 05 and Jan 06) saw a large-scale flood, second only to the 1997 winter flood in recent decades. After spawning in the American River occurred during a steady flow of 2000-2500 cfs during the fall, flow reached 35,000 cfs in late December and early January, likely washing out much of the spawn. Only winter 1997 and 2017 have had similar Dec-Jan floods since 1975. Such a flood could have washed out the eggs/embryos spawned in fall of 2005, thus contributing to the poor 2008 run.
  2. Egg viability during the fall 2005 spawn may have been poor because water temperature was high (at or greater than 60°F) during most of the spawning season from mid-September through mid-November.
  3. Poor ocean conditions may have reduced survival of smolts rearing in the ocean in summer-fall of 2006.
  4. During the 2008 spawning season, flows were low, near 1000 cfs, and water temperatures exceeded 65°F through mid–October, likely leading to high pre-spawn mortality and lower than expected escapement. Poor conditions in the river may have attracted fewer spawners to the American or delayed their migration, leading to greater pre-spawn mortality or increased straying to other spawning rivers.

Floods during the wet winters of 1982 and 1986 may have contributed to the lower than expected runs in 1984 and 1988, respectively. Though not as strong as the Dec-Jan floods of 1997 and 2006 water years, winter floods in 82 and 86 were still substantial.

The hatchery practice of trucking smolts to acclimation pens in the Bay likely contributed to the strong runs in years 2000-2004. Lack of pen acclimation from 2003 to 2005 likely contributed to reduced runs from 2005 to 2007.

In summary, recruitment to the fall-run salmon population in the American River is a complex process affected by multiple factors. However, there are several actions that serve to keep recruitment-escapement and the contribution of the American River to California fisheries high.

  1. Trucking hatchery smolts to acclimation pens to San Pablo Bay contributes substantially to good salmon recruitment from the American River. Releases to pens in the Delta may reduce costs, but this comes at the expense of substantially less recruitment. Releases to the Bay allow DFW to grow fish longer in the hatchery, which contributes to higher ocean survival.
  2. Improvements to flow and water temperatures from September through November will reduce adult pre-spawn mortality, improve egg viability in hatchery and wild spawners, and increase wild embryo survival in redds.
  3. Improved late-winter and early-spring flows will improve growth and survival of juveniles rearing in the river, and improve transport of wild juveniles to Delta rearing areas.
  4. Though the jury may still be out on the contribution of habitat improvements to the salmon population, spawning and rearing habitat restoration in recent decades in the American River have likely helped sustain higher recruitment in good and poor water years alike. Habitat improvements increase the recruit-per-spawner capacity of salmon in the American River, especially given the relatively fixed contribution of the hatchery program. The wild or non-hatchery component of the American River salmon population also depends on Delta habitat and migratory conditions, which may also change in coming years.

Figure 1. Chinook salmon rivers. Source: Chinook salmon – species profile (USDOI 1986).

Figure 2. Fall run Chinook salmon escapement (river and hatchery counts) to the American River 1975-2016. Data Source: CDFW GrandTab.

Figure 3. “The American River is a death trap for fall run salmon” because of high water temperatures. Source: http://water4fish.org/res/pdf/salmon_status_and_needs_2011.pdf

Figure 4. Recruits (escapement in numbered year) per spawners (escapement three years earlier) for years 1978 to 2016 (log10 transformed). Red number denotes rearing conditions in a dry water year two years earlier. Red circle denotes dry water year in spawning year. Green denotes normal water year. Blue denotes wet water year. For example: Spawning year 2011 had dry rearing conditions in 2009, wet year during its spawning run in 2011, and the lowest number of parents in 2008. Orange rectangle represents years having poor ocean rearing conditions. Note that for recruit years 00-04, hatchery smolts were trucked to Bay acclimation pens (1998-2002), whereas in 03 to 05 they were trucked to Bay for direct release or to Delta pens.

