Category Archives: Northern California

Park Fire – Spring-Run Salmon’s Worst Nightmare

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The fire that started on July 24 has burned most of the lower foothill and middle reaches of the affected streams as of August 8th.  It is now actively encroaching on the mountain spawning reaches of Mill and Deer creeks on the south slopes of Mt Lassen, the two most important of the affected spawning streams (see maps below).  It will likely slow only when it reaches the boundary of the 2021 Dixie Fire and its lower levels of fuels.

Map of Park Fire in northeast Sacramento Valley dated 8/3/2024.  Red arrows indicate further fire growth as of 8/6, mainly in the upper Mill and Deer creeks watersheds.  Green stripes indicate spring-run salmon summer holding and fall spawning reaches.

Spring-run salmon populations in the Central Valley, including the core Battle, Mill, Deer, and Butte Creeks populations, are at recent historic lows.  It is essential to rehabilitate previously burned watersheds as soon as possible.  The California Department of Fish and Wildlife should expand the Deer Creek Spring-Run Conservation Hatchery Program begun in 2023 at UC Davis to include the other spring-run salmon streams in the Sacramento Valley. 

At the same time, it is important to attack the causes of poor survival of juveniles migrating to the ocean and poor survival of adults returning to the spawning grounds.  In this regard, comments on the Environmental Impact Statement for the Long-Term Operations of the Central Valley  Project and the State Water Project are due on September 9.  Operations of these water projects play a major role in the survival of Central Valley salmon to and from the ocean.  With the acceleration of climate change, it is important to re-evaluate the present and future effects of these water projects and potential operational changes to protect salmon under this new climate change baseline.

For more on Mill and Deer creek salmon see:  https://www.facebook.com/CaliforniaDFW/videos/spring-run-chinook- salmon/306327998810027/

Park Fire active zone moving northeast in the upper Mill Creek watershed on August 8th, 2024.  CALFIRE hopes to stop the Park Fire advance at highways 32/36 and the boundary of 2021 Dixie Fire (see next map).

Park Fire active zone moving northeast in the upper Mill Creek watershed on August 8th, 2024.  CALFIRE hopes to stop the Park Fire advance at highways 32/36 and the boundary of 2021 Dixie Fire (see next map).

Western boundary (extent) of Dixie Fire in summer 2021.

Klamath River Update – July 2024

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It is the first summer without the reservoirs on the Klamath River.  Upper river flows at Iron Gate are now at summer lows (900 cfs, Figure 1).   The flow, water temperature, and turbidity in the river without the reservoirs (the dams have not all been removed) is shown in the following figures.  Two major concerns are sporadic turbidity events from dropping flows and higher water temperatures that are a consequence of unshaded former reservoir reaches and loss of cold-water dam releases.

Extensive gaging data are available for the lower Klamath River from the USGS and Karuk Tribe (Figure 2).  The focus here is on the reach below the four-dam-removal project where the dams were drained in early 2024, leaving the river free-flowing.

Late spring and early summer gage data show the upper reaches below Iron Gate had the warmest water in 2024 (Figures 3-5).  Water temperatures reached 25oC/77oF, lethal to salmonids.  Further downstream, water temperatures were gradually cooler as the river progressed toward the mouth, generally remaining in the 68-70oF maximum range after receiving cool tributary water and cooler air temperatures.  Further upstream above Iron Gate, water temperatures were similar those immediately below Iron Gate (Figure 6).

Prior to dam removal, the upper reaches below Iron Gate had the lowest water temperatures in 2022 and 2023 (Figure 7 and 8), reflecting the release of cold water from the bottom of Iron Gate Reservoir.  Without this source of cold water, the upper reaches are now significantly warmer in late spring and summer. 

Because the water temperatures were similar in 2024 above and below the former Iron Gate Reservoir (see Figures 4 and 6), there seems to be little warming in the unforested former Iron Gate reservoir reach.  The upper reach of river below Iron Gate Dam now generally reflects historic warm water characteristics of the 6-dam project reach between Klamath Lake and Iron Gate Dam.  Future riparian forest restoration of the three former reservoir reaches may lead to some cooling of the upper river in the future.

