Category Archives: Bay-Delta

More on the Delta Threat to Winter-Run Salmon – Fall 2021

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During early November, juvenile winter-run salmon were moving into the Delta after two short fall rainfall pulses (Figure 1). The allowed export of 65% of Delta inflow is not protective of these wild young winter-run salmon, which are in short supply this year. My October 30 post, in which I warned about the threat of rising Delta exports on this year’s production of juvenile winter-run salmon entering the Delta, is being borne out.

From November 9-12, south Delta exports exceeded 70% of Delta inflow,1 with about 2000 cfs of calculated Delta outflow. The USGS measurement of Delta outflow on November 8-9 was as low as -3000 cfs. Delta exports were simply drawing from the Delta’s freshwater reservoir supplied by the recent rains. The cries of San Joaquin Valley farmers for the capture of the runoff before it was “wasted” into the Bay and Ocean were indeed being answered. The Delta export pumps were shipping 15,000-20,000 acre-feet of water south each day.

Up at the Delta Cross Channel (open) and Georgianna Slough, over half the daily flow was being diverted into the central Delta. With the False River Barrier installed, most of the diverted water (and young salmon) flowed south toward the export pumps. Since no young salmon were showing up in the export fish salvage collections, it is likely that few successfully made the 50-mile journey from the northern Delta through the predator-laden central Delta corridor.

Hopefully, the several hundred thousand winter-run hatchery smolts will have better circumstances when they are released this winter near Redding for their 300-mile migration to the ocean.

Figure 1. Capture of juvenile winter run salmon in the lower Sacramento River in 2021.

Delta Smelt Status 2021

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The Enhanced Delta Smelt Monitoring (EDSM) caught only 1 Delta smelt in 2200 smelt-targeted net tows in 2021.  This compares to 49 captured in 2020 and hundreds in prior years.  None were captured in the Spring Kodiak Trawl 2021 survey (Figure 1).  This year’s results indicate that Delta smelt are likely virtually extinct in the wild.

Figure 1. Spring Kodiak Trawl survey index of Delta smelt (2004-2021), in which none were caught in 2021. Only one was captured in 2020. (source)

Longfin Smelt 2021

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In a 6/15/21 post, I had a grim outlook for longfin smelt for the summer of critical drought year 2021.  My concern has proven warranted.

The June Townet Survey (6/7-6/10) found longfin juveniles concentrated in the Sacramento River channel of the western Delta (Figure 1) in water temperatures of 19-21ºC (Figure 2), very close to stressful, low growth, poor survival conditions for longfin (>20ºC).  The area was within the low salinity zone, where juvenile smelt concentrate in spring.  In conditions of low Delta outflow in drought years like 2021, the low salinity zone encroaches into the western Delta, where the zone is prone to warming without the cooler Bay air temperatures.  The zone remained in the western Delta through the summer of 2021, with sustained water temperatures of 21-23ºC.

The September Midwater Trawl Survey collected only one longfin smelt, a minimum catch for that survey (Figure 3).  This catch total was similar to those observed in late summer of other drought years (07-08, 15, and 20).

A 2017 paper by UC Davis scientists concluded that extinction of Delta smelt and longfin smelt was not inevitable if the necessary recovery actions were soon implemented.  The paper’s recommended actions have as yet not been implemented, and conditions have even become worse in recent years, especially in the 2021 drought.  Delta smelt are now virtually extinct in the wild, with longfin smelt likely to follow soon.

Figure 1. Catch per unit effort of longfin smelt in survey #1 of CDFW/IEP Townet Survey in June 2021.

Figure 2. Water temperature in lower Sacramento River channel in western Delta in early June 2021.

 

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.