Low Delta Outflow Not Keeping Bay Salt Water out of the Delta

Low Delta outflows at the beginning of summer 2021 (Figure 1) are not adequately keeping brackish Bay water out of the west Delta (Figures 2-4). One reason salt is intruding is the high “spring” tides (Figure 5). Another factor is the State Water Board’s Order granting a Temporary Urgency Change Petition (TUCP) to the Department of Water Resources (DWR) and the Bureau of Reclamation. The Order allowed the installation of the False River Barrier in early June that helps force freshwater Delta inflow from the Sacramento and San Joaquin rivers to the south Delta pumping plants. It also allows lower summer Delta outflows and weaker salinity standards in this critical water year. The normal critical summer outflow criteria is a monthly average 4000 cfs. The outflow requirement was reduced to 3000 cfs. The normal salinity standards for a critical dry year are 14-day-average 2.78 EC at Emmaton and 2.2 EC at Jersey Point. The Emmaton compliance point was moved upstream to Three Mile Slough. Even at the upstream compliance point, the criteria limit has been exceeded (see Figure 2).

In the 2014 and 2015 drought years, Delta smelt almost disappeared entirely when the State Water Board granted a series of TUCPs that moved the salinity compliance points in the Delta upstream. Delta smelt have in no sense recovered.1 In the 2021 TUCP, DWR and Reclamation were unable to show the recent distribution of Delta smelt in the Delta: there are too few Delta smelt left to meaningfully count.

Figure 1. Daily average Delta outflow during June 2021.


Figure 2. Salinity (EC, mean daily) at Three Mile Slough near Rio Vista during June 2021.

Figure 3. Salinity (EC) and water temperature (C) in the lower Sacramento River channel near Emmaton during June 2021. Note spring/neap tide effects with warmer, fresher water draining the Delta on neap tides.

Figure 4. Salinity (EC) in the lower San Joaquin River channel near Jersey Point in the west Delta during June 2021.

Figure 5. River stage in the lower Sacramento River channel near Rio Vista in the west Delta during June 2021.

  1. See for example https://calsport.org/fisheriesblog/?p=2709. This blog (see the “Smelt” tab to the right) has chronicled the catastrophic decline of Delta smelt since 2015.

Hatchery Delta Smelt 2021

Efforts continue to gain approval for releasing hatchery-raised delta smelt in the San Francisco Bay-Delta Estuary. However, given a poor prognosis for a successful introduction, the chances of approval are not good.1  The biggest obstacle is the absence of a location to release the hatchery-raised fish that will allow their survival and thus contribute to the species’ recovery. Another problem is the potential detrimental effect on the remaining wild smelt from genetic compromise.

To me, the answer to the second issue is clear. With few if any “wild” delta smelt left on Earth, it is essential to get as many hatchery smelt out into the wild as soon as possible to save the species. Let the genetics get worked out later by Mother Nature.

Two locations for release of hatchery smelt seem most plausible: the low salinity zone in the west Delta/eastern Suisun Bay and the Deep-Water Shipping Channel in the north Delta. These are primary late spring and early summer nursery areas that are most likely to have the right habitat conditions (water temperature and low salinity) and food supply. These two locations were the last known concentrations of juvenile delta smelt (Figure 1) from the last strong adult spawn in 2012 (Figure 2).

The better of the two sites is the eastern-Bay/west-Delta location, because the ship-channel gets too warm by summer (Figure 3). In contrast, the region between Collinsville in eastern Suisun Bay and Decker Island in the west Delta is cooler and within the low salinity zone (Figures 4 and 5). A nighttime near-bottom release into cooler, deeper channel waters would give the hatchery smelt at least a minimum opportunity to acclimate to the warm Bay-Delta waters.2

Figure 1. Last known prime late spring and early summer nursery area of delta smelt (2012, 20-mm survey). Red lines denote approximate location of X2 (~2000-4000 EC) at the time.

Figure 2. Adult delta smelt catch index from monthly winter trawl surveys 2002-2021.

Figure 3. Water temperature (ºC) and salinity (EC) in spring 2020 in Deep Water Ship Channel.

Figure 4. Water temperature (C) and salinity (EC) in spring 2021 in Sacramento River channel near Collinsville in eastern Suisun Bay.

Figure 5. Water temperature (ºC) and salinity (EC) in spring 2021 in Sacramento River channel near Decker Island in the western Delta.

Drastic Measure to Meet Delta Outflow

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

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

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.