Category Archives: Northern California

State Water Board to Decide Fate of Shasta and Scott River Salmon and Steelhead – Part 2, the Scott River

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On July 1, 2021, staff from the State Water Resources Control Board (State Board) held a public Zoom meeting to provide information and solicit input on potential actions that could be implemented to address low flows in the Scott River and Shasta River watersheds (Figure 1) during the ongoing drought.  The Scott and Shasta rivers are major salmon and steelhead producing tributaries of the Klamath River. The State Board’s July 1 workshop sought input and options prior to taking action.   

 CSPA is providing comments through this three-part series.  Part 1 was the introduction, with a description of the general problems and solutions.  This is Part 2, with specific comments on the Scott River.  Part 3 will cover the Shasta River.

The Scott River Problem

The Scott River has a chronic low streamflow problem that occurs in the summer and fall of most years.  Only in very wet years, do ranchers and fish for the most part get the water they need.  In most years, nearly all the water in the watershed goes to agriculture, while the lower river and its tributaries run virtually dry.  Fish survive in the upper reaches of the river and in the lower tributaries that receive snowmelt and spring water from the adjacent Marble and Trinity mountains.  There are also spring-fed refugia in the middle sections of the river and In tributaries to the lower sections of the river.  But at many locations in the watershed, a large portion of the surface-water flow goes underground into near-surface aquifers, only to resurface as springs and be further diverted or extracted by wells, or go back underground.

The California Department of Fish and Wildlife is recommending summer minimum flows from 30-50 cfs at the lower end of the river to protect over-summering juvenile Chinook and Coho salmon, and steelhead.  These recommended flows represent roughly half of the available summer baseflow water supply in the Scott River.  Without a minimum flow requirement, almost the entire summer baseflow is  consumed by a carefully distributed water supply extraction system regulated by seniority-based surface water rights and overseen by the State Board or by minimally regulated groundwater pumping.  A large portion of the consumption occurs by means of minimally regulated shallow well pumping from the valley’s alluvial floodplain aquifer.  This supplies water for stock watering, pasture irrigation, or large scale sprinkler irrigation of hayfields.  The aquifer is recharged by surface flows and applied irrigation, and in places is augmented by beaver dam flooding.  The floodplain was once known as “beaver valley”.  However, much of such wetland floodplain habitat has been lost to channelization to enable irrigated agriculture.

There are many areas in the watershed that provide refugia for over-summering salmon and steelhead.  The extent of these refugia decreases over the summer as the surface water supply declines and springs cease flowing.  The loss of refuge habitat over the summer is greatest in drought years.  As the extent of refuge habitat declines, juvenile salmon and steelhead become more concentrated or succumb to “catastrophic stranding” where they die from refugia drying up or overheating.  Many refugia are on private lands.  Many are unidentified.  They need to be identified and surveyed to determine their characteristics and need for protection.

Drying rivers also pose problems for emigrating juvenile and immigrating adult salmon and steelhead in the fall and winter.  When fall rains and winter snow are lacking or late, juvenile fish are hindered or blocked from moving downstream to the Klamath River.  Adult fish cannot move upstream to spawning grounds in the valleys.

General Solution Options for the Scott River

Other than CDFW’s recommended minimum instream flows to save the fish (which would be successful), there are further options to help the fish.  One major option is to protect through the summer-fall season the many refuge areas that are present and functioning at the end of the spring snowmelt season. This can be accomplished in several ways:  (1) not allowing any diversion of surface or groundwater within or near the designated refuge; (2) pumping well water directly into the refugia; (3) diverting other surface waters into the refugia; and (4) protecting and enhancing refuge habitat (e.g., cattle fencing, riparian plantings, channel improvements).  The basic concept is to protect and enhance cold-water habitats of the refugia.  Each refuge will have its own prescription.  Some may benefit from introduced beaver colonies.  Note that some landowners working with CDFW and local stakeholder groups have accomplished some of these actions at varying scales of effort and with varying degrees of success.

