Category Archives: Bay-Delta

The Next Threat to Winter-Run Salmon – Rising Delta Exports

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A modest production of winter-run salmon fry was achieved in the Sacramento River near Redding this summer (Figure 1).1 With the recent storm that peaked on October 24, these young salmon are now moving down the river toward the Delta (Figure 2).

Upon entering the Delta, these young salmon face the grim fate of passing through the Delta Cross Channel (DCC)/and Georgiana Slough into the central and south Delta, where they are drawn to Delta pumps by sharply increased exports (Figure 3).

The diversion of Sacramento flows increases with the periodic opening of the Delta Cross Channel (Figure 4). On an outgoing tide, the diversion via the DCC and GS can be higher than 50% under these circumstances.

Once they enter the interior Delta, it is difficult for young salmon to navigate out to the Bay. Many are drawn with reverse net flows to the south Delta, especially in periods when the DCC is closed. The risks to salmon fry in Clifton Court Forebay (predation) and at fish facility screens are severe.

Closing the DCC during the flow pulse only increases flow through Georgiana Slough and traps any diverted salmon in the interior Delta. Keeping the DCC open minimizes the reverse flows in the interior Delta, but draws more salmon in. It is a tough call either way. So the best option for this first fall pulse of winter-run fry is to minimize exports. This type of protection has been considered many times in the past. It is currently required in the Incidental Take Permit (p. 80) for the operation of the State Water Project, but not until after December 1.

Figure 1. Passage of juvenile winter-run salmon past Red Bluff, September-October 2021.

Figure 2. Catch of winter-run fry in lower Sacramento River near Wilkins Slough (RM 120) in fall 2021.

Figure 3. Graphic depiction of Delta net flow (cfs) conditions in late October 2021.

Figure 4. Hourly flows through Delta Cross Channel in October, 2021.

The Delta – Where do we go from here?

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(Editor’s note: The opinions expressed in this post do not necessarily represent the positions of CSPA.)

The Delta is still here, albeit not what it used to be.  Yes, the Delta smelt are gone, the striped bass are at historic lows, and largemouth bass and bluegill abound.  Plankton densities are way down and their species-composition is highly altered.  Waters are warmer and saltier, and less turbid in dry-year summers.  Invasive aquatic plants are taking over.  Tidal flows now dominate over river inflows and Delta outflows.  Winter flushes still occur in odd years, but droughts predominate.  Climate change, heavy water use, and pollution have taken a toll.  But the Delta is still home to a vast array of native fish and other aquatic organisms, and remains a seasonal critical rearing and migrating habitat of endangered salmon, steelhead, sturgeon, lamprey, and smelt.  So what does the future have in store for the Delta, and how can we influence the outcome, especially for the aquatic ecosystem and its fish community?

To me, it has always been a simple solution involving the following array of strategic actions, although they are a very hard sale.  I have seen little progress and further damage to the Delta in my nearly 50 years working on the Delta issues, because of uncertainties and high costs, slow planning processes, and oh so many delays.

  1. Stop exporting from the south Delta. Most of the water supply comes in from the north, so why pull it through and export it from the south?  It has always been the main problem.
  2. Cut back on taking water from the Delta. Projects take a quarter of inflow and other users take another quarter or more (Figures 1 and 2).  In early June 2021, just 2000 cfs was reaching the Bay, out of 6000 cfs of Delta inflows.
  3. The Delta needs more inflow in most years. The Delta is too warm in summer (Figure 3), and now more prone to blue-green algae blooms.  Inflow from the San Joaquin is especially important to the Delta ecosystem.
  4. The Delta needs more nutrients to produce more plankton and benthos; it lacks nutrients because nutrients and aquatic productivity are exported/diverted and replaced by reservoir water that is very low in nutrients and productivity.
  5. The low salinity zone should be located west of the Delta in the cooler eastern Bay where it can be more productive – more outflow is needed. This is especially important in spring of dry years (Figure 4), when low outflow results in the low-salinity zone being located in the Delta.
  6. Invasive aquatic plants should be cut back as much as possible – this will help improve plankton, lesson water clarity, lower water temperature, and reduce habitat of non-native fishes.
  7. The biomass and productivity of non-native fishes should be reduced by whatever means possible.
  8. Pollutant inputs to the Delta should be minimized. Herbicides and pesticides and other pollutants inputs are too high.
  9. Ship-channel dredging and shoreline-shoal habitat degradation should be lessened.
  10. The tidal-prism should be increased with expansion of flow-through Delta tidal channels. Avoid shallow floodplain enhancements that increase water temperatures.
  11. Restore Delta channel riparian habitats to increase shoreline protection, provide shade, and increase aquatic and terrestrial food for fish.
  12. Release hatchery-raised delta smelt in optimal habitats in the Delta to reduce the imminent threat of their extinction.

There are more planning and restoration efforts today than 50 years ago.  So much more information is available.  It should not be this hard.

Figure 1. Delta outflow (DTO) plus major sources of Delta inflow in May-June 2021. Wilkins Slough (WLK) is contribution from upper Sacramento River system (mainly Shasta/Trinity reservoir water). Freeport is Sacramento channel in north Delta including Feather and American system reservoir inputs (total Sacramento Valley inputs minus its diversions). Vernalis (VNS) is San Joaquin Valley inputs to Delta. Flow through Georgianna Slough is water crossing over from Sacramento to San Joaquin channel including some from Delta tributaries (primarily Mokelumne River). In early June, only slightly over 2000 cfs was reaching the Bay out of slightly more than 6000 cfs of Delta inflows.

