Author Archives: Tom Cannon

Salmon Rescue in Yolo Bypass

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A December 23, 2015 article in the Sacramento Bee1 describes salmon rescues occurring in the northern Yolo Bypass near the outlet of the Knights Landing Ridge Cut. The online SacBee article provides a video of the trapping and hauling process. I posted earlier about the stranding of salmon in the Bypass.2

It is encouraging that the California Department of Fish and Wildlife is addressing the immediate situation and that this effort is getting coverage in the press. However, the SacBee article contains several misconceptions about the problem:

  1. “Salmon are having problems with the drought identifying which route to go right now.” This problem is by no means unique to the drought. This stranding problem is far worse in wetter years when higher flows into the Yolo Bypass and Colusa Basin Drain attract far more salmon (and steelhead and sturgeon).
  2. “Beginning in 2013…” – the problem has been known for many decades.
  3. “That spring, biologists discovered that some 600 endangered winter-run salmon had gotten trapped 70 miles off course in the Colusa Basin Drain system” – the estimate was very rough, given that the agencies acknowledged the problem late in spring and surveyed only a few areas of the Colusa Basin. In addition, they were unable to count all the fish concentrations and to identify the genetics of all the fish.
  4. “Although conservationists captured and returned many of the fish to the river” – though the effort was commendable, many of the stray fish were not captured and returned.
  5. “Since then, we’ve started building seasonally these traps that we can put in the channel to allow us to move them pretty efficiently” – when flows got high last winter in the Colusa Basin Drain, the trap was removed because it was ineffective. Many salmon passed the trap location (to die upstream in the Colusa Basin), and hundreds were stranded nearby and died (see photo below).
  6. “The traps are a temporary solution, but efforts are underway to permanently stop the fish from going off-course.” – The traps are better described as a Band-Aid than a solution. They do not work at higher flows when fish passage is greatest. Permanent solutions were prescribed in the 2008 National Marine Fisheries Service Biological Opinion for operation of the federal Central Valley Project and the State Water Project. If a permanent solution is in fact completed next summer as the SacBee article suggests, it can’t be soon enough.
Picture of stranded salmon

Salmon stranded at Knights Landing Ridge Cut Outlet in northern Yolo Bypass after high flows in December 2014.

It is Too Early to Turn On the Delta Pumps

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Delta export pumping has increased, jeopardizing endangered Winter Run salmon and Delta smelt. Yes, there is a lot of fresh water (and young salmon) pouring into and through the Delta from the recent storms. Delta outflow has risen from 5000 cfs to 22,700 cfs this month (Figure 1). So the state has started pumping more from the south Delta. State exports have risen from 500 cfs on 12/21 to 4000 on 12/23.

The problem is that the Low Salinity Zone (LSZ, 500-10,000 EC1) so critical to the Delta ecology has yet to be flushed west, out of the Delta. Turning up the pumps has actually increased the concentration of salt in export water (Figure 2) by pulling LSZ water from the north and west into the central and south Delta (Figure 3). Smelt and salmon concentrate in this zone. The LSZ has moved west from Rio Vista in the north Delta on the Sacramento River (Figure 4), but not from the west and central Delta on the San Joaquin side (Figure 5). Export pumps in the south Delta are pulling LSZ waters from the San Joaquin channel through False River and Dutch Slough (Figure 6).

Remnants of the Delta smelt population are in the central Delta.2 Winter Run salmon smolts began showing up at the export fish facilities in Clifton Court on 12/23. Both occurrences should be a stern warning, given the present poor state of these two endangered fish populations. Closure of the Delta Cross Channel earlier in December to protect migrating salmon actually aggravated the problem by limiting flushing of the central and west Delta and by trapping salmon and smelt in the central Delta. Exports should not be increased until the LSZ is west of Jersey Point. The Delta Cross Channel should remain open until the LSZ is west of Jersey Point. It is better for everyone if exports are pumping fresh water (

Graph of Delta outflow 2015

Figure 1. Delta outflow in December 2015.

Graph showing Electrical Conductivity at Clifton Court

Figure 2. EC of water exported from Clifton Court Forebay in south Delta in December 2015.

