Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Scott River Chinook Crisis

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Klamblog1 recently reported that the Scott River Chinook salmon are again delayed from ascending the lower Scott from the Klamath River because of low water flow. This major Klamath tributary to the west of Mt. Shasta and Weed, CA that flows most winters with thousands of cubic feet per second (cfs) from rain and snow from the Trinity and Marble mountains has been flowing at less than 10 cfs this summer and fall. The salmon simply cannot migrate up this large, steep river with such low flow, especially in dry years when there is no snowmelt after June. The salmon simply wait for rain at the mouth of the Scott. Rains often come by December, just in time for California’s last viable run of Coho salmon, but too late for the Chinook.

As usual the blame is on irrigators in Scott Valley who draw down the water table with heavy groundwater pumping and surface water diversions in the summer for hay and pastures. The State Board did restrict most surface diversions this summer, but with little snowpack there was little streamflow to restrict. Scott Valley often has high groundwater, but with little snowpack recharge, less flood irrigation, and heavy pumping, groundwater seepage and ag returns to the river have virtually ceased, leading to the low flows.

Surprisingly, there is a solution that ranchers are willing to do – pump groundwater into the river in the fall after the summer irrigation season. There is more than enough pumping capacity and groundwater available. Ranchers only want payment for the electricity – a reasonably modest cost. In years like this we are talking about 8 to 10 weeks of a nominal amount of pumping and groundwater storage with a high likelihood that the groundwater used would be replaced/recharged this coming winter and spring.

The concept and proposal have fallen on deaf ears, and the ranchers have circled their wagons much like the salmon in the video link below. As the political fight over water goes on, we should take every opportunity like this one to save the salmon from extinction.

 

Trap and Haul –a better Central Valley option

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Last month, CalTrout’s blog had a post on a federal government program to trap-and-haul salmon and move them upstream of Shasta Reservoir.1 Earlier we also commented on trap-and-haul (http://calsport.org/fisheriesblog/?p=334). The National Marine Fisheries Service’s (NMFS) Recovery Plan for Central Valley Salmon and Steelhead prescribes trap-and-haul, as does their biological opinion for operation of state and federal Central Valley water projects.

Transporting adult salmon above dams and the offspring back below the dams is an expensive and difficult task. No one loves trap-and-haul, but NMFS considers it necessary to ensure that endangered salmon and steelhead do not go extinct. The prescription comes out of frustration that the populations are declining below the dams. Given the choice of extinction or doing something that no one is thrilled with, NMFS has chosen a set of actions in the latter category. The feds have again begun raising Winter Run Chinook in the fish zoo at Livingston Stone Hatchery to ensure there is some genetically pure stock available in the future. Having a wild stock above Shasta in the McCloud River seems a wiser option, given that those fish would be wild even if they spend some time in a truck. It is a further hedge against conditions like the past two years when the Bureau of Reclamation failed to keep their promise to protect the Winter Run downstream of Shasta.

NMFS has also prescribed trap-and-haul to pass Spring Run Chinook and Steelhead around Shasta Reservoir and other Central Valley dams. Stakeholders on the Yuba are developing a plan to carry out the prescription.

In a second blog post, CalTrout recently asked: “Will winter run go the way of the bull trout?”2 Most assuredly, trap-and-haul can help maintain populations while we get our act together below the dams. It’s a better option than a zoo.

Save the Winter Run Salmon

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By now most everyone has seen the newspaper articles on the catastrophic decline in Winter Run Chinook salmon production in the Sacramento River below Shasta Reservoir in 2015. The number of Winter Run juveniles passing downstream past Red Bluff is down substantially from last year, when the estimated survival rate was 5%.  Many blame the drought  – the fourth year of drought.  I have blamed poor water management and the weakening of water quality standards prescribed to protect the salmon (see previous posts).

It is now time for extreme actions to save these fish.  This coming year’s winter adult run will be made up primarily of the 2013 spawn, with some from 2012.  These spawns were marginally successful and could produce enough spawners next summer to help fix this debacle.

The responsible agencies plan to take more eggs and increase smolt production at the Livingston Stone Hatchery near Redding.  They also plan to truck these hatchery smolts to the Bay to maximize their survival.  They will likely severely limit commercial and recreational fisheries that may harvest Winter Run.  They plan to again start raising a rescue population in captivity to ensure they have some fish in the future to draw on for recovery.  A new drought plan will again address how flows and water temperatures will be managed below Shasta.  The State Board may resist weakening Sacramento River and Delta water quality standards designed to protect Winter Run, unlike what they did in the last two years.  All of these actions together will indeed help Winter Run from further decline, but it will not be enough even if the El Niño brings abundant rain and snow.