Figure 2. The major inputs and outputs from the Delta in summer 2021. DTO = Delta outflow. VNS = San Joaquin River inflow to Delta at Vernalis. FPT = Sacramento River inflow to Delta at Freeport.

Figure 3. Water temperatures in Delta plus Delta outflow in June-July 2021. FPT = Freeport. DLC = Delta Cross Channel. OH4 = Old River in central Delta.

Figure 4. Salinity (specific conductance or EC) in the western Delta near Jersey Point 2014-2021. Note three April-July periods highlighted in drought years 2014, 2015, and 2021.

Addendum to the State Drought Plan — August 31, 2021, Part 1: the Art of the Euphemism

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The California Department of Water Resources (DWR) and the U.S. Bureau of Reclamation (Reclamation) released a Central Valley Drought Contingency Plan Update on August 31, 2021, stating:: “Project operations are still tracking with the operations forecast included in the July Drought Plan addendum. August has been fairly typical, with operations primarily controlled by system-wide depletions and Delta salinity.”  This is like a dispatch from the captain of the Titanic saying: the ship was tracking course since the last report, and yes, it hit the iceberg.  As is fairly typical under such circumstances, it sunk, primarily due to the hole in the hull.

The “depletions” that caused the current gaping hole in Shasta Reservoir’s storage and the resulting lethal downstream water temperatures, to reach full effect in September, didn’t just happen.  These glibly described “depletions” are primarily the excessive deliveries to Sacramento River Settlement Contractors to which this blog, CSPA, and others have been vociferously objecting since March.  And, of course, what is sunk is not the good ship Reclamation.  It is the year’s cohorts of Sacramento River salmon, just like in the disasters of 2014 and 2015.

Shasta-Keswick Storage Releases to the Upper Sacramento River

In 2021, Reclamation has not heeded the lessons learned in the 2013-2015 drought.  In 2021, Reclamation has not even implemented the feeble salmon-saving drought actions it applied in 2014 and 2015.

  1. April-May Keswick storage releases were higher in 2021 than 2014 (+257 TAF) and 2015 (+185 TAF) (Figure 1). Reclamation restricted releases in 2014 and 2015 in April-May to preserve Shasta’s cold-water pool.  It did no such thing in 2021.
  2. The higher releases in 2021 led to depleted storage in Shasta Reservoir (Figure 2). Storage at the end of May 2021 was 200 TAF lower than in May 2014, after having been 200 TAF higher at the beginning of April.
  3. The measures to maintain steady flow/stage and water temperature prescribed for drought year 2015 were not applied in 2021. In 2021 operations reverted to the 2014 regime, or worse.

Spawning Conditions for Winter Run Salmon

Winter-run salmon spawn from April to August, with a June-July peak in the ten miles of river downstream of Keswick Dam.  Early season (April-May) flow and water temperature conditions were erratic in 2014, 2015, and 2021 (Figures 1-4).  Rising flows and water temperatures stimulate the spawning migration and maturation leading up to the spawn.  Water temperature above 65ºF hinder migrations and stress adult spawners.  Water temperatures above 60ºF delay spawning and stress eggs in female salmon and eggs/embryos in redds.

  1. Conditions in 2014 proved devastating for the salmon spawn because of high water temperatures in late summer as Reclamation lost access to Shasta’s cold-water pool due to low storage. In addition,  a late summer drop of 2-3 feet in the stage height of the Sacramento River downstream of Keswick Dam caused spawning interruption and redd stranding (Figure 3).
  2. Despite concerted efforts in 2015 to retain storage, to maintain steady flows (and stage), and to sustain colder water releases, water temperature proved too high (>55ºF) for good egg/embryo survival. The lesson learned led to the current target for good survival of <53ºF in Keswick releases.
  3. Operations in 2021 were devastating, starting with high spring water temperatures, followed by a short period of good conditions in late June designed to stimulate spawning, before higher water temperature (Figure 4) and falling stage height greeted later winter-run spawners and egg/embryos/fry in redds.

Migration Conditions for Adult Salmon in Lower Sacramento River

Water temperatures in the lower Sacramento River 100-200 miles downstream of Shasta Dam remained far from typical in 2021 (Figure 5).  For the most part, water temperature from May through August were above the minimum stress level of 68ºF, and above the 72ºF avoidance level for weeks at a time.  These conditions not only affected the late migration of winter-run salmon, but also that of the spring-run (in spring) and fall-run (in summer) who spawn in early fall.

Summary

In summary, Reclamation’s operations of Shasta Reservoir have been as bad in 2021 as they were in 2014 and 2015, or worse.

Future posts will discuss more aspects of the failures of Reclamation’s Shasta operations in 2021.

Figure 1. Water releases from Keswick Dam (river mile 300) to the lower Sacramento River near Redding CA, April-August 2014, 2015, and 2021.

Figure 2. Shasta Reservoir storage (acre-feet) April-August in 2014, 2015, and 2021.

Figure 3. River Stage in Sacramento River below Keswick Dam April-August in 2014, 2015, and 2021.

Figure 4. Water temperature in Sacramento River below Keswick Dam April-August 2014, 2015, and 2021.

Figure 5. Water temperature in the lower Sacramento River at Wilkins Slough (river mile 120) May-August 2021, along with average for past 13 years. Note that the State’s year-round water quality standard for the lower Sacramento River is for water temperature to remain below 68ºF.

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

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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

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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.