Map of flows

Figure 3. Aerial photo of Delta showing high Delta freshwater inflow and outflow from Sacramento River (blue arrow) and South Delta exports pulling brackish Low Salinity Zone water from central and west Delta San Joaquin channel to south Delta export pumps at Clifton Court Forebay (center bottom). The two eastward red arrows represent the False River (upper arrow) and Dutch Slough connections.

Graph of electrical conductivity at Rio Vista

Figure 4. EC at Rio Vista in north Delta on Sacramento River 12/19-12/26, 2015.

Graph of electrical conductivity at Jersey Point

Figure 5. EC at Jersey Point in the western Delta on San Joaquin River 12/19-12/26, 2015.

Graph of electrical conductivity at Dutch Slough

Figure 6. EC at Dutch Slough between the west and central Delta 12/19-12/26 2015. Note spike on 12/23 when south Delta exports were increased to 4000 cfs.

  1. EC is electrical conductivity expressed as microsiemens ↩
  2. http://calsport.org/fisheriesblog/?p=570 ↩

Scott River – Crisis Update

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In a recent post1 I related that the Scott River, a major salmon producing Klamath tributary in northern California near Yreka and Fort Jones, is again in crisis due to low fall flows in the present drought. I suggested that normal December storms might be too late to save the Fall Run Chinook, but would likely accommodate the later spawning Coho.

Two December storms (Figure 1) have come and helped the salmon. Counts near Fort Jones recently reached near 400 for Chinook and 200 for Coho. Neither number is good, but the Chinook number, though preliminary, is very low, as it should be several thousand or more. Waiting for several months to ascend the river to spawn has likely taken its toll on the Chinook. The storms were also nearly too late for Coho, but these circumstances are fairly normal for Coho.

Graph of December streamflow in Scott River below Fort Jones

Figure 1. December streamflow in Scott River below Fort Jones. (Source: CDEC)

The late storms made things very difficult for Chinook. In a recent newspaper article2 on the Scott, it was noted that late runs usually spawn in the lower river, downstream of the good spawning reaches. The lower river spawning grounds are subject to winter storm scouring. In the article, some sources blamed the low fall flows on agricultural groundwater pumping during the summer and fall, which lowered the water table in Scott Valley. Lack of summer snow storage in the adjacent mountain ranges was also a key factor.

But the article and its sources miss what my previous post suggested as a solution to the problem. Groundwater could have been pumped into the river in the Valley in substantial amounts in the fall using some of the irrigators’ idle pumps. A concerted pumping effort in October and November, for one to several weeks, could have gotten the Chinook up from the mouth into the Valley to the perennial flowing spawning tributaries and river reaches. The salmon could have spawned or have been ready to spawn when the rains did come.

The winter rains are already recharging the groundwater basin in the Scott Valley, so the costs of the effort in terms of next year’s water supply would have been minimal. The cost of electricity is minuscule in comparison with the loss of production of one of the Klamath’s most prolific salmon-producing tributaries.

Some Delta Smelt Back in the Delta

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The US Fish and Wildlife Service’s early winter survey1 recently detected the first adult Delta Smelt of the water year in the Delta at Jersey Point on the lower San Joaquin River (Figure 1). The number collected in the survey through December 15th is 3, compared to 26 for the same period last year. Their appearance is on schedule and likely related to the first storm flow of the winter (Figures 2 and 3), and the freshening of the Delta (Figure 4).

Table of Smelt Count

Figure 1. Catch of adult Delta Smelt in early warning survey at two lower San Joaquin River stations in December 2015.

Graph of Delta freshwater outflow in December 2015

Figure 2. Delta freshwater outflow in December 2015. (Source: CDEC)

Graph of Turbidity of water at Jersey Point in December 2015

Figure 3. Turbidity of water at Jersey Pt in December 2015. (Source: CDEC)

Graph of Salinity (EC) at Jersey Point in December 2015

Figure 4. Salinity (EC) at Jersey Pt in December 2015. (Source: CDEC)

More on Spill

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In a recent post I suggested “spill” (targeted reservoir releases) to enhance salmon production in Central Valley rivers. Well, it is now time to employ spill to help Winter Run and Spring Run Chinook salmon in the upper Sacramento River below Shasta near Redding. Waiting for El Niño to help these fish may be too late. Confidence and early indications that El Niño will come this winter should make the necessary commitment for spill now more palatable. Spill releases could have already been made from Shasta Reservoir with these recent storms to support emigration of young salmon from the spawning and rearing reach.

