Category Archives: Bay-Delta

The Future Potential of San Joaquin River Salmon

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In an August 21 blog post, Dr. Peter Moyle described recent Delta fish science and the future of San Joaquin River salmon.  Dr. Moyle summarized five papers with relevance to the Central Valley.  Below, I comment on the discussion on the San Joaquin smolt salmon tagging study.

The first bullet point in Dr. Moyle’s blog post reads:  “Flows do not improve San Joaquin salmon survival but salvage does.”  He then makes observations, shown below in italics.

  •  “The study nevertheless shows that juvenile Chinook from the San Joaquin region are not surviving passage through the south Delta and that increased flows are not likely to increase their survival.” Comment: It is generally true that juvenile San Joaquin Chinook are not surviving passage.  However, the conclusion that increased flows are unlikely to increase survival is based on a series of six years with mostly low flows and one wet year, 2011, a year with record exports.  There is no doubt that San Joaquin salmon do better in wetter years.1  The survival of the relatively small number of radio-tagged hatchery smolts in the cited study was low because south Delta exports minimize the ability of smolts to escape the San Joaquin side of the Delta.  Most of the San Joaquin water (and salmon) goes to the export pumps.  Once there, putting the smolts in a taxi to the Bay does obviously help them escape the Delta.  Moyle fails to note that San Joaquin salmon are “ocean type”, meaning they move to the Delta often as fry or fingerlings, and rear in the Bay-Delta before moving to the ocean.  These fry/fingerlings were not included in the study and most certainly benefit from higher winter flows.
  • “Large-scale improvement of habitat in the south and central Delta is likely the key to improved survival, as shown by higher survival rates of fish from the Sacramento River that pass through the north Delta.” Comment:  Yes, if he means flow-habitat improvements by eliminating south Delta exports and improving positive flows.  Physical habitat improvements in the central and south Delta will not help without sufficient winter inflows to carry young salmon downstream to the Delta and to stop misdirected movement toward the export pumps if young salmon reach the Delta.
  • “The basic results showed such low survival of salmon passing through the Delta that returning adults would be too few to sustain the salmon populations in the San Joaquin basin.” Comment:  San Joaquin salmon do well in wet years. 1   Under current water operations in most years, river and Delta survival is low because most of the watershed’s water is diverted, held in reservoirs, or exported from the Delta.
  • The study indicates that the lack of decent habitat for juvenile salmon in the Delta means that most are picked off by predators (as shown in part by tagged fish moving in the wrong direction because the tags are in the stomachs of predators). Comment:  No, these were smolts, not smaller juveniles, and they were trying to find the ocean, not decent habitat.  They had to spend too much time trying to find the escape route from the Delta.  Eventually, they succumbed to a wide range of stressors.
  • “Essentially, fall-run Chinook populations in the San Joaquin basin are being sustained by straying hatchery fish from the Sacramento River system.” Comment:  All Central Valley salmon fall-run salmon populations are sustained directly or indirectly by hatcheries.  The San Joaquin has its own hatcheries whose smolts also benefit from higher flows. 3 While gene flow among the populations has been high, it does not preclude individual populations from developing river/watershed-specific characteristics through natural selection.
  • “How badly do we want to restore self-sustaining salmon runs to the San Joaquin and its tributaries? This question has to be asked in the context of future scenarios of climate change with increasingly variable conditions and likely permanent flooding of Delta islands.” Comment:  Moyle seems to suggest that restoring “self-sustaining” San Joaquin runs may not be worth the effort.  While “self-sustaining” may be very difficult to achieve for all Central Valley salmon populations given all the dams, loss of habitat, and water diversions, a balance of “wild” and hatchery salmon (and dependent fisheries) has been possible and will be so in the future if water resources are shared as required by federal and state laws.

  1. Salmon production is on average ten times better in wetter years. http://calsport.org/fisheriesblog/?p=1518 ↩
  2. Salmon production is on average ten times better in wetter years. http://calsport.org/fisheriesblog/?p=1518 ↩
  3.  http://calsport.org/fisheriesblog/?p=1403 ↩

Delta Smelt Summer 2018

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After catching over 800 Delta smelt in 2011 (Figure 1) and near 30 in 2017 (Figure 2), the Summer Townet Survey captured only 3 in 2018 (Figure 3). The pattern is consistent with the spring 20-mm Survey collections

The only option now other than extinction is stocking hatchery smelt in large numbers in their primary summer-fall habitat, the Low Salinity Zone of the Bay-Delta. Release should be near the 2 ppt (3800 EC) location, commonly referred to as X2, which recently has been moving tidally back and forth between Collinsville and Sherman Island in the Sacramento River channel just downstream of the Emmaton gage (Figures 4 and 5). The X2 location has optimum salinity, water temperatures (<70oF), turbidity, and food for Delta smelt.