Another solution option is a program to scale back seasonal agricultural water use based on the needs of fish and their habitat, as well as those of the landowners.  For example, a major problem for Scott River salmon is not being able to ascend into Scott Valley in the fall because of low streamflows.  Unlike the Shasta River Watershed, in which irrigation is disallowed after October 1, irrigation is allowed into December in the Scott watershed.  Scott Valley hay-crop irrigators in particular could cease irrigating a month or two earlier, foregoing late season cuttings.  This option was suggested by a landowner of a large ranch who was even willing to use his large-capacity wells to help water the river during the fall salmon migration.

Specific Recommended Solutions

The following recommendations offer large potential benefits with limited impacts and costs.

1.      Focus on the surface water irrigation diversions – all should cease in summer of dry years

Two large diversions with large canal distribution systems make up the bulk of the surface water diversions in Scott Valley, at least in wetter years or spring of drier years.  If these have not as yet cut back diversions as in most dry years, their diversions should cease.  The largest diversion, Young’s Dam, is a relatively large concrete structure with a fish ladder (Figure 2).  In summer of dry years, it usually does not divert, but does back up water in the river channel, causing significant rises in water temperature.  More flow would minimize such heating.  More flow is necessary to provide upstream passage of adult salmon in late summer and fall through the dam’s fish ladder, even when the dam is not diverting water.

The second largest surface diversion is Farmers Ditch, which diverts directly from the Scott River channel (Figure 3).  It too usually does not divert in summer of dry years, due to lack of surface flow.  Prior to ceasing its diversions, it contributes to drying up the river in the downstream tailings reach.

There are many small diversions1 in the middle and upper valley from reaches of the river and lower tributaries that retain flows in the summer.  Locally, they divert significant portions of the available streamflow.  Some are crudely designed and operated, and are unregulated (Figure 4).  All surface diversions should cease operating, since most are from spring-fed stream reaches supporting rearing salmon and steelhead.  In many cases, such diversions contribute to the dewatering of downstream reaches.  One such example is lower Shackleford Creek, where multiple small diversions in flowing spring-fed sections in the several miles upstream contribute to the drying up of the creek near its mouth on the Scott River (Figure 5).

2.      Middle and lower reaches of Scott River affected by groundwater pumping – all well pumping from locations contributing to dewatering of the main channel of the Scott River or lower tributaries should cease pumping.

Most free-flowing reaches of the middle and lower Scott River and its lower tributaries are over-summering juvenile salmon and steelhead refugia.  Even warm low flows provide some cooler hyporheic flow to sustain young salmon and trout in microhabitat areas of the stream channel (Figure 6; also see videos referenced at the end of this post).  Such locations cannot support high population densities for long and thus could use added flow to sustain them.

3.      Refugia in middle and lower reaches of Scott River and lower tributaries affected by groundwater pumping could be supported by pumping cold groundwater into stream channels to help sustain refuge habitat.

In reaches where groundwater pumping is no longer needed, idle wells can pump cold groundwater directly into stream channels to sustain specific refugia or to provide added flow for fish migrations.  Many ponds situated within the Valley’s water table have cold water that could be drained or pumped to refuge areas.  The tailings reach in the upper end of the Valley has many such ponds.

Summary and Conclusions

All surface diversions from free-flowing reaches of the Scott River should cease in summer-fall of 2021.  All such reaches are fed by snowmelt or springs, and are most likely refugia for over-summer rearing salmon and steelhead.  All well pumping near the river and lower tributaries that may affect springs or hyporheic flow in refugia should be cut back to help sustain the refugia.  All refugia should be identified and classified to value and need.  Where feasible, wells or surface waters can supply supplemental water to sustain refugia.  All refugia should be mapped, surveyed, and characterized for need; high value  options should be identified and implemented.  All irrigation in the Scott Valley (not including stock watering) should cease by October 1, as is already done in the Shasta Valley.  Cutbacks of well pumping for Scott Valley irrigation should commence on a graded scale on August 1 and September 1.

Figure 1. The Scott River and Shasta River Valleys in northern California west of Yreka, CA (Yreka is located in the Shasta River Valley). The Scott and Shasta Rivers flow north into the Klamath River, which runs west to the ocean. The Salmon River watershed is immediately west of the Scott River watershed. The upper Trinity River watershed is immediately to the south of the Scott River watershed.