Finally, the drop in river flow in early July 2024 (see Figure 1) appears to have caused additional reservoir-footprint erosion and scouring, leading to high turbidity levels below Iron Gate (Figure 9).  Such turbidities like the warm water are generally lethal to salmonids.

Figure 1.  Upper Klamath River flow at Iron Gate gage in June and early July 2024.

Figure 2.  Lower Klamath River gauging stations from Klamath Lake downstream to mouth.  Blue marker denotes gage below JCBoyle Dam.  Numbers in green and yellow circles denote multiple gage locations.

Figure 3.  Water temperatures in lower Klamath River in June 2024.  Iron Gate Dam is uppermost location and Turwar Gage is lower-most location near mouth.  Note greatest water temperatures were recorded from the two uppermost reaches:  Iron Gate and Walker Bridge.

Figure 4.  Water temperature recorded at Iron Gate gage 6/15-7/7 2024.

Figure 5.  Water temperature recorded at Walker Bridge gage 5/20-7/7 2024.

Figure 6.  Water temperature recorded at Fall Creek gage 6/1-7/7 2024.

Figure 7.  Water temperatures in lower Klamath River in June-July 2022.  Iron Gate Dam is uppermost location and Turwar Gage is lower-most location near mouth.  Note lowest water temperatures were recorded from the two uppermost reaches:  Iron Gate and Walker Bridge.

Figure 8.  Water temperatures in lower Klamath River in June-July 2023.  Iron Gate Dam is uppermost location and Turwar Gage is lower-most location near mouth.  Note lowest water temperatures were recorded from uppermost reach: below Iron Gate.

Figure 9.  Turbidity (suspended sediment) concentrations measured at Iron Gate Gage in 2024.  Note original reservoir drawdown and subsequent reservoir sediment deposit erosion January-

Klamath River Salmon and Steelhead Recovery – The Future

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After dam removal, the plan for recovering Klamath River salmon and steelhead is relatively straightforward.

Oregon is going to focus on watching to see how steelhead repopulate the upper watershed and on having a more active role in developing spring-run Chinook salmon populations.  Without an existing spring-run stock, Oregon will try establishing one by out-planting stock from California’s Trinity River Hatchery.

California will focus on recovery of existing lower river spring-run Chinook and fall-run Chinook, Coho, and steelhead stocks.  The new Fall Creek Hatchery will sustain the fall-run Chinook, Coho, and steelhead stocks formerly produced at the now-closed Iron Gate Hatchery.  Lower and middle river wild spring–run and fall-run Chinook, Coho, and mainstem and tributary steelhead stocks should expand with improved water quality and access to new habitat.  Historical tributaries offer great potential as does the spring-fed reach of the mainstem near the Oregon border.

In the decades ahead, as the populations and habitat recover, state, federal, tribal, and stakeholder groups will work together toward Klamath salmon and steelhead recovery.

There will be a need to coordinate management of the three H’s:  hatcheries, harvest, and habitat.  Existing hatchery programs should be converted to a single conservation hatchery program focused on salmon and steelhead recovery.  Such a program will need a new hatchery to support the recovery of Klamath spring-run Chinook, as in the San Joaquin River Restoration Program.  The Pacific Fishery Management Council and the two states will have to protect the recovering populations with strict harvest regulations.  Considerable funding will be needed to restore fire-damaged and drought-damaged watersheds, former reservoir footprints, mainstem and tributary fish passage, and spawning and rearing habitat.

Water supply management will remain contested and challenging.  Adequate funding, cooperative efforts, and adaptive management will bring success.

Klamath Dam Removal Update – April 6, 2024

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Video Screen Grab of lower Jenny Creek ASSISTED SEDIMENT EVACUATION PROJECT

In a March 20 post, I related events in the Jan-Feb 2024 period of the Klamath Dam Removal Project.  The initial four-reservoir drawdown in January led to abrupt increases in streamflow, suspended sediment, and low dissolved oxygen levels above and below Iron Gate Reservoir (the lower reservoir).  This was followed by lower stable streamflow, high dissolved oxygen, and declining suspended sediment.  Streamflow pulses from upstream Klamath Lake in late February and early March resulted in (short-term) elevated suspended sediment from exposed sediment erosion in the four reservoir reaches.  These circumstances were expected as part of the four Dam Removal Project.