Figure 1. Summer Townet collections of Delta smelt 2011.

Figure 2. Summer Townet collections of Delta smelt 2017.

Figure 3. Summer Townet collections of Delta smelt 2018.

Figure 4. Water temperature at Emmaton late August 2018. High tide X2 water is 68-69oF.

Figure 5. Salinity (EC) at Emmaton late August 2018. High tide water is near X2 salinity (3800 EC).

Sacramento Valley Salmon Resiliency Strategy

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The Sacramento Valley Salmon Resiliency Strategy, June 2017, is the state’s strategy to improve the resilience of listed salmon to its activities, including water rights permits, State Water Project actions, CESA implementation, and CDFW management.

The document states on page 2:

Specific biological objectives have been identified for the Sacramento River that support the general need to increase survival and productivity of salmonids in the Sacramento Valley and to increase life history and genetic diversity. A summary of these biological objectives:

  1. Increase productivity by improving spawning and incubation conditions (habitat and water quality).
  2. Increase productivity by increasing juvenile salmonid survival.
  3. Support the full range of juvenile migration conditions to maintain life history diversity.
  4. Support the full range of adult migration conditions to maintain life history diversity.
  5. Maintain genetic integrity by limiting genetic influence from hatchery-produced fish and interbreeding of genetically or behaviorally distinct runs.

The Strategy is an aggressive approach to improving species viability and resiliency by implementing specific habitat restoration actions. (Emphasis and bullet numbering added)

The Strategy is defined as a “resiliency” strategy and not a recovery strategy for a reason. It does not include the actions necessary for recovery. It won’t fix the activities that caused the crisis in the first place. Over the past several decades, much restoration has occurred, yet fish populations continue to decline. Much stronger and more immediate management actions are needed to save the salmon populations. Habitat restoration alone will simply not suffice.

So what is missing?

  1. Spawning and incubation conditions – Missing are actions to maintain cold water temperatures and sufficient spawning flows in the reaches below all the major dams during spawning and incubation. A. Eliminate the water temperature increases caused when water from Whiskeytown Reservoir is routed through Spring Creek Powerhouse to Keswick Reservoir. B. Maintain cold water in the Sacramento River downstream to Red Bluff, not just to Redding. C. Eliminate dewatering of winter, spring, and fall–run salmon redds in the Sacramento River. D. For the American and Feather rivers, take actions similar to A through C that maintain cold water and eliminate redd stranding. E. Better manage reservoirs to place more emphasis on cold water pools and less on water deliveries.
  2. Juvenile salmon survival – Maintain adequate flows and water temperatures in rearing reaches to sustain growth and to reduce stress and predation.
  3. Full range of juvenile migration conditions – Maintain adequate flows and water temperatures in the lower rivers and the Delta throughout emigration seasons. Do not shave off early and late seasons.
  4. Adult migrations – Maintain adequate flows and water temperatures to assure adult survival, egg survival and gonad development during migration. Do not shave off early and late seasons.
  5. Genetic integrity – Move more toward conservation hatchery activities, reduce straying by barging smolts, implement natural floodplain rearing, mark all hatchery smolts, and introduce mark-selective recreational fisheries.

As for other planned actions like completing projects on Battle Creek and reintroducing salmon upstream of Central Valley rim reservoirs, let’s get on with it. If we keep the present snail’s pace, there is little hope for future salmon generations.

Sacramento River Low Flows and High Water Temperatures Violate State Standards for lower Sac River and Delta - Lethal for Salmon and Smelt

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Low flows in the lower Sacramento River above the Feather River and warm flows from the Feather River are compromising the summer habitat of smelt and salmon in the lower Sacramento River and the Delta, violating state and federal water quality standards.

Lower Sacramento River at Wilkins Slough

The Sacramento River at Wilkins Slough at river mile 118, 63 miles upstream of the Sacramento Delta, has low flows and high water temperatures (Figure 1).  The high water temperatures are a violation of the 68oF (average daily) water quality standard and are stressful to migrating salmon.

