Category Archives: Bay-Delta

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.

July-Aug 2020 Delta Outflow – New State Standard Needed

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The State’s Delta outflow standard for July and August varies from 3000 to 8000 cfs on a 14-day average. The standard in in the drier years is 3000 cfs. The standard in wetter years is 8000 cfs in July and 4000 cfs in August.

These standards have been met for the most part over the past five years (Figure 1). Outflow was greater in 2017 and 2019 than these numeric outflow standards since the State also had to meet the Delta salinity standard that in wet years extends into August. The outflow standard in August 2015 (3000 cfs) was not met under a State Board emergency order in the third year of drought.

The July and August Delta outflow standard should be a 10,000 cfs minimum daily average tidal flow at Rio Vista in the Sacramento River (Figure 2) and 2000 cfs minimum daily average tidal flow at Jersey Point in the San Joaquin River (Figure 3). In addition, a standard of -2000 cfs in False River (Figure 4) is needed to protect endangered smelt and salmon, as well as to protect water quality in the central Delta.1

Standards should also be set to protect against extreme events and circumstances. An example is salt intrusion and high water temperatures in the Delta, such as occurred in a heat wave in mid-August 2020 (Figure 5 and 6). Water temperatures of 23-25oC in the low salinity zone (500-6000 micro-mhos conductivity) are rare and highly detrimental if not lethal to smelt and salmon. Delta exports were raised from 6,000 cfs to 10,000 cfs from 8/10 to 8/22. Delta inflows were raised 4000 cfs during the period to accommodate increased exports (Figure 7). The increasing inflows helped bring warm water from the interior Central Valley into the Delta (Figure 8).

Such conditions should be avoided at all costs. This can be achieved by limiting exports, reservoir releases, or both. August is a peak month of the fall-run salmon migration into the Sacramento Valley. Such high water temperatures would be lethal or avoided with the run being delayed and salmon holding in the Bay. The Delta smelt population concentrates primarily in the low salinity zone, and water temperatures higher than 25oC are lethal to Delta smelt.

I acknowledge the difficulty in meeting these proposed standards, especially in drier years, but they must be adopted to protect the salmon and smelt. New standards are essential for the Delta’s recovery.

Figure 1. Delta outflow in summer of years 2015-2020. Note difference in August between wet (2017, 2019) and drier (2015, 2016, 2018, 2020) years.

Figure 2. Daily average (tidally filtered) flow in the Sacramento River channel at Rio Vista in the north Delta in summer 2020 and average of last 22 years.

Figure 3. Daily average (tidally filtered) flow in the San Joaquin River channel at Jersey Point in the west Delta in summer 2020 and average of last 22 years.

Figure 4. Daily average (tidally filtered) flow in the False River channel in the west Delta in summer 2020 and average of last 22 years.

Figure 5. Water temperature and salinity (specific conductance) at Jersey Pt in the San Joaquin channel of the west Delta in summer 2020.

Figure 6. Water temperature and salinity (specific conductance) at Decker Is in the Sacramento River channel of the west Delta in summer 2020.

Figure 7. Daily average flow in the Sacramento Rivers channel in the north Delta near Freeport in July-August 2020. Note the flow pulse in late August from reservoir releases to meet Delta export increase.

Figure 8. Hourly water temperature of the Sacramento River at Rio Vista in July-August 2020.

  1. A tide gate on False River would help accomplish this objective. ↩