Category Archives: Bay-Delta

Striped Bass Comeback Stalls in June

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In a June 1 post, I wrote of an apparently strong year class of striped bass developing in 2016.  This analysis was based on May surveys.  I suggested then the comeback could fall short after higher exports began in June.

The results of the two DFW 20-mm Surveys for June are in, and these results indeed show a sharp decline in the densities of juvenile striped bass between early and late June (Figure 1), coincident with a rise in south Delta exports over the month (Figure 2).  Some of the greatest changes occurred in the interior Delta (900 stations), where the effect of exports would be greatest.

The late June densities, though higher than 2014 and 2015, are consistent with densities over the previous decade of striped bass decline and are lower than the prior decade of striped bass recovery.  With the demise of the Delta smelt population, it may be appropriate to consider striped bass once again as the Delta’s “canary-in-the-coal-mine.”

Figure 1. Striped bass juvenile density in the Delta in June 2016 20-mm surveys. The 700 stations are from the lower Sacramento River channel of the west and north Delta. The 800 stations are from the lower San Joaquin River channel of the west and central Delta. The 900 stations are from interior Delta channels. ( http://www.dfg.ca.gov/delta/data/20mm/stations.asp )


Figure 1. Striped bass juvenile density in the Delta in June 2016 20-mm surveys. The 700 stations are from the lower Sacramento River channel of the west and north Delta. The 800 stations are from the lower San Joaquin River channel of the west and central Delta. The 900 stations are from interior Delta channels. ( http://www.dfg.ca.gov/delta/data/20mm/stations.asp )

Figure 2. Reverse flow in Old and Middle Rivers in central Delta in June 2016. Reverse flows are representative of the direct effects of south Delta exports on central Delta channels. The survey periods of the two DFW 20-mm surveys are shown.

Figure 2. Reverse flow in Old and Middle Rivers in central Delta in June 2016. Reverse flows are representative of the direct effects of south Delta exports on central Delta channels. The survey periods of the two DFW 20-mm surveys are shown.

Central Valley Salmon Require Improved Resilience

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A suite of disturbances in the Central Valley has eroded many of the inherent characteristics that once conferred resilience1 in historically abundant salmon populations.  Resilience is provided by natural abundance, diverse run timing, multiple habitats, and broad habitat availability and connectivity.  Last November, I recommended a dozen specific actions to save winter-run salmon.  This post focuses on long-term actions to restore resilience in Central Valley salmon populations and fisheries.

Resilience has declined due to the narrowing of optimal adult migration conditions, the confinement of spawning to localized areas and time periods, the limitation of outmigration periods and regional conditions, the confinement of rearing periods, and the amount of and connectivity of geographical habitats.

Confinement of salmon below dams constructed in the 1940’s  took away much of the resilience in the salmon populations.  In the past 70 years, the populations have depended upon a narrowing range of habitat conditions in time and space in the limited spawning habitat below Shasta and other major rim dams, as well as in the migration and rearing habitat between these spawning areas and San Francisco Bay.  The development of the State Water Project further diminished Central Valley salmon’s remaining resilience.

Resilience has been lost in following ways:

  1. Spawning habitat has gradually declined below dams due to lack of new gravel recruitment and the gradual armoring of spawning riffles.
  2. Spawning habitat has declined with weakened management of water temperature below Shasta, narrowing the spawning reach from 40 miles to as little as 10 miles. Early spawning of winter-run salmon in April and May has been lost even in wetter years like 2016 because of flow reductions in these months and because the temperature of water released from Shasta in these months has been increased.
  3. Embryo survival in redds and fry survival in rearing reaches has been compromised by low, warm summer and fall flows. More redds are dewatered with more frequency as water deliveries for irrigation taper off in the fall.
  4. Winter flows that carry juveniles to and through the Delta are lower and more sporadic. Fall and early winter flows and pulses that occurred historically and enhance smolt emigration no longer occur to the extent they once did, particularly in the spawning reaches immediately below the major reservoirs that regulate all the inflow.
  5. With lower and warmer river and Delta flows, salmon predators have become increasingly more effective.
  6. The quality of the physical habitat of salmon, and winter-run salmon in particular, has been adversely modified over time.

Hatcheries can reduce resilience over time if specific precautions are not taken to avoid weakening the gene pool and population diversity, and to avoid interactions with wild fish.  But hatcheries can also be used to strengthen resilience by increasing genetic diversity and spreading populations in time and geographical range.

Habitat restoration can increase resilience by limiting bottlenecks such as lack of spawning gravels or migration corridor connectivity.  Flow and water temperature remain the two most important habitat factors in the Central Valley.  The availability of floodplain rearing habitat is also important.  Reduced winter flooding resulting from global warming and lower reservoir carryover storage levels has reduced habitat resilience over time.  The gradual decline of large wood in Valley rivers over the decades has reduced the rearing capacity of streams and rivers.  River and stream channels have gradually degraded due to scour and the lack of large wood and natural sediment supplies.