Lower Sacramento River at Verona below mouth of Feather River

The lower Sacramento River 50 miles downstream of Wilkins Slough at Verona, just downstream of the mouth of the Feather River, has near lethal water temperatures, far above the water quality standard (Figure 2).  The high temperatures are likely due in part to recent increased releases from Oroville Reservoir to lower water levels for the spillway repair project.

Lower Sacramento River in Delta

The lower Sacramento River at Freeport in the north Delta, 25 miles downstream of Verona, has near lethal water temperatures for Delta smelt (Figure 3).   The high temperatures are likely due in part to recent increased releases from Oroville Reservoir to lower water levels for the spillway repair project.  The north Delta water temperatures are also high in part due to lower than normal net river flow (as measured at Rio Vista 20 miles downstream of Freeport – Figure 4).  The low flows have also led to encroaching salinity at Emmaton several miles downstream of Rio Vista (Figure 5), also in violation of water quality standards.

Figure 1. Sacramento River at Wilkins Slough flow and water temperature in May-June 2018. The water temperature standard for the lower Sacramento River is 20°C (68°F).

Figure 2. Sacramento River at Verona water temperature 6/15-6/26, 2018. The water temperature standard for the lower Sacramento River is 20°C (68°F).

Figure 3. Sacramento River at Freeport water temperature 6/15-6/26, 2018. The water temperatures above 72°F are stressful to Delta smelt.

Figure 4. Rio Vista daily average historical and 2018 flow May-June.

Figure 5. Salinity (EC) at Emmaton near Rio Vista. The standard of 450 EC (uS/cm) was exceeded from 6/15 to 6/18, 2018. The standard is necessary to keep the low salinity zone, critical habitat for Delta smelt. west of the Delta.

Enhancing Pelagic Habitat Productivity in the North Delta Is it too late to save the Delta smelt?

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The Bureau of Reclamation recently released an Environmental Assessment for the Sacramento Deep Water Ship Channel Nutrient Enrichment Project. The proposed project would directly release nitrogen nutrients into the Ship Channel, which runs from West Sacramento to Cache Slough, north of Rio Vista.  The project is designed to stimulate plankton blooms in the North Delta as part of the Delta Smelt Resilience Strategy, which describes the goal as follows:

The purpose is to determine if the addition of nitrogen can stimulate plankton (fish food organisms) production in a section of the ship channel, which is isolated from the Delta in terms of water flow.

Adding nitrogen to the ship channel will indeed stimulate plankton productivity.  Only a few miles away, regional governments have spent decades in removing nitrogen (most recently, ammonia) from the effluent of the Sacramento Regional Wastewater Treatment Plant to reduce production of blue-green algae in the Delta.  The City of West Sacramento already seasonally releases high nutrients, metals, and salts into the Ship Channel.  Adding more nitrogen could easily increase toxic blue-green algae problems in the Delta, similar to the bloom that recently led to the recreational closure of southern California’s Diamond Valley Reservoir, which receives Delta water.

There is higher plankton productivity in the Ship Channel than in nearby Delta channels because the Ship Channel has longer residence time, higher nutrients,  and higher water temperatures.  The broken gate on the Ship Channel’s northern entrance contributes to these conditions.  However, lack of circulation also leads to nitrogen depletion and declining plankton production, and there is limited seasonal replenishment of nitrogen.

The Delta Smelt Resilience Strategy is considering increasing flows into the north Delta from the Colusa Basin Drain, Fremont Weir, and the Ship Channel to stimulate Delta plankton blooms.  The biggest problem with these sources is high spring-through-fall water temperatures (Figures 1-3).  Water temperature is certainly the greatest limiting factor in the north Delta for Delta smelt; adding nitrogen will not fix this problem.

Fixing the gate at the north end and allowing cooler Sacramento River water (strong American River influence) into the channel (Figure 4) would reduce water temperatures in the Ship Channel.  Just a few degrees can be life or death for Delta smelt.  Increased entry into the Ship Channel of Sacramento River water would also introduce more nitrogen, potentially reducing the need to fertilize the Ship Channel with crop dusters.

Figure 1. Water temperature in the Yolo Bypass downstream of the entrance of the Colusa Basin Drain.

Figure 2. Water temperature in the Sacramento River Deep Water Ship Channel.

Figure 3. Water temperature in the lower Yolo Bypass toe drain canal near Liberty Island.

Figure 4. Water temperature in the Sacramento River near Freeport downstream of the entrance to the Sacramento River Deep Water Shipp Channel.