Category Archives: Bay-Delta

Drastic Measure to Meet Delta Outflow

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For seven days in mid-March 2021, the Bureau of Reclamation substantially increased Folsom Lake storage releases. Roughly, the releases tripled in volume (Figure 1). The release of over 20,000 acre-feet of water is significant for a year in which Folsom storage is not much better than it was in the worst year on record – 1977 (Figure 2).1 With the release in mid-March, the lake level dropped 3 feet. Yes, there was rain in the forecast and a decent snowpack, but certainly no flood concerns. So why? The reason was to meet state water quality requirements for Delta outflow. Delta outflow increased from 7,000 cfs to 12,000 cfs for a few days (Figure 3).

The outflow pulse was needed to meet an obscure and complicated provision in the Bay-Delta’s D-1641 Water Quality Control Plan called “footnote 11.” The footnote (Figure 4) specifies a formula for determining minimum daily Delta outflow for February through June in different water year types. The base requirement is 7100 cfs 3-day running average minimum (that was being met – Figure 3). What was not met is the requirement in Table 4 to increase Delta outflow from Feb-Jun for the general ecological benefit from higher natural Delta outflow. That requirement is met by meeting a specified average number of days of obtaining an electrical conductivity level (EC) of 2640. Since even that requirement was not met either (Figure 5), the Executive Director of the State Water Board allowed Reclamation and the Department of Water Resources not to meet it.

The primary problem with this Delta Outflow requirement is the abrupt and arbitrary way it is met. If all that is needed to relax the requirement is a “BOGSAT,”2 then all stakeholders need to be involved. Why did Reclamation place the burden primarily on Folsom Reservoir? Why did Reclamation release all the water over just a few days? The abrupt releases likely affected steelhead spawning. The lost storage will likely make salmon migration and spawning in the fall worse as well. At a minimum, Reclamation should have provided some form of notice of this major action. Reclamation should also document the effects.

Figure1. Streamflow in the lower American River at Fair Oaks gage March 8-18, 2021

Figure 2. Storage level in Folsom Reservoir in 2021. Source: CDEC.

Figure 3. Delta outflow in Feb-Mar 2021. Source: CDEC.

Figure 4.  FOOTNOTE 11 in D-1641:  Bay-Delta Water Quality Control Plan

Figure 5. EC at Chipps Island Station D10 in winter 2021.

Figure 6. Daily average Oroville reservoir release in winter 2021.

  1. Lake Oroville provided something less than 10,000 acre-ft, while Shasta Lake provided none. ↩
  2. BUNCH OF GUYS SITTING AROUND a TABLE ↩

Central Valley Steelhead 2021

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The Delta Science Program plans to host a Steelhead Workshop on February 17 – 19, 2021.  The purpose of the workshop is to “identify challenges to managing and monitoring Central Valley steelhead with the goal of identifying collaborations that are needed to improve the monitoring and science network for the species in the San Joaquin basin.”  While commendable and needed, such a workshop could and should cover the entire Central Valley Evolutionary Significant Unit (ESU), all of which must pass through the Delta on the way to and from the Pacific Ocean.

Although Central Valley steelhead science and management can succinctly be described as a mess, there are a few basic facts and misconceptions worthy of note that are useful in considering steelhead management in the Central Valley.

First, the facts:

  1. Steelhead are rainbow trout that have the genetic inclination to spend some of their life cycle in the ocean. Most rainbow trout have such an inclination, but some populations have long ago given up on that inclination (g., redband rainbow trout).

  2. In the Central Valley, all rainbow trout residing in anadromous waters are considered steelhead and are thus protected unless their adipose fins are clipped, which definitively shows hatchery origin.

  3. Rainbow trout of a wide range of origin, stocked or wild, live in or above dams in the Valley and are not designated steelhead. Some are remnants of steelhead trapped behind dams.  Other were hatchery raised or perhaps are remnants of long-ago geologically isolated populations.  Many of these non-steelhead pass over or through the dams and mix with steelhead, essentially becoming steelhead and influencing steelhead population genetics.