After the salmon spawning, irrigation, and water transfer season ended in October, there have only been minimum flows and no spills to enhance young salmon emigration. Flow from Shasta-Keswick (river mile 302) has remained near the minimum requirement of 4000 cfs (Figure 1).

Recent Storms – December 2015

The recent storms have sharply increased flow in the Sacramento River downstream of the spawning reach at Bend Bridge at river mile 258 (Figure 2) below the input of four large creeks entering the Sacramento River below Redding (Figure 3). Inflow to Shasta Reservoir has nearly quadrupled during the two storms, reaching 8,000-10,000 cfs. A prescriptive “spill” release of 5-10% of inflow (500-1000 cfs) is needed. That would raise Keswick releases to about 5000 cfs, which would help stimulate emigration from the spawning reach into the higher flow reach below the tributaries, and down into and through the Delta.

December 2003 Case Study and Precedent

December 2003 had similar circumstances. Screw trap catch of Winter Run salmon at Knights Landing (RM 90) had a sharp increase coincident with flow increases in December 2003 (Figure 4). Spill in December 2003 (Figure 5) helped increase the river flow.

Concern for Young Salmon in the Delta

Higher freshwater inflows from the storms in 2015 have already pushed the Low Salinity Zone out of the Delta into Suisun Bay. Winter Run and Spring Run salmon (as well as Late Fall smolts and Fall Run fry) are likely now entering the Delta in large numbers (comparable monitoring results from 2003-4 are shown in Figure 6). Spill wouldl help move fish through the Delta and west to the Bay. The Delta Cross Channel remains open, allowing the emigrating salmon to spread into the Central Delta. This increases the need for spill to keep these fish moving west before the DCC is closed and south Delta exports divert freshwater inflow and emigrating salmon away from the Bay and toward the Delta pumps.

Spill is also needed from other reservoirs on the Feather, Yuba, and American Rivers that have also received significant inflow during the recent storms. Spill from these reservoirs is needed to stimulate migration of young salmon from their tailwaters as well as to contribute more to the combined Delta inflow and outflow.

Though it is a hard decision not to store all of the inflow from these first storms of the season in reservoirs, releasing 5-10% as spill would go a long way to help saving the wild endangered salmon that depend on the early winter flows.

Graph of releases from Keswick fall 2015

Figure 1. Flow releases to Sacramento River from Keswick Reservoir fall 2015. Minimum prescribed outflow to Sacramento River is approximately 4000 cfs in drought years like 2015. Keswick Dam is at rivermile 302, nine miles below Shasta Dam.

Graph of flow spike

Figure 2. Flow in the Sacramento River at Bend Bridge (RM 258) 44 miles below Keswick Dam fall 2015. Flow spikes from recent storms come from local tributary creeks upstream of Bend Bridge.

Map of winter run spawning location

Figure 3. Location of Winter Run spawning and rearing reach (green hatched line) below Keswick Dam (RM 302) near Redding, CA. Four major tributary creek inputs are shown below Redding. The mouths of Cottonwood and Battle Creeks are about RM 270.

Graph of catch index in Knights Landing

Figure 4. Catch index of older juvenile (non-fry) in Knights Landing (RM 90) rotary screw trap Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

Graph flow from Keswick 2003

Figure 5. Flow releases to Sacramento River from Keswick Reservoir fall 2003. Releases were approximately doubled to 9000 cfs at mid-month, ostensibly to help stimulate young salmon emigration and allow greater Delta exports 1.

Graph of trawls 2004

Figure 6. Catch index of older juvenile (non-fry) in trawls and seines in the Sacramento River near Sacramento, Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

  1. High exports in December03-January04 did result in substantial counts of juvenile Winter Run salmon at South Delta Fish Salvage Facilities during the period. ↩