Author Archives: Tom Cannon

Saving Shasta, Trinity and Klamath Salmon in 2016

Posted on by

Salmon in the Sacramento, Klamath, and Trinity rivers depend on maintaining cold water releases from Shasta and Trinity reservoirs through the summer and early fall. Major die-offs of salmon on the lower Klamath and lower Sacramento below Shasta have occurred under conditions of low flows and high water temperatures. In summer and fall of dry years, flows and water temperature cannot be maintained if there is too little reservoir storage, especially the cold-water portion in the bottom of the reservoirs.

The biggest overall threat is that one of the reservoirs will run out of cold water in September and October when salmon eggs and embryos are in the gravel spawning beds in the rivers. For Winter Run salmon in the Sacramento, eggs are in the gravel from June through August. For Klamath-Trinity and Sacramento Spring Run salmon, eggs are in the gravel beginning in September or October; Fall Run eggs in each river are in the gravel beginning in November. In addition to the high water temperatures that can kill any of the eggs, flow reductions in the Sacramento in September and October can also dewater spawning beds after initial spawning in higher flows has occurred.

Government agencies have typically blamed large scale mortality events on the more than a decade-long series of droughts and competition between irrigation demands and water for salmon. But better water management of the Shasta and Trinity divisions of the Central Valley Project by the Bureau of Reclamation and other federal and state agencies can reduce mortality. Massive salmon die-offs in the Klamath, such as the one that occurred in 2002, have been avoided by targeted late summer and early fall cold-water releases from Trinity Reservoir during the past two multiyear droughts. However, failures of the 2014 and 2015 Winter Run broods below Shasta on the Sacramento River were not avoided.

Salmon runs continue to decline during droughts, with hatcheries making up a greater proportion of the runs in both river systems. On the Trinity, wild Spring and Fall Run salmon are at only 32% and 17%, respectively, of restoration program goals.1 All the Sacramento runs are down, especially the Winter Run, and prognosis for future years is poor based on broodyear failure the past two years. Ocean stocks of Klamath-Trinity and Central Valley salmon are also down this year, which will likely lead to severe sport and commercial fishery restrictions.2

So what measures are in the works for 2016 for protecting salmon? Depending on what precipitation falls in the remainder of winter and this spring, there has been speculation of further restrictions on irrigation deliveries and water supplies, and the allocation of more colder water below the dams for salmon.

In addition to the many actions I identified in previous posts,3 there are several further options that should be considered for 2016 to benefit salmon:

  1. The Klamath-Trinity system should get more emphasis because of potential risks to its salmon, and because it has not fared as well as the Sacramento system in the latest multiyear drought. Shasta Reservoir has reached 60% of capacity as of 1 March (Figure 1). Trinity Reservoir has reached only 40% (Figure 2). This summer, less water could be delivered to the Sacramento River from Trinity Reservoir via Whiskeytown Reservoir to the Sacramento River below Shasta Reservoir than last summer (Figure 3). Water delivered through Whiskeytown is warmer than water delivered from Shasta; reducing deliveries through Whiskeytown would thus save Trinity storage and the cold-water pool supplies in both Trinity and Shasta reservoirs.
  2. Increasing the relative contribution of Trinity Reservoir to the Sacramento River in April and May (and reducing the summer contribution) would save the cold-water pool supplies in both Trinity and Shasta reservoirs. April-May releases from Whiskeytown Reservoir to the Sacramento River below Shasta are colder (<53°F) than the summer releases (58-59°F) (Figure 4) that threaten Winter Run salmon.
  3. Reducing hydropeaking power production during summer would reduce the demands on the cold-water pools. Much of the water released from Shasta, Trinity, and Whiskeytown reservoirs in summer is released in the hot afternoon hours for hydropower production peak demands, leading to warmer waters in Keswick and Lewiston reservoirs. To ensure water that released from these two reservoirs is not too warm for salmon in the rivers below, Bureau of Reclamation operators should optimize daily water deliveries through powerhouses for water temperatures rather than for the value of power.
Figure 1. Shasta Reservoir storage March 2014 to March 2016. (Capacity is 4,552,000 AF.)

Figure 1. Shasta Reservoir storage March 2014 to March 2016. (Capacity is 4,552,000 AF.)