  4. All steelhead populations in the Valley have some degree of domestication from more than 100 years of hatchery influence and manipulation. Hatcheries (federal, state, and private) continue to influence population genetics.  Valley hatcheries have brought in eggs from many sources (g., Columbia River, coastal stocks, interior stocks such as Kamloops rainbow trout).  Hatcheries manipulated many important natural traits through selective breeding (e.g., run timing, age of maturity, growth rate).  Such changes affected the genetic integrity of locally adapted populations, adapted traits gained over thousands of generations.  Some hatchery sources were selected for traits better suited for hatchery managers or anglers than for natural diversity and population endurance.

  5. Valley steelhead come in many different breeds and colors, with distinct characteristics, traits, behaviors, and appearance. The basic breeds are often described by run timing:  winter, spring, summer, and fall, although most spawn in winter or spring.  Some examples are shown in attached figures below.

  6. Natural selection continues to adjust to human influences, albeit in competition with hatchery domestication.

Some misconceptions:

  1. Hatcheries are managed for benefit of natural, wild, or native steelhead populations. No. Hatcheries are managed to meet mitigation smolt production quotas at minimal cost, with some consideration for angler preferences (e.g., trophy size).  Hatchery domestication effects on genetic integrity are severe and not lessening.

  2. Central Valley steelhead are not in danger of extinction. Wrong.  They are in danger, which is why they are state and federally listed, and why no wild (unmarked) rainbow trout can be harvested in the anadromous zone of the Central Valley.  Wild “native stocks” are rare and declining.

  3. Spawning and rearing habitat in rivers and dam tailwaters are maintained to protect wild steelhead.   Protective standards are inadequate or often unmet.  Natural spawning and rearing habitats are degraded and are further deteriorating or being lost.  Flows are too low, and water temperatures too high.

  4. Steelhead are compatible with introduced non-native sportfish. No.  Striped bass, black bass, catfish, sunfish, and American shad all prey upon steelhead – the total population effect is substantial.  Since predatory fish cannot be eradicated, the interaction between steelhead and predators needs to be managed.

  5. Climate change is the cause of declining natural populations. Though climate change is real and exacerbates harmful conditions for steelhead, blaming climate change for the decline of steelhead is just a convenient excuse.

Management needs:

  1. Improved monitoring of steelhead population dynamics is needed. Despite the angler-funded steelhead stamp program, there is minimal monitoring of adult spawners or juvenile  Screw traps are for migrating fry, but steelhead fry don’t migrate like salmon.

  2. River habitats should be restored and improved. Rivers should not be treated just as conduits from hatcheries to the ocean.  Steelhead over-summer at least one year before emigrating to the ocean.

  3. Mitigation hatcheries should be converted to conservation hatcheries. The hatchery programs need a cleansing.  Also, hatchery rainbows released above dams should be marked.

  4. Spawning habitat should be for wild, native steelhead. Steelhead sanctuaries are needed.  Every effort should be made (selective barriers) to limit access to these areas by hatchery or stray steelhead, and by migratory non-native predators and competitors such as shad and stripers.

  5. Flows are needed to increase survival of wild steelhead fry and smolts. Steelhead are genetically adapted to emigrate with the natural flow pulses of fall, winter, and spring.  Reservoirs have eliminated or reduced such flows.  Without the flows, smolts won’t migrate or survive the predator gauntlet.  Trap and hauling wild smolts around the lower river and Delta predator gauntlet is an option for dry years.

  6. Flows are needed to improve attraction of adult migrants to spawning rivers. Again, steelhead need the flow pulses.

For more on steelhead see:

Native rainbow-steelhead from the lower Yuba River. Many wild rainbow trout do not migrate, choosing to remain in the cold tailwaters of dams, where they sustain high-quality sport fisheries.

An early fall run hatchery steelhead from the lower American River in October. Battle Creek hatchery steelhead smolts were stocked in the American River for one year to determine if they would be a viable more-native alternative to the American hatchery’s coastal Eel River origin stock. They were fine sport, susceptible to dry flies.

The American River hatchery program uses coastal origin stock that spawn in winter. Many spawners enter the river in late fall when fishing is closed to protect spawning salmon. Fishing is open in winter spawning season. This female caught in January was likely actively spawning. Native steelhead are spring spawners.

