Sacramento Valley Salmon Resiliency Strategy

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

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?

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.

And then there were none…


In late April and early May 2018, 20-mm Surveys collected no Delta smelt (Figure 1) in the San Francisco Bay-Delta estuary. It’s a new low for Delta smelt since the survey began in 1995, worse even than the 2017 survey catch (Figure 2). The outlook for the population as indexed by the summer and fall surveys looks grim after record lows from 2012-2017. Despite good conditions in spring 2018, the number of adult spawners was too low, indicating a weak recovery potential.

Figure 1. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2018. None were collected in surveys 4 and 5

Figure 2. Catch and lengths of Delta smelt collected in the 20-mm Survey in spring 2017.

Pacific Herring and Bay Productivity

In past posts I have focused on salmon, smelt, sturgeon, and striped bass, even zooplankton, but have yet to discuss Pacific herring. Pacific herring are the Bay-Delta estuary’s most abundant fish and like the other fishes previously mentioned also depend on the estuary for spawning, rearing, or migration. They also support an important commercial fishery in the Bay. 1

Herring larvae and juveniles are also important prey for young salmon and other estuarine and marine fish from winter into summer. Sub-adult and adult herring are key elements of the coastal marine food web of the northern Pacific, from California to Alaska. Herring populations of the northern Pacific, including the Bay’s population, have been generally managed by controlling harvests (usually with quotas or effort limits) and stock-fishery models.2 Like most fish stocks managed by harvest, the populations tend to become overfished with subsequent difficult recovery. The role of the environment in juvenile fish recruitment is often overlooked because it can be very complicated.

Unlike the freshwater spawning smelt, salmon, and sturgeon, herring spawn in coastal marine and estuarine bays including San Francisco Bay, and their larvae move upstream in winter with tidal and estuarine circulation into brackish waters to rear. Some larvae born in San Francisco Bay even drift with tides up into the Delta. Most rear in brackish waters of the North Bay (San Pablo and Suisun bays) feeding on estuarine plankton whose productivity is positively related to freshwater outflow from the Delta and coastal ocean upwelling (enhanced feeding from turbidity and nutrient driven plankton blooms3). When winter storms and associated pulses of freshwater into the Bay are generally common, Bay productivity in winter is generally dependable, as is herring production regardless of the water year type.

However, at some point herring and general Bay productivity will suffer (if not already) if larger portions of freshwater outflow to the Bay are stored in reservoirs or directly diverted for water supply, especially in drier water years. Proposed projects like California WaterFix (Delta Tunnels) and new storage reservoirs will do just that – take more of the water that would normally enter the Bay, especially in drier years with limited runoff to the Bay.

One potential clue about herring productivity is density patterns of larval herring in the winter during peak abundance. Figures 1-4 show February herring densities versus salinity concentration in four recent years of the Smelt Larval Survey. Figure 5 shows long-term trend in Pacific herring densities in April Bay midwater trawl survey. Taking into account biased-low catch in very wet years (1983, 1995, 1996, 1998, 1999), there is a clear downward trend, with very low catch in 2015-2016. With limited data like this it is hard to see real abundance patterns let alone factors that have led to observed differences. There are so many important factors acting together and independently, it is (and will) be hard to determine cause and effect.

Is the pattern in Figures 1-5 a start of a trend of lower densities and more near zero densities in certain areas of the estuary? More analyses and synthesis are needed to answer the question. More science in the form of studies and comprehensive surveys is needed if we are to understand the role of freshwater outflow to the Bay and coastal waters. Is freshwater outflow to the Bay being “wasted” at the expense of human endeavors, or is it a critical element of the coastal ecosystem productivity? I would guess the latter. Pacific herring would be a good ecological indicator or canary in the coal mine, as Delta smelt once were.

Figure 1. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2011, a wet water year.

Figure 2. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2012, a below normal water year.

Figure 3. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2014, a critically dry water year.

Figure 4. Density of Pacific herring in larval surveys of the Bay-Delta versus surface salinity in February 2018, a below normal water year.

Figure 5. Long term trend in Pacific herring average April catch per trawl in stations 100-500s in Bay in Bay midwater trawl survey.