In March, the Assisted Sediment Evacuation Project began in the Jenny Creek floodplain of the Iron Gate Reservoir footprint.   That project has led to lethal doses of suspended sediment (turbidity) in the lower Klamath River below the Iron Gate Dam site (Figures 1-3).  Project approvals, such as the National Marine Fisheries Service’s (NMFS) biological opinion quoted below, included provisions to stabilize sediments after the January drawdown, but not to flush sediments into creeks and the Klamath River.

Post drawdown and dam removal, crews will be working to actively restore the exposed reservoir footprints and tributary mouths that flow into the former reservoirs. To reduce elevated suspended sediment concentrations (SSCs), the Renewal Corporation will take active measures to flush sediment from the reservoirs during drawdown and then immediately begin stabilizing remaining sediment after drawdown has been completed. Revegetation, channel construction, and placement of habitat features such as logs and boulders will minimize erosion and allow passable channels to form in preparation of fish presence. (NMFS Biological Opinion p. 14)

The origin of the high suspended sediment levels was likely from the exposed bed of Iron Gate Reservoir (particularly the Jenny Creek arm), not upstream reservoir erosion during the Klamath Lake flow pulses.  Sediment levels below Iron Gate Dam were low during the flow pulse that diluted the high sediment loads from Iron Gate Reservoir (Figure 1).  Gages below Copco and JC Boyle reservoirs were lower, generally below lethal levels (Figure 4).

Chinook salmon fry are abundant and most prevalent in the lower Klamath River below Iron Gate Dam in late winter (February-March).  Coho and steelhead fry are more abundant later during spring.

The Assisted Sediment Evacuation Project is slated to end on April 15.  I recommend that it cease immediately, with efforts shifted to “stabilizing remaining sediment,” in order to minimize impacts of the project on Klamath River salmon and steelhead.

Figure 1. Turbidity and streamflow in the Klamath River below Iron Gate Dam (rm 193) in January to March 2024. Note turbidity of 300-500 SBU is roughly 1000-2000 mg/l total suspended sediment (TSS). Such levels are considered lethal for juvenile salmon and steelhead.

Figure 2. Turbidity and streamflow in the Klamath River near Seiad Valley below the mouth of the Scott River (rm 145) in March 2024.

Figure 3. Turbidity and streamflow in the Klamath River near Seiad Valley about ten miles upstream from the mouth of the Scott River (rm 145) in March 2024.

Figure 4. Turbidity and streamflow in the Klamath River just upstream of Iron Gate Reservoir and below Copco dams in March 2024.

Scott-Shasta River Salmon Update – February 2024

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The upper Scott River near Callahan in early spring of drought year 2013.

At the end of November 2023, the Beaver Moon, the last full moon before December, appeared. The Beaver Moon was so named because it was the last chance for trappers to catch beaver with full coats before winter set in. The Beaver Moon also occurs at the peak of the Coho and Chinook salmon runs in the Scott River Valley, once named Beaver Valley. The beaver were once very abundant before being “removed” by ranchers and trappers. Today, beaver are slowly coming back. The beaver help maintain the local groundwater tables, streamflow, water temperatures, riparian vegetation, and create good coho salmon rearing habitat.1

The State Water Resources Control Board took up the Scott and Shasta Rivers water issues again in fall 2023,2 following its adoption of emergency drought regulations in 2022 and a 2023 petition from the Karuk Tribe and environmental organizations3 to protect salmon and steelhead in the Scott river in all water years.

The emergency regulations for 2022 called for summer minimum flows of 30-50 cfs in the Scott River and 50 cfs in the Shasta River. Such minimums were not achieved on the Scott River (Figure 1), but for the most part were achieved on the Shasta River (Figure 2). Such flows were necessary for two key flow functions: (1) maintaining connectivity between spawning and rearing areas in the valleys and the Klamath River, and (2) sustaining over-summering rearing habitat of salmon and steelhead throughout the two rivers and their tributaries.

Without adequate summer flows, salmon fry become trapped in upstream spawning areas without access to productive spring-fed Valley rearing habitat. Maintaining flow in Valley spring-fed habitats provides connectivity and rearing refuges. Late summer and fall minimum flows are necessary to provide access to the valleys from the Klamath River canyon for salmon and steelhead adult spawners.