Another Fall-Run Salmon Crash – Bad Ocean Conditions Again? Or Bad River/Delta/Bay Conditions?

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NOAA Fisheries’ Northwest Fisheries Science Center states on its website1: “Similar to 2015, many of the ocean ecosystem indicators suggest 2016 to be another poor year for juvenile salmon survival, the second consecutive year of poor ocean conditions. The PDO2 was strongly positive (warm) throughout 2016, coinciding with the continuing of the anomalously warm ocean conditions in the NE Pacific initiated by the “The Blob” that began in the fall of 2013. Strong El Niño conditions at the equator also persisted throughout 2015 until May of 2016. Sea surface and upper 20 m water temperatures off Newport Oregon remained warmer than usual (+2°C) throughout most of 2016 continuing two consecutive years of anomalously warm ocean conditions.” See Figures below and at end for more details from NMFS presentation.

Mother Nature has once again dealt California salmon a deadly set of circumstances. There is not much that can be done at this point, because much of this bad hand has already been played during the 2012-2016 drought and the bad ocean conditions in 2015 and 2016. Reduction of the 2017 sport and commercial fisheries has been prescribed again to save the patient. Cutting salmon harvest is like applying a tourniquet to an amputation, yet it is necessary. Have we not learned to better prepare for such circumstances?

Once again, the blame for poor resource management is being shifted to poor ocean conditions. Evidence clearly indicates that poor inland river, Delta, and Bay conditions were also a major factor in the poor survival of salmon during the recent drought. Furthermore, evidence indicates that the fall-run hatchery salmon populations that make up most of the commercial and sport fishing catch were sustained through the drought by the transport of hatchery smolts to the Bay avoiding the poor river and Bay-Delta conditions. There was very poor survival of smolts released near upriver hatcheries during the drought compared to smolts trucked to the Delta or the Bay. This is strong evidence that the rivers and Delta are the key factors in Central Valley salmon viability.3

The same circumstances occurred in the 2004-2008 period, leading to the 2008 “salmon crash”. First came a sequence of drier years, 2001-2005; two bad ocean years, 2004 and 2005; then a flood year 2006; followed by drought years 2007 and 2008. The salmon populations did recover with better runs in 2012 and 2013 because of normal-wet river conditions in 2010-2012 and good ocean condition in 2010-2013, but the runs have since declined sharply, beginning in 2014 and culminating in the expected 2017 crash. So far, the 2017 fishery is better than expected because of the expanded hatchery transport efforts in 2014. The prognosis is not as good for the wild salmon that were not trucked to the Bay.

Declining runs in the drought years 2014 and 2015, poor young production from 2013-2015, and the poor run of two-year-old (jacks) from brood-year 2014 in 2016 are indicators of a population crash. The brood-year 2014 jacks were the consequence of cumulative bad conditions: (1) in their spawning run (summer-fall 2014), (2) during incubation and first year rearing-emigration (winter-spring 2015), (3) during their first two summers in the ocean (2015-2016), and (4) poor conditions during their run from the ocean in summer-fall 2016 from the drought hangover. Three-year-olds from the 2014 brood year are also expected to return in poor numbers in 2017, because of droughts during their parents’ spawn, poor river rearing conditions (2015), and then poor ocean conditions in 2015 and 2016.

The prognosis for brood-years 2015-2017 (2018-2020 runs) is not good for some of the same reasons, especially the expected poor numbers of spawners. These runs will carry hangovers from poor river and ocean conditions in 2015 and 2016.

One thing is lessening the overall effect on fisheries: trucking hatchery smolts to the Bay. While that is not helping the wild salmon populations in the Central Valley, or those hatchery populations not included in the trucking program, it is helping.

What can be done to improve all the salmon populations in the Central Valley?