Figure 3. Farmers Ditch diversion located in upper middle valley on Scott River.

Figure 2. Young’s Dam and diversion located on the Scott River in mid-Valley.

Figure 4. An unnamed small diversion located in spring-fed reach of Scott River below tailings reach. Both the river and diversion ditch contained large numbers of juvenile coho salmon.

Figure 5. The mouth of Shackleford Creek on Scott River in late summer.

Figure 6. Reach of the lower Scott River upstream of Fort Jones near Eller Bridge, nearly dewatered by groundwater pumping and lowering of the groundwater table. Despite lack of flow, the reach retains some over-summering refuge pools sustained by groundwater and hyporheic flow. Eventually, these areas become too warm, and many thousands of juvenile salmon and steelhead die. Such areas would benefit from a cessation of irrigation with water sourced from adjacent wells. Idle wells could be employed to add cold water to sustain the refugia.

Available Videos of Scott River Refugia

 

 

 

  1. There are approximately 800 water right holders in the Scott River watershed. ↩

State Water Board to Decide Fate of Shasta and Scott River Salmon and Steelhead

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On July 1, 2021, staff from the State Water Resources Control Board (State Board) held a public Zoom meeting to provide information and solicit input on potential actions that could be implemented to address low flows in the Scott River and Shasta River watersheds (Figure 1) during the ongoing drought.  The Scott and Shasta rivers are major salmon and steelhead producing tributaries of the Klamath River.

Low flows in the Scott and Shasta have led to the recurring mortality of salmon and steelhead due to high water temperatures, stranding, or hindered migration.  The recurrence, duration and intensity of mortality events now threatens the extinction of salmon and steelhead in these rivers. 

Low flows in both watersheds are caused by surface diversions and groundwater extraction by local agriculture.  Although low flows are often attributed to drought and climate change, they have become a regular occurrence even in wetter years.  Drought and climate change intensify and increase the frequency of low flow conditions that have become the norm each summer and fall. 

The State Board under the governor’s drought emergency declaration could limit water use to help save the fish.  This would come at substantial cost to local agriculture and communities.  The State Board July 1 workshop sought input and options prior to taking action.

The California Department of Fish and Wildlife is recommending summer minimum flows near 50 cfs to protect over-summering juvenile Chinook and Coho salmon, and steelhead.  Such flows represent roughly half of the available water supply in both rivers.  Absent action by the State Board, this water would be nearly completely consumed by a carefully distributed water supply extraction system regulated by seniority-based state water rights overseen by the State Board.

In this three-part report, CSPA provides a general strategy plus watershed-specific recommendations to help address the issues and save the fish.  In this introduction, we address the general problems and solution strategies.  We will follow up with by two watershed-specific parts, one on the Scott and one on the Shasta.

General Problem

The low-flow problem in the Scott and Shasta watersheds occurs in most years.  In exceptional high flow, high snowmelt years, ranchers and fish for the most part get the water they need.  So in most years, nearly all the water goes to agriculture ,and the lower rivers and their tributaries go virtually dry.  Fish survive in the upper river and tributaries, and in middle portions of the mainstem rivers that convey water to the more downstream users.  Overall, large portions of the flow go underground into near-surface aquifers, only to resurface and be further diverted or extracted by wells.

There are many areas in both watersheds that provide refuges for over-summering salmon and steelhead.  The extent of these refuges decreases over the summer as the surface water supply declines and springs cease flowing.  The loss of refuge habitat over the summer is greatest in drought years.  As the extent of refuge habitat declines, juvenile salmon and steelhead become more concentrated.  Many succumb to “catastrophic stranding,” where they die because refuges dry up or get too hot.

Drying rivers also pose problems for emigrating juvenile and immigrating adult salmon and steelhead in the fall and winter.  When fall rains and winter snow are lacking or late, juvenile fish are hindered or blocked from moving downstream to the Klamath River.  Adult fish cannot move upstream to spawning grounds in the valleys.