The State Board should have kept some emergency order elements in place after the orders ended in July 2023, even though 2023 was a wet year. In 2023, both rivers and their salmon were stressed again by low flows (Figures 3 and 4).

Because base flows from mountain and valley springs are just over 100 cfs in both streams, stressful conditions are brought on by the cumulative effects of small water diversions and groundwater pumping. Surface water diversions and groundwater extraction for agricultural and domestic water use draw from this supply, with peak use in the summer-fall irrigation season. On the Shasta River, the irrigation season ends at the beginning of October, allowing flows from springs to fill the river channel for returning salmon. On the Scott River, the irrigation season extends through November to water pastures and to get in the last crop of hay.

In the Shasta River, flows in October are sufficient for Chinook spawners passage to spawning areas around Big Springs in Shasta Valley. But in the Scott Valley, Chinook often do not have adequate passage flows to ascend from the Klamath Canyon up to Scott Valley until the first late-fall rains. In most years, early December rains accommodate the Coho run in the Scott River. Young salmon from the prior year’s spawning also need the fall flows to emigrate from the Valley to the Klamath River and ocean.

2023 Karuk et. al. Petition for Scott River4

On May 22, 2023, the Karuk Tribe, Environmental Law Foundation, Pacific Coast Federation of Fishermen’s Association, and Institute for Fisheries Research petitioned the State Water Board to initiate a rulemaking to establish permanent (not just emergency) instream flows on the Scott River.

As an initial response, the State Water Board re-adopted, on an emergency basis, the emergency minimum instream flows previously in effect in both the Scott River and Shasta River.

Comment: The State Board did not readopt the emergency regulations in wet year 2023 and the salmon suffered.

2024 Coastkeeper et al. Petition for Shasta River

On January 17, 2024, California Coastkeeper Alliance, Friends of the Shasta River, Mt. Shasta Bioregional Ecology Center, Water Climate Trust, Shasta Waterkeeper, Save California Salmon, and Environmental Protection Information Center petitioned the State Water Board to initiate a rulemaking to establish permanent (not just emergency) instream flows on the Shasta River.

Recommendations

As an initial matter, the State Water Board should adopt as permanent the minimum instream flows it adopted on February 1, 2024 as emergency instream flows.5 This will put an immediate end to dry streambeds in the summer and fall as shown in Figures 3-5 below. This will admittedly also significantly reduce water available for human use and cause a conflict between groundwater and surface water users, as well as among water right holders.

In the longer term, there are some relatively straightforward additional measures that could help create solutions to the problems in Scott and Shasta Valleys and potentially reduce the water supply impacts. Whether these actions are equitable, reasonable, cost-effective, and/or politically doable is open to question and evaluation. The adoption of the flow requirements as shown must not be contingent on the implementation or effectiveness of such actions.

Possible additional measures include:

  1. Create additional instream or off-stream storage to capture winter water for summer release to meet demands and needs.
  2. Make concerted efforts to recharge groundwater storage with the often-plentiful winter-spring runoff.
  3. Deepen the river channel by removing accumulated fine and course sediments to enhance channel access to groundwater. Removing Young’s Dam in the middle Scott Valley would deepen channel upstream and alleviate the dam’s impediment to salmon and steelhead migration.
  4. Eliminate all surface water diversions from stream channels. There are many small water diversions from the Scott and Shasta rivers that divert streamflow and juvenile salmon. Surface diversions should be replaced by a regulated groundwater extraction program.

    Small water diversion on a Scott River tributary. All small and larger surface diversions should be eliminated. The present system was controlled by the state watermaster program that no longer covers the Scott River and its tributaries.

    Small water diversion on a Scott River tributary. All small and larger surface diversions should be eliminated. The present system was controlled by the state watermaster program that no longer covers the Scott River and its tributaries.

  5. Use unused well capacity to temporarily augment surface water flow in the streams in late summer to help with salmon migrations and to accommodate spawners. In Scott Valley, many hay producers cease pumping from wells at the beginning of August or September. A monitoring and evaluation program would be required to avoid long-term impacts to groundwater levels. The target flow in both the Scott River and Shasta River should be near 100 cfs by October 1 at the Fort Jones and Yreka gages, respectively.
  6. Enhance and restore water storage in mountain and valley meadows through watershed management, including introductions of beaver.
  7. Institute an aggressive water conservation program in the two watersheds.