  1. Reduce harvest of adults in ocean and rivers (being implemented).
  2. Increase hatchery production (take more eggs and rear more smolts).
  3. Diversify hatchery smolt production by rearing some fry in natural floodplain habitats.
  4. Increase hatchery smolt survival by trucking and barging to the Bay and pen acclimating in the Bay.
  5. Improve migration and pre-spawn holding conditions for wild and hatchery adult spawners by maintaining spring-fall migration conditions (flow and water temperatures) in lower rivers and spawning reaches.
  6. Maintain adequate water levels and water temperatures to sustain eggs and embryos until hatching and emergence.
  7. Provide optimum flows and water temperatures in rearing areas for growth and survival (minimize predation).
  8. Provide flow pulses to attract spawners to spawning rivers below major rim dams.
  9. Provide winter and spring flow pulses to stimulate juvenile emigration and to provide floodplain rearing opportunities.
  10. Limit South Delta exports during late fall to spring peak emigration periods.

With so many factors potentially affecting salmon survival and production, it is hard to say which of these prescriptions will be most effective. We should focus on doing them all, at least in this plentiful water year (2017).

Ocean condition indicators 1999-2016. Source: see footnote 1.
Red = poor conditions. Green = good conditions. Yellow = intermediate conditions.

MWD’s Dreams: a Nightmare for Fish

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The Metropolitan Water District of Southern California, commonly known as MWD, recently released a series of information papers on the California WaterFix (Delta Tunnels). In this first in a series of posts I address MWD’s “assessment” of what will happen to the Bay-Delta environment and fish community if the WaterFix is built and operated.

One figure from MWD’s papers demonstrates the primary flaw in its assessment.

This key figure from the MWD’s papers accurately portrays the WaterFix’s potential “benefit.” But it leaves out the back story. The “uncontrolled” winter flows from Mother Nature’s few-and-far-between miracle rain events in drought years like 2013, as portrayed in the figure, were long ago allocated to the Bay-Delta as a small compensation for all the water taken from potential Bay inflow not shown in the chart.1 The proposed new WaterFix exports shown by the white line would take a good-sized bite out of what was left for the Bay. The proposed Sites Reservoir would take another large bite.

What is not shown is that this increase in export water would come from un-dammed tributaries to the Sacramento River such as Cow, Cottonwood, Battle, Deer, and Mill creeks, and the partially dammed Yuba and Cosumnes rivers. Most of the total inflow to the Valley from the storms shown on this graph was captured and stored in the large reservoirs on the main rivers (Sacramento, San Joaquin, Feather, American, Mokelumne, Stanislaus, Tuolumne, Merced, and Trinity), before it ever got to the Delta. Diversions to storage and exports from the Valley captured over 20 million acre-ft in Water Year 2013, including carryover storage.

It is true that exports from the south Delta were only about 2 million acre-ft for water year 2013: export water rights are among the last in line, especially in very dry years. About 2 million acre-ft, roughly the same amount of water as exports, flowed to the Bay from the uncontrolled winter flow. The other Delta outflow for the year was water that was released from storage to repel salinity and thus keep water for exports and Delta farming fresh enough to use.

The caption at bottom left of the figure attributes the loss of 800,000 acre-ft to biological opinions for fish, and suggests that WaterFix would “recover” these “losses.” The “loss” is not real and “recovery” of this water would only be possible at the further expense of fisheries already in collapse. The present (and past) restrictions on exports are needed to protect (1) the tens of millions of young hatchery and wild salmon and steelhead moving from rivers to the Bay-Delta and ocean during the flow pulses, and (2) the spawning runs of Delta and longfin smelt, which are also keyed to the flow pulses. Screening the WaterFix intakes is not going to protect the flow needs of the fish that depend wholly on the storm flows moving through the Delta to the Bay and ocean.

  1. Past water rights and water quality control plans, as well as various water project operating agreements, recognized the important role played by uncontrolled Delta inflows and outflows. Qualifiers to such agreements commonly stated that further allocation or access to these uncontrolled would not be made without careful review of the environmental consequences. ↩