A resilience-based approach is likely to be more successful than traditional mitigation or restoration approaches “by seeking to rebuild suites of disturbance-resistant characteristics” that were historically present in the Central Valley.  A resilience-based strategy “emphasizes the diversification of life history portfolios” and “would seek to maintain a diversity of habitat types, including less productive habitats that may have primary importance only as refugia or alternate spawning habitat during disturbances.”  The ultimate goal is to get salmon smolts to San Francisco Bay and the ocean, which offer cold waters and abundant food.

Historically, resilience occurred at all life stages, beginning with an abundance of adults.  With the present depressed adult runs, resilience is thus already handicapped.  Building runs requires restoring resilience of all life stages, starting with egg survival.  Turning around the decades of decline in resilience and increasing it, especially in the short term to avoid extinctions, is a therefore a major, expensive undertaking.  First, we should focus on stopping further declines in resilience.  Second, we should improve resilience where we can to begin the healing.  The following are some suggestions:

  1. Increase the salmon spawning reach below Shasta in time and space by providing better flows and water temperatures. Extend the spawning reach back down to Red Bluff and diversify timing with better early season conditions (e.g., April-May winter run spawning).  Improve physical habitat further downstream toward Red Bluff, not just near Redding.  Extend habitat improvements where possible into tributaries (e.g., Clear and Battle Creeks).
  2. Extend the range of salmon into former habitats, such as the planned improvements on Clear and Battle creeks, and in the reaches above selected rim dams.
  3. Expand the conservation hatchery program to diversify genetics and support expanded range. Select for specific natural genetic traits that have been lost or changed to increase diversity.
  4. Develop and implement a river flow management plan for the Sacramento River downstream of Shasta and Keswick dams that considers the effects of climate change and balances beneficial uses with the flow and water temperature.
  5. Increase the range in time and space of rearing and migratory habitats that accommodate diversity.
  6. Develop and implement a long-term large wood and gravel augmentation2 plan consistent with existing plans and flood management to increase and maintain spawning habitat for salmon and steelhead downstream of dams. Diversify habitats and reduce habitat bottlenecks.  Expand rare and important habitat types.
  7. Counteract where possible the effects of climate change. Where changes in flow and water temperature changes delay smolting, make changes that return diversity.
  8. Provide a more natural diversity of flow pulses immediately below major dams during the emigration season (i.e., December-April) to diversify the timing and life stages of the emigration of juvenile salmon.

A final note:

Instead of improving resilience, the Delta “WaterFix” will only cut further into and adversely modify the resilience of the salmon populations.  There will be more demands on Shasta storage to meet new Tunnel diversion capacity.  Flows below the Tunnel intakes will be lower, further reducing resilience by warming through-Delta spring migration routes (Figure 1).  Less freshwater flow into the Delta will further alter Delta habitats and make them more conducive to non-native invasive species of plants and animals.  Delta habitat will be warmer earlier in the season, less turbid, and more brackish.

Figure 1. Water temperature versus mean daily flow at Rio Vista in spring 2016. (Source of data: CDEC). Resilience in terms of Delta migration survival would be reduced by the effects of the proposed WaterFix on water temperature in the Delta spring migration route.

Figure 1. Water temperature versus mean daily flow at Rio Vista in spring 2016. (Source of data: CDEC). Resilience in terms of Delta migration survival would be reduced by the effects of the proposed WaterFix on water temperature in the Delta spring migration route.

  1. Resilience Approach or Portfolio Effect – The “portfolio effect,” is the coexistence of multiple life history strategies within a population – how diversity in life history can increase resilience and stability.
    http://fisheries.org/2016/03/a-resilience-approach-can-improve-anadromous-fish-restoration/
    ↩
  2.  http://www.redding.com/news/local/gravel-work-to-aid-salmon-2bcbc5bc-999f-2cba-e053-0100007fbf34-369363581.html ↩

July 1 Smelt Update

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The Smelt Working Group packed its bags for the summer after its last meeting on May 31, just when it was most needed.  The water temperature in the South Delta had reached 77°F/25°C in the first week of June, forcing the Working Group to close shop, consistent with the biological opinion.  The 5000 cfs June south Delta export limit in the biological opinion also departed.  Exports soon rose above the earlier 3000 cfs limit, reaching nearly 7000 cfs later in June (Figure 1).

Figure 1

Figure 1. Old and Middle River net flows in June 2016. Negative flows generally correspond with export rates at the south Delta pumping plants. The limit in the Delta Smelt biological opinion is -5000 cfs for June, but the limit does not apply once the south Delta water temperature reaches 77°F/25°C.

The two June DFW 20-MM surveys showed that small numbers of Delta smelt remained in their normal northwest Delta nursery area (Figures 2 and 3) in slightly brackish, cooler (20-22°C) water. Still directly and indirectly vulnerable to the effects of exports, these smelt were sustained by a bare minimum of Delta outflows (7000-7500 cfs). What they needed and are still failing to receive are higher outflows to move them west to Suisun Bay.1 With exports soon to rise in July up to the full 11,400 cfs maximum capacity, and without further hope of higher outflow to the Bay, these last smelt may soon succumb to the rigors of the Delta as they did during the past four years of drought.