What else?  The answer to that question should be everything that is reasonably possible to increase production and survival.  Here are some suggestions:

  1. Do not weaken Sacramento River and Delta water quality standards that protect Winter Run. (This alone would have averted the catastrophes below Shasta the past two years.)
  2. Minimize warm water inputs to the Sacramento River in summer from the Trinity River to keep Sacramento River temperatures lower and save Shasta’s cold-water pool.
  3. Alter peaking hydropower management and system infrastructure in Shasta-Trinity CVP system to improve water temperatures in the Sacramento River and the conservation of reservoir cold-water pools.
  4. Further limit Shasta-Trinity reservoir releases to water contractors to conserve cold-water pools and maintain flow requirements for salmon.
  5. Enhance natural winter and spring flow pulses from tributaries below Shasta with flow releases from Shasta to increase survival of emigrating wild juvenile salmon migrating downstream in the Sacramento River, to and through the Delta, and to and through the Bay to the ocean.
  6. Conduct an aggressive rescue program of adult Winter Run that migrate into Sacramento Valley bypasses only to be blocked below overflow weirs, or that migrate into dead-end basins, or that stray into other tributaries including Battle Creek, Feather River, and American River salmon hatcheries.
  7. Capture wild juvenile Winter Run in an enhanced trapping program at fish screen bypasses, screw traps, and other techniques in the Sacramento River in fall and winter migration period, and transport these juveniles to the Bay to avoid lower river and Delta sources of mortality.
  8. Modify Delta operations to maximize juvenile Winter Run survival through the Delta. This may involve further changes to Delta Cross Channel operations and Delta export schedules, as well as Delta inflow and outflow.
  9. Maximize egg taking and rearing capacity in hatchery system.
  10. Barge wild and hatchery young from the Sacramento River through the Delta for release in the Bay to avoid future straying problems associated with trucking fish.
  11. Raise juvenile hatchery salmon in floodplain habitats in winter in the Sacramento Valley (e.g., Sutter and Yolo Bypasses).
  12. Conduct egg injection or fry releases in appropriate locations in Battle Creek to jumpstart its prescribed new population; this can be managed at the Battle Creek hatchery.
  13. Develop and implement an emergency comprehensive plan with appropriate agencies with the necessary authority to carry out these actions. Include stakeholders in the plan development and review process.  Obtain necessary funding from available sources.

Sturgeon and the Drought

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The State Water Board’s weakening of the water temperature standards in the Sacramento River below Shasta at the request of Reclamation and concurrence by NMFS this late spring and early summer has likely led to excessive take during this spawning season of listed Green Sturgeon, increasing their risk of their extinction. Lower flows and higher temperatures in the Sacramento River’s Green Sturgeon spawning reach from Anderson (RM 280) to Hamilton City (RM 200) has likely resulted in a substantial mortality of eggs and larval Green Sturgeon, as well as White Sturgeon, during and following their May-June spawning season.

Water temperatures below Red Bluff (RM 240) exceeded the upper thermal optimum for Green Sturgeon embryos (17-18°C, 62-65°F1) from late spring to early summer 2015 (Figure 1), but rarely in 2012, the first year of the present drought (Figure 2), when standards were not weakened. Water temperatures exceeded 62°F nearly to Anderson at times this summer (Balls Ferry and Jelly’s Ferry). Approximately half the spawning reach has been severely degraded by warm water from weakened standards (Figure 3). Lower flows and higher water temperatures have likely led to earlier spawning and more concentrated spawning in the upper end of the spawning reach. The river below Hamilton City, where eggs and fry drift and many young rear, is degraded with high water temperature even above 100% lethal levels (23°C, 73°°F) at Wilkins Slough (RM 120) (Figure 4). In 2012, when standards were not weakened, conditions at Wilkins Slough were much better and near optimum (Figure 5). However, even in 2012 (the first year of the present drought cycle) Green Sturgeon tended to spawn further upstream in the spawning reach than in previous years2 because of lower river flows and/or higher water temperatures.

What applies to Green Sturgeon also applies to the non-listed White Sturgeon, whose spawning and rearing requirements, timing, and locations are similar to those of the Green Sturgeon3. Concerns for the White Sturgeon are ever increasing4. The risks extend to adult White Sturgeon, which have undergone a die-off in the Columbia River under similar circumstances5.

Figure 1

Figure 1. Water temperatures at Red Bluff on Sacramento River late spring and early summer 2015. (Source: CDEC)

figure 2

Figure 2. Water temperatures at Red Bluff on Sacramento River late spring and early summer 2012. (Source: CDEC)

Figure 3

Figure 3. Green Sturgeon spawning reach in the Sacramento River (green highlight). Reach degraded by high water temperature in 2015 (red highlight).