General Solution

The general solution is to focus on maintaining summer refuges and providing fall and early winter flows.  Refuges can be maintained on a general or individual basis by protecting natural surface and spring flows or providing supplemental flows where feasible.  Each watershed has specific options for sustaining or supplementing streamflows.

Each watershed has about 100 cfs of base streamflow in summer, maintained by permanent springs or higher-elevation snowmelt.  Maintaining a 50 cfs flow as recommended by CDFW is a matter of cutting surface diversions and groundwater extractions.  To minimize restrictions on water users, flows can be supplemented from various limited surface storage sources or from groundwater aquifers.  Both these options can be accomplished to a great extent in the short term.

Since opportunities to save fish this year exist, quick action is necessary.  An intensive survey-monitoring program is needed to (1) best allocate available resources, (2) effectively apply necessary restrictions, and (3) evaluate the effectiveness of actions taken.

In the next two parts, we address watershed-specific problems and solutions for the Scott River and Shasta River watersheds. 

Figure 1. The Scott River and Shasta River valleys in northern California. Yreka, CA is located near the northwest corner of the Shasta River valley. The Scott River valley is west and somewhat south of Yreka. The Scott and Shasta rivers generally flow north into the Klamath River, which generally runs west to the ocean. The Salmon River watershed is immediately west of the Scott River watershed. The upper Trinity River watershed is immediately south of the Scott River watershed.

Peaking Power at Shasta Dam in Summer 2021 – Saving Winter Run Chinook Salmon

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In a recent 6/13/21 post, I discussed various tradeoffs of Shasta Reservoir operations on water supply deliveries, power production, and salmon survival for summer 2021. In that post I made reference to tradeoffs with peaking power production at the Shasta hydropower system. This post provides more information on those potential tradeoffs.

Peaking Power Production

Peaking power refers to the release of varying amounts of water through power turbines on a within-day schedule to meet the peak power demands of the regional electric grid. Inflows into Keswick Reservoir near Redding show the peaking power production schedule from Shasta Dam and Whiskeytown Dam into Keswick Reservoir on the Sacramento River (Figure 1). Over a recent two-day period, June 12-14 2021, hourly inflows to Keswick Reservoir ranged from 1900 cubic feet per second (cfs) to 17,500 cfs. Peak inflows were in late afternoon and evening, reflecting peak power demands. Minimum inflows were in the early morning, when power demand is low.

Peaking Power and Water Temperature from Shasta Dam

High releases for peaking power at Shasta Dam can draw warm water from near the surface of Shasta Reservoir (Figure 2). Water temperature below the dam increased from 50ºF to 56ºF in the recent example peaking periods, June 12-14. The positive relationship between dam release flow and water temperature is obvious (Figure 3).1

Peaking Power and Water Temperature from Whiskeytown Dam

In contrast to Shasta Dam, there was minimal influence on water temperatures when there were peaking releases from Whiskeytown Dam from June 12-14. The release water temperatures into Keswick Reservoir through the Spring Creek Powerhouse are minimally influenced by the flow rate (Figures 4 and 5). On June 13, there was no peaking through Spring Creek Powerhouse, but there was little variation in water temperature from peaking days on June 12 and 14.

Summary of Shasta-Keswick Operations

Shasta-Keswick operations is about to enter a new phase of summer operations. Under the Bureau pf Reclamation’s planned operations, there will be larger volumes of exports from the Trinity River system through Whiskeytown Reservoir over the summer. There will also be larger release volumes from Keswick Reservoir to meet increasing downstream contractor demands (Figure 6).

Proposed Operations

The proposed CSPA Temperature Management Plan2 for June-October, 2021 would provide a lower Keswick Dam release. First, Trinity exports would end, except for releases of 300 cfs down Clear Creek, because Trinity water releases through Spring Creek Powerhouse are already pushing the threshold temperature of 53ºF. Second, Shasta release would be limited to releases from coldwater pool at 52ºF to provide 5000 cfs total Keswick release, thereby saving Shasta storage. Third, peaking power at Shasta Dam would be minimized to ensure that warm surface waters are not drawn into the TCD gates (Figure 7) during peaking operations.