Delta Smelt – 2020 Status

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In a March 2020 post, I described the status of the Delta smelt through 2019.  This post updates the status with the most recent 2020 information.  Delta smelt continue to be absent from the standard long-term surveys and their related indices.  However, some Delta smelt were collected in 2020 in selected locations of the Bay-Delta during focused intensive special surveys designed to find remaining survivors.  Larval and juvenile Delta smelt were collected in low numbers in the Bay and north Delta (Figure 1).  Pre-adult Delta smelt were also collected in summer trawl surveys (Figure 2).

The north Delta habitats where a few Delta smelt persevere continue to be plagued by constant stressful if not lethal water temperatures (Figures 3 and 4).

As I stated in a prior post, Delta smelt would benefit from increased net flows through the north Delta during the spring and summer.

Figure 1. Numbers of larval and juvenile Delta smelt collected in the spring Enhanced Delta Smelt Monitoring (EDSM) 20-mm nets. Source.

Figure 2. Numbers of pre-adult Delta smelt collected in the summer Enhanced Delta Smelt Monitoring (EDSM) Kodiak trawls. Source.

Figure 3. May through September 2020 water temperature and net tidally-filtered flow in the lower ship channel near Rio Vista. Note water temperatures fall 1-2ºC when net flows increase.

Figure 4. May through September 2020 water temperature and net tidally-filtered flow in Cache Slough near Rio Vista. Note water temperatures generally fall 1-2ºC when net flows increase.

The Delta as Salmon Nursery

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The Delta is an important nursery area for Central Valley Salmon. This fact continues to be ignored or under-appreciated. The phenomenon is fully consistent with the general science on salmon in their southern range in the eastern Pacific. Nearly all California Chinook salmon are “ocean-type,” meaning that juveniles reach the ocean in their first six months after rearing for extended periods in estuaries. To grow, young salmon fry need to rear in winter in warm productive areas of floodplains and tidal estuaries (Bay and Delta). Flood control infrastructure limits floodplain habitat except in wetter years. Water management, mainly reservoir storage, limits transport of fry to the Bay except in wetter years.

That leaves the Delta as the key nursery area in non-wet years. Thus, the state of the Delta in non-wet years largely determines the success of Central Valley salmon. Salmon smolt production to the ocean is one to several orders of magnitude lower in drier years, which is the fundamental cause of salmon run declines over the past several decades during periods of drought (Figure 1).

Getting salmon fry to the Delta, successfully rearing them in the Delta, and then getting them to the Bay and Ocean are keys to their success. Peaks between droughts, and even small runs during droughts, are driven by trucking smolts from the hatcheries to the Bay and Ocean, bypassing the Delta survival sink. Without hatchery contributions, the underlying pattern for wild-natural salmon would show drastic declines during and after droughts. Improving Delta-derived smolt production is the key to improving the wild component of Central Valley salmon.

For nearly four decades, I have been promoting Delta salmon habitat improvements.1 I have also helped show the importance of winter rearing of salmon fry in the Delta.2 I have also conducted a comprehensive review of Delta salmon rearing habitats and restoration.3 In other posts in this blog, I have offered much discussion on the role of the Delta in salmon production and survival.

The State Water Resources Control Board is in a multi-year process of updating decades-old water quality standards. Focusing on salmon as a key public trust resource is the way to go. The new standards need to assure that fry get to the Delta, do well in the Delta, and then get to and through the Bay to the Ocean.

Figure 1. Over the past several decades the Central Valley fall-run Chinook salmon has declined sharply during and shortly after three major periods of drought: 1987-1992, 2007-2009, and 2013-2016. Source: CDFW Grandtab.