Figure 2. Trinity Reservoir storage March 2014 to March 2016. (Capacity is 2,447,650 AF.)

Figure 2. Trinity Reservoir storage March 2014 to March 2016. (Capacity is 2,447,650 AF.)

Figure 3. Water deliveries to Whiskeytown Reservoir from Trinity Reservoir via Lewiston Reservoir outlet to Carr powerhouse March 2014 to March 2015. Water then proceeds to Keswick Reservoir immediately below Shasta Reservoir on the Sacramento River. Approximately 100-200 cfs of these flows is also released to Clear Creek, which flows into the Sacramento River below Redding.

Figure 3. Water deliveries to Whiskeytown Reservoir from Trinity Reservoir via Lewiston Reservoir outlet to Carr powerhouse March 2014 to March 2016. Water then proceeds to Keswick Reservoir immediately below Shasta Reservoir on the Sacramento River. Approximately 100-200 cfs of these flows is also released to Clear Creek, which flows into the Sacramento River below Redding.

Figure 4. Water temperature in Spring Creek Powerhouse June to September 2015.

Figure 4. Water temperature in Spring Creek Powerhouse June to September 2015.

Spring Run Salmon Restoration in San Joaquin River – Some Questions

Posted on by
Pilot study release of Feather River hatchery smolts at the Golden Gate. (DFW photo)

Pilot study release of Feather River hatchery smolts at the Golden Gate. (DFW photo)

50,000 Spring Run Chinook smolts from the Feather River Hatchery will soon be released into the San Joaquin River near Merced, as was the case in 2014 and 2015. The action is part of the effort to restore Spring Run to the lower San Joaquin below Friant Dam near Fresno. The smolts each have a coded-wire tag in their nose and an adipose fin clip so their survival can be monitored.

So how have the first two releases fared? Were any collected in Delta surveys, at south Delta pump salvage facilities, in Chipps Island trawls, ocean fisheries, spawning surveys? Data available now from these surveys should be providing early indications of success rates for comparison with other restoration programs. After all, it is an adaptive management program.

Given that the last three years have been dry years especially in the San Joaquin, I do not hold out much hope for the survival of these three years of smolt releases. I hope I am wrong, but information is lacking on the first two releases. Did any make it down the river to the South Delta pumps? Did any make it to the Bay (Chipps Island trawls)?

If not, then some adjustments should be made this year.

  1. Hatchery trucks from Fresno could travel further downstream to the Delta or Bay.
  2. Smolts could be barged from Merced or Stockton to the Golden Gate (see photo above).1

At a minimum, some early indicators would help us all see some progress for the program and deflect the naysayers who would write off the whole program.2

An Opportunity Missed?

Posted on by

The U.S. Fish and Wildlife Service has released 400,000 Winter-Run Chinook salmon smolts from the Livingston Stone Fish Hatchery into the Sacramento River near Redding. But according to the US Fish and Wildlife Service’s Steve Martarano, “The release won’t occur until we see a significant increase in density and flow in the Sacramento River. It’s based on a rain event.” 1

Last year Reclamation released some water from Shasta for the “event” (Figure 1). This year there was no such an “event” (Keswick release) (Figure 2). The real question is whether they missed the “real” flow event in January (Figure 3) when storm flows from Cow, Cottonwood, and Battle Creeks downstream of Redding brought flows near Red Bluff to 10,000-40,000 cfs. Why didn’t Reclamation and the Service coordinate release of water from Keswick and the salmon smolts at Redding in late January? Shasta inflows in January reached 40,000 cfs.(Figure 4.) Such a release would have also helped the wild salmon emigrate from their spawning reach at Redding to San Francisco Bay and the Ocean.

Keswick Reservoir releases into the upper Sacramento River near Redding in winter 2015

Figure 1. Keswick Reservoir releases into the upper Sacramento River near Redding in winter 2015.

Keswick Reservoir releases into the upper Sacramento River near Redding in winter 2016

Figure 2. Keswick Reservoir releases into the upper Sacramento River near Redding in winter 2016.

Upper Sacramento River flow near Red Bluff winter 2016

Figure 3. Upper Sacramento River flow near Red Bluff winter 2016.

Shasta Reservoir inflow during January storms

Figure 4. Shasta Reservoir inflow during January storms.