Figure 4

Figure 4. Water temperatures at Wilkins Slough (RM 120) on Sacramento River late spring and early summer 2015. (Source: USGS)

Figure 5

Figure 5. Water temperatures at Wilkins Slough (RM 120) on Sacramento River late spring and early summer 2012. (Source: USGS)

  1. “Water temperature for spawning and egg incubation is near optimal (15oC/ 59oF)) from RBDD upriver during the spawning season. Below RBDD, water quality, in terms of water temperature, gradually degrades and eventually exceeds the thermal tolerance level for egg incubation, when egg hatching success decreases and malformations in embryos increase above 17 oC/62 oF, at Hamilton City”. (NMFS OCAP Biological Opinion p276) ↩
  2. William R. Poytress, Joshua J. Gruber, Joel P. Van Eenennaam & Mark Gard (2015) Spatial and Temporal Distribution of Spawning Events and Habitat Characteristics of Sacramento River Green Sturgeon, Transactions of the American Fisheries Society, 144:6, 1129-1142, DOI: 10.1080/00028487.2015.1069213 ↩
  3. White Sturgeon generally spawn lower in the river than Green Sturgeon. ↩
  4. http://www.scout.com/outdoors/fish-sniffer/story/1563429-ca-dfw-considers-slashing-sturgeon-fishing
    https://cdfgnews.wordpress.com/2015/08/11/responsible-angling-practices-help-conserve-sturgeon-populations/
    ↩
  5. http://www.cbbulletin.com/434540.aspx ↩

Knights Landing Outfall Gates New Screens – Only a Start

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A SacBee article on October 22, 20151 describes the nearly completed Knights Landing Outfall Gates (KLOG or Outfall Gates) screening project on the Sacramento River: “local, state and federal officials are close to completing a $2.5 million project that will block an entrance wayward salmon use to get into the Colusa Basin Drain”. The operative word here is “an”, because the other entrance, and by far the more important, is the Knights Landing Ridge Cut (KLRC or Ridge Cut) outlet into the upper Yolo Bypass (Map 1).

Upstream-migrating Winter Run Chinook Salmon bound for spawning grounds below Shasta Dam near Redding in the Sacramento River can be attracted into irrigation and stormwater drainage system outfalls and eventually lost. The two largest outfalls are the Yolo and Sutter bypasses (see my previous blog on the bypass attraction – http://calsport.org/fisheriesblog/?p=421 ). Of lesser importance are a series of agricultural outfalls from low-lying basins adjacent to the Sacramento River. Chief among these are the Knights Landing Outfall Gates, which drain the Colusa Basin on the west side of the Sacramento River Valley.

The new screens on Outfall Gates will ensure that no salmon leave the river for the basin through the gates. But that is not the big problem. The Colusa Basin Drain (CBD or Drain) is also a stormwater drain that can flow mightily in winter storms even in drought years such as 2013-2015 (Charts 1 and 2). When stormwater-driven high flows in the Drain occur, the Outfall Gates’ outlet is usually closed because the river is higher than the gates during storm runoff. Under these high flows, water in the Drain is forced down the Knights Landing Ridge Cut into the upper Yolo Bypass (see Map 1).

Storm runoff that passes through the Ridge Cut into the Yolo Bypass attracts many salmon, steelhead, and sturgeon into the Drain and to their eventual demise in the dead-end Colusa Basin. Storm flow to the Yolo Bypass reaches 4000-6000 cfs in drought years, while non-storm flows through the Outfall Gates are usually only several hundred cfs (Charts 1 and 2). Flows leaving the Yolo Bypass and entering the Delta at Cache Slough (Map 2) attract many salmon, steelhead, and sturgeon moving through the Delta. During floods, the Sacramento River spills into the Yolo Bypass, adding even more attraction flows through Cache Slough. With limited passage options past the Fremont Weir at the upper end of the Yolo Bypass (Map 1 or 2), many of fish moving up the Yolo Bypass are attracted to and migrate up the Ridge Cut.

In short, the Knights Landing Ridge Cut outlet also needs to be blocked to keep fish from migrating into the Colusa Basin and being lost. The threat is serious not only to Winter Run Chinook, but also to Fall Run, Late Fall Run and Spring Run Chinook, as well as Steelhead, Green Sturgeon and White Sturgeon. Fish passage facilities at Fremont Weir are also needed so that adult fish that migrate up the Yolo Bypass are not stranded in the Bypass.

Map 1

Map 1. Location of Knights Landing Outfall Gates (KLOG) on Sacramento River and Knights Landing Ridge Cut (KLRC) outlet in the Yolo Bypass near Knights Landing, CA. Red arrows point out routes taken by salmon into the Colusa Basin.

Chart 1

Chart 1. Flow in the Colusa Basin Drain Nov 2013 through May 2014. Red line depicts flow when KLOG were closed due to high Sacramento River stage. (At flows above about 900 cfs in the CBD the KLOG were closed and flow diverted to Yolo Bypass via KLRC.)

Chart 2

Chart 2. Flow in the Colusa Basin Drain Nov 2014 through May 2015. Red line depicts flow when KLOG were closed due to high Sacramento River stage.

Map 2

Map 2. Route salmon take from the Delta via Cache Slough up the Yolo Bypass when attraction flows are input from either the Knights Landing Ridge Cut or the Fremont Weir.