 

  1. Cannon , T. C. 1982. The importance of the Sacramento-San Joaquin estuary as a nursery area of young Chinook salmon. Unpublished NMFS report. ↩
  2. http://www.fisheryfoundation.org/Reports/2005-2006%20Western%20Delta%20seine%20survey%20report.pdf ↩
  3. https://calsport.org/news/wp-content/uploads/Overview-Habitat-Restoration-in-Delta-LowRes.pdf ↩

May-September Delta Water Temperature Standard Needed

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In a 9/22/20 post, I suggested summer Delta outflow standards. In this post I suggest a spring-summer water temperature standard for the Delta as further protection for salmon and smelt. Water temperatures above 23oC (73oF) are harmful to salmon and smelt, which live and migrate through the north and west Delta throughout the summer. Much of the Delta smelt population that remains is located in these regions especially in dry years.1 Spring-run and winter-run salmon migrate upstream through the area in late spring. Fall-run salmon migrate upriver through the summer.

Harm occurs as stress, higher predation, avoidance reactions, poor growth, and reduced long-term survival and reproduction. At higher temperatures (>23oC) migration blockage and mortality occurs. Such temperatures are commonly reached or exceeded in the north Delta even in wetter, water-abundant years.

High water temperatures occur in the Delta when there are high air temperatures and/or low freshwater inflow and outflow. Such conditions are becoming more frequent with climate change. A good example occurred in water year 2020, which featured low precipitation, low snowpack, and high air temperatures.2 Because water managers cannot control air temperatures or watershed precipitation, they must manage Delta inflows from reservoir releases and outflows through the Delta to improve water temperature control in May-September, especially in drier years.

To protect smelt and salmon, there need to be reasonable water temperature standards in the Delta. The existing water temperature standard in the lower Sacramento River above the Delta is 68oF, but managers of the state and federal water projects pay it almost no heed. There is no existing standard for the Delta. The north Delta water quality standard for the Sacramento channel in wet years should be 70oF (21oC) at Freeport and at Rio Vista. In normal and dry water years, the standard should be 72oF (22oC) at Freeport and at Rio Vista. In critical drought years, the State Water Board needs to require additional Delta inflow and curtail exports as needed to respond to extreme events (e.g., water temperatures greater than 75oF during heat waves). At critical times, a change of only a degree or two will help limit fish stress and mortality.

Higher Delta outflow and lower exports are appropriate prescriptions for maintaining reasonable water temperatures in the Delta (see Figures 1-3 and caption notes). For example, in July and August 2020 (Figures 1-3), increased inflow into the 14,000-16,000 cfs range from 12,000 cfs at Freeport could have held water temperature below 22oC. Note in Figure 3 that increased inflow can be captured by south Delta exports (Figure 3). However, during heat waves under extreme drought conditions, the State Board should also limit exports to retain outflows from the Delta to keep the low salinity zone out of the warmer Delta. Otherwise, exports will reduce the portion of Delta inflows (Freeport flows) that reach Rio Vista.

Such standards are achievable, albeit at significant water supply cost. They are worth the effort. High summer water temperatures, such as those that occurred in wet year 2019 and dry year 2020, must be mitigated. The 23-25oC conditions in summer 2020 (portrayed in Figures 1-3) should not occur, and would not under the suggested Delta water temperature standard. For wet years such as 2019 (Figure 4) and 2017 (Figure 5), water temperatures should be kept at or below 70oF (21oC) by maintaining Freeport near 20,000 cfs as needed.

In summary, Delta water quality standards should be adopted for inflow, outflow, and water temperature to protect salmon and smelt in the warmer months of the year, May-September. Such standards are needed because of recent changes in water project operations and the effects of climate change.

Figure 1. Water temperature and salinity in the west Delta near Rio Vista in spring-summer 2020. Note Delta draining in neap-tide periods generally brings warmer water downstream into the west Delta, except in mid-August event when a heat wave drove water temperatures up into 23-25oC range. This event was accentuated by higher exports and associated high Delta inflows.3

Figure 2. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of dry year 2020. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 3. Sacramento River flow at Freeport (FPT), water temperature at Rio Vista (RVB), and south Delta exports at Tracy (TRP) and Banks (HRO) pumping plants in south Delta from May-Oct 2020.

Figure 4. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of wet year 2019. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 5. Sacramento River flow at Freeport (FPT-Y1) and water temperature at Freeport (FPT-Y2) and Rio Vista (RVB-Y2) from May-Oct 2017.