Instead of the prescribed standard of 6,500 cfs Delta outflow in July, an outflow of at least 8,000 cfs is necessary to protect the remaining smelt.

Figure 2. Survey 7 of 20-MM Survey results for Delta smelt.


Figure 2. Survey 7 of 20-MM Survey results for Delta smelt.

Figure 3. Survey 8 of 20-MM Survey results for Delta smelt.

Figure 3. Survey 8 of 20-MM Survey results for Delta smelt.

State Board: Increase Sacramento River Flow

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The State Water Resources Control Board is responsible for enforcing water rights and the Sacramento River Basin Plan that protects beneficial uses including fish and water quality.1 The Basin Plan’s 68°F objective for the lower Sacramento River is clearly being violated right now because of low Sacramento River flows brought about by lower than normal Shasta releases and a 100 % allocation of water to Sacramento Valley water contractors. The State Board has jurisdiction over both of these factors through control of water rights. The State Board is about to review Reclamation’s Water Temperature Plan (WTP) for summer 2016, which calls for a 10,500 cfs release in July, several thousand cfs below normal, to conserve Shasta’s cold-water pool for salmon through the summer and fall. The WTP however has no provisions for cutting downstream water use. Thus, flows in the lower Sacramento River will be lower, with higher water temperatures that violate the Basin Plan. The flows must be raised at Wilkins Slough (RM 125) by either increasing Shasta releases or reducing water diversions, or a combination thereof.

The Basin Plan objective of 68°F is there to protect salmon and sturgeon migrating and rearing in the lower Sacramento River. Water temperatures above 68°F are stressful to the fish, affecting growth, survival, and subsequent reproduction. Present water temperatures in the lower river (Figure 1), caused in part by low flow (Figure 2), are lethal to salmon and sturgeon. In 2010 and 2012, water years similar to 2016, flows were higher and water temperatures were lower in early summer (Figures 3-6).

The State Board, in reviewing the WTP, must explicitly consider flows and water temperatures in the lower Sacramento River under its broader responsibilities to protect fish as prescribed in the Basin Plan and in various water rights orders.

Figure 1. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2016.


Figure 1. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2016.

Figure 2. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2016.

Figure 2. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2016.

Figure 3. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2010.

Figure 3. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2010.

Figure 4. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2010.

Figure 4. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2010.

Figure 5. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2012.

Figure 5. Water temperature of lower Sacramento River at Wilkins Slough (RM 125) in early summer 2012.

Figure 6. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2012.

Figure 6. Sacramento River flow at Wilkins Slough (RM 125) in early summer 2012.

June Protection Lost for Delta Smelt

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In a May post and again in an early June post, I offered some hope for Delta smelt.  But the Smelt Biological Opinion and the Smelt Working Group failed the smelt once again.  The only protection afforded Delta smelt in June is the -5000 cfs Old-Middle River negative flow limit, which has the practical effect of limiting Delta exports to about 5000-6000 cfs.  Historically (from 1978-1994), D-1485 water quality standards limited June exports to 6000 cfs in order to protect Delta fish, but there are no June export limits in the existing D-1641 standards.

The last Smelt Working Group meeting was May 31.  The only biological opinion criterion left to manage, the -5000 cfs OMR limit, was gone because of a little known trigger in the opinion that dropped the OMR limit when the water temperature in the South Delta first reaches 25°C or 77°F (Figure 1).  The reasoning behind this trigger in the biological opinion was that exports would no longer hurt smelt because 25°C/77°F water temperatures would kill them anyway.  The problem with this logic is that exports can still pull smelt from their cooler nursery in the west and north Delta (Figures 2 and 3) into warm water killing zone in the central and south Delta.  Fortunately, export pumping in June 2016 was limited (Figure 4) by Reclamation’s holding back Shasta Reservoir storage releases to conserve cold-water for salmon.  Otherwise June exports and negative OMR flow would likely have been higher.

Reclamation has begun consulting with fishery agencies on a new biological opinion.  We can only hope that they improve protections for smelt and other Delta fish in spring and summer.  I suggest strong OMR restrictions any time the Delta Cross Channel in the far north Delta is closed, as this will help minimize (1) the draw of smelt from their nursery area and (2) the degradation of the Low Salinity Zone by south Delta exports.

Figure 1. Water temperature in Clifton Court Forebay in the South Delta in June 2016.

Figure 1. Water temperature in Clifton Court Forebay in the South Delta in June 2016.

Figure 2. Water temperature at Jersey Point in the west Delta in June 2016.

Figure 2. Water temperature at Jersey Point in the west Delta in June 2016.

Figure 3. Water temperature in the lower San Joaquin River at Three Mile Slough in June 2016.

Figure 3. Water temperature in the lower San Joaquin River at Three Mile Slough in June 2016.

Figure 4. June OMR flow. The Smelt Biological Opinion limit is for June is -5000 cfs, but that provision does not apply once south Delta water temperature reaches 25°C/77°F.

Figure 4. June OMR flow. The Smelt Biological Opinion limit is for June is -5000 cfs, but that provision does not apply once south Delta water temperature reaches 25°C/77°F.