February Delta Smelt Update

Posted on by

The February trawl survey indices are in – there are a few Delta Smelt left (Figure 1).

The Smelt Working Group, created as prescribed in the Smelt Biological Opinion issued by the US Fish and Wildlife Service (in the Department of Interior), has stated following its meetings on February 15 and 22: “The fact that sporadic Delta Smelt catches have continued to occur at Prisoners Point under the lowest February SKT survey on record indicates that the risk of entrainment remains high and is incompatible with current pumping levels.” 1

After its February 22 meeting, the Working Group added: “Salvage: Four delta smelt on February18, geographic influence of the pumps extends to the lower San Joaquin River at the more negative end of this flow range, especially affecting the southern bank near Jersey Point. Recent salvage of adult Delta Smelt confirms that entrainment into the export facilities has occurred and likely is continuing…. The Working Group concluded that any salvage observed at either facility will be of high concern because Delta Smelt abundance is at a historic low, contributing to low detection probability of Delta Smelt in salvage under RPA compliant operations (BiOp page 338). One fish was detected in salvage sampling on January 21 and February 18, counting as eight salvaged Delta Smelt due to an expansion factor of four.”

Following these meetings, the US Bureau of Reclamation (also in the Department of Interior), which operates the federal export pumps in the South Delta, exported more than double the recommendation of the Smelt Working Group. Together the state and federal exports were nearly triple the recommended amount (<2000 cfs). This situation, where the state and federal experts in the Smelt Working Group were ignored by their managers, who instead maximized Delta exports in February, is a gross violation of the intent of the state and federal endangered species acts and species protections in the biological opinion. Graph of Kodiak Trawl Figure 1. Record low indices for Jan-Feb 2016 in Kodiak Trawl Survey2

Few Smelt Left are at High Risk

Posted on by

This third week of February 2016 the Smelt Working Group concluded “the risk of entrainment remains high and it is incompatible with current pumping levels”1. Basically as Delta inflows decline after the early winter stormwater recedes in early February and South Delta exports increase, the risk to Delta Smelt is high with the onset of spawning imminent. Despite the high risk assessment, state and federal managers have decided to raise exports to the maximum allowed under the Delta Smelt Biological Opinion, to 6,000 cfs, which is triple the 2000 limit suggested by the working group, and about a third of Delta inflow. The working group warns the managers that just because there are few smelt being seen in Delta surveys does not mean that the remnants of the populations are not at risk.

The working group is also concerned with what may soon occur once smelt do start spawning. As Longfin Smelt have begun spawning, I have summarized recent data to specifically look at that risk. Figure 1 shows the recent early February Smelt Larval Survey results along with annotations of net flows. Under 6000 cfs exports negative upstream net flows occurs throughout the central Delta (red arrows). The larval smelt in this area will transport to the south Delta over time. With spawning smelt in this area, their offspring will also likely move south to the pumping plants.

With most of the larval Longfin in Suisun Bay because of the earlier storm flows, the risk to the population is low. Yet, these are a state endangered species with these export operations causing a measurable take. With Delta Smelt yet to spawn, they are more likely to be found further upstream because of lower Delta inflows, thus putting their larvae at greater risk than Longfin, especially given ripe adults are present in the central Delta.

One final note, with these operations and declining Delta inflow, the low salinity zone where smelt larvae concentrate will be drawn ever eastward from eastern Suisun Bay into the central Delta. This pattern will increase the risks to smelt. The upstream edge of the low salinity zone is moving upstream in the lower San Joaquin channel with the higher exports as seen at Antioch (Figure 2) and False River (Figure 3).

February Longfin Smelt densities from Larval Smelt Survey

Figure 1. Early February Longfin Smelt densities from Larval Smelt Survey2 with added annotations of net flow in the Central Delta zone of influence (red circle) of the South Delta exports. Blue circle shows catch at Jersey Pt station (809). Red arrows depict net negative flows on the order of 400-5000 cfs3. (Note these early February Longfin larvae densities are by far the lowest observed in the eight years of surveys.)

Feb Salinity (EC) at Antioch

Figure 2. Salinity (EC) at Antioch in the San Joaquin channel of the west Delta during February 2016. (Source: CDEC)

Salinity (EC) in False River

Figure 3. Salinity (EC) in False River in the central Delta during February 2016. (Source: CDEC)