Latest Actions

 The petitioners requested the following:

Drought emergency minimum flows are specified below:

 Scott River:

  Shasta River:

 The State unveiled the California Salmon Strategy for a Hotter, Drier Future:  Restoring Aquatic Ecosystems in the Age of Climate Change on January 31, 2024.  The Strategy describes state actions for the Scott and Shasta rivers, as follows:

 Scott/Shasta:

  • Designate Salmon Strongholds: the Klamath River and its tributaries including the Salmon, Scott, and Shasta rivers.
  • In April 2023, CDFW awarded $20 million in Drought Emergency Salmon Protection Grants to 10 projects demonstrating support from and collaboration with Tribal Nations and landowner interests in the Shasta and Scott rivers and their watersheds. These include habitat improvement, removal of barriers to fish passage, and groundwater recharge projects that help ensure streamflow.
  • The State Water Board, acting upon a petition from the Karuk Tribe, began consideration of an emergency regulation in 2023 to set emergency minimum flows for the Scott and Shasta rivers while a longer, inclusive process evaluates long-term strategies for these salmon strongholds.
  • By early 2024, commence work to establish minimum instream flows in the Scott and Shasta Rivers, working with local partners on locally driven solutions and coordinating on options for incentivizing the reduction of diversions and groundwater pumping. (SWRCB, CDFW)
  • Currently, with state funding support, the Yurok Tribe, the Karuk Tribe, California Trout, Scott River Water Trust, and Farmers Ditch Company are developing a design-build project to restore habitat in the Scott River and improve water diversion infrastructure for on-farm water utilization and efficiency.

 For more on the Scott River issues see: https://calsport.org/fisheriesblog/?p=1608 .

Figure 1. Scott River streamflow in 2021 and 2022 at Fort Jones gage. Note the end of the irrigation season in November-December. Note also prescribed emergency flows were not met in 2022.

Figure 2. Shasta River summer 2021 and 2022 streamflow at the Yreka gage. Note the end of the irrigation season on October 1st. Note also prescribed emergency flows were met in 2022 with the exception of about a one-week period in August.

Figure 3. Scott River streamflow in summer-fall 2023 at Fort Jones gage. Note the July 2023 flow reduction when the emergency flow regulations ended. Note also the end of the irrigation season on December 1st.

Figure 4. Shasta River summer 2023 streamflow at the Yreka gage. Note the July 2023 flow reduction when the emergency flow regulations ended. Note also the end of the irrigation season on October 1st.

Figure 5. Scott River in Scott Valley in August 2013. The riverbed is perched above the water table that was low due to groundwater extraction for hay and pasture watering.

Figure 6. Lower Valley location of Scott River at the mouth of Shackleford Creek, a major salmon spawning tributary, on October 26, 2013.

Figure 7. Young’s Dam and fish ladder. Portions of the dewatered Scott Valley stream are located in the perched channel upstream of Young’s Dam. Under low late-summer streamflows, the ladder at Young’s Dam is not functional and blocks the Chinook migration. The channel upstream of the dam is wide and perched above the water table, so it is often too warm, with insufficient flow and cover, for rearing salmon. In contrast, the channel below the dam is deep and shaded with spring-fed juvenile salmon refugia.

  1. Beaver dams sometimes block salmon migrations.  In Alaska, biologists sometimes resort to blowing up dams with dynamite.  On the Yuba River near Brownsville, biologists in recent decades had to “dismantle” some dams to allow salmon access to tributary creek spawning habitat. ↩
  2. https://www.times-standard.com/2023/08/22/minimum-flows-set-for-scott-river-in-state-water-board-meeting/ ↩
  3. https://www.waterboards.ca.gov/drought/scott_shasta_rivers/docs/2023/petition-minimum-flows.pdf ↩
  4. https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/scott_shasta_rivers/docs/2022/klamath-reg-2022.pdf ↩
  5. State Water Board, Emergency Regulation Scott River & Shasta River Watershed, February 1, 2024:  https://www.waterboards.ca.gov/drought/scott_shasta_rivers/docs/2024/scott-shasta-reg-oal-approval-2024.pdf. ↩