Sustaining the cold-water pool in Shasta through the summer is a function of (1) maintaining total storage and cold-water-pool volume in storage: (2) reducing Whiskeytown releases when they become too warm (>53ºF); and (3) minimizing warm water from peak power releases. Such a strategy would help save winter-run salmon eggs in the summer spawning season.

Figure 1. Inflow (cfs) to Keswick Reservoir from Shasta Dam and Spring Creek Powerhouse (cfs), June 12-14, 2021.

Figure 2. Water temperature (ºF) of the water released from Shasta Dam, June 12-14, 2021.

Figure 3. Relationship between water temperature and Shasta Dam release volume, June 12-14, 2021.

Figure 4. Total reservoir release (cfs) from Whiskeytown Dam, June 12-14, 2021. Note that of the minimum 250 cfs release, about 125 cfs were released to Clear Creek to maintain base flows and were not releases through Spring Creek Powerhouse.

Figure 5. Water temperature of water exiting the Spring Creek Powerhouse into Keswick Reservoir, June 9-14, 2021.

Figure 6. Summary of Shasta operations, June 1-13, 2021. Note SAC is gage station 5 miles below Keswick Dam on Sacramento River. Source: https://www.usbr.gov/mp/cvo/vungvari/sactemprpt.pdf

Figure 7. Shasta Dam operations and reservoir storage conditions on June 10, 2021. Source: https://www.usbr.gov/mp/cvo/vungvari/sactemprpt.pdf .

  1. At other times, depending on specific conditions and operations, the opposite relationship is true.  See https://calsport.org/fisheriesblog/?p=3596, Figure 6, for example from 2014 when higher temperatures were associated with lower release volumes. ↩
  2. Referenced in https://calsport.org/fisheriesblog/?p=3714.  The May 23, 2021 CSPA Temperature Management Plan proposed limiting Trinity exports to 300 cfs for the entirety of the June-October period, to be released exclusively down Clear Creek.  In addition to the water temperature benefits in the Sacramento River, such operation would also conserve cold water and overall storage in Trinity Reservoir. ↩

Shasta Reservoir Operations, April 2021 Recap – A Bad Start to an Awful Year

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April 2021 is a month for the record books. Central Valley Project (CVP) operations of the Shasta-Trinity Division were beyond the pale. Water year 2021 began as a critical drought year after a dry year, with everyone scrambling to save the winter-run salmon in the Sacramento River below Shasta and provide water for downstream CVP contractors. The two opposing goals have proven impossible to meet. With no approved operations plan, the US Bureau of Reclamation (Reclamation) moved ahead to fulfill its water contractor needs at the expense of the federally-and state-listed endangered winter-run salmon, other fisheries, and carryover storage for 2022.

Water releases in April to the Sacramento River below Shasta were significantly higher in 2021 than in the most recent critical drought years 2014 and 2015 (Figure 1). With these higher releases, Shasta storage, which began ahead of 2014, ended up lower than 2014 (Figure 2). As a consequence, Shasta’s cold-water pool has also fallen behind what it was in both 2014 and 2015 (Figure 3). In both 2014 and 2015, releases of warm water from Lake Shasta led to extremely high spring-summer egg mortality, devastating the winter-run spawning year cohort. In both years, the cold-water pool in Shasta simply gave out before the end of summer.

In 2021, water temperatures in the Sacramento River below Shasta have already risen well above the safe level (Figure 4) as Reclamation began releasing warm surface water from Shasta in mid-April to meet contractor demands.1 Reclamation seems to accept sacrificing endangered salmon again in 2021. There has been little mention of the similar fate this year for green and white sturgeon, and for spring-run and fall-run salmon.

Figure 1. Daily average flows (cubic feet per second) in Sacramento River below Shasta Reservoir in April 2014, 2015, and 2021.

Figure 2. Daily average storage (acre-feet) in Shasta Reservoir in April 2014, 2015, and 2021.

Figure 3. Daily average cold-water-pool (<52ºF) volume in Shasta Reservoir in 2014, 2015, 2021 (black line), and other selected years.

Figure 4. Daily average water temperature in Sacramento River below Shasta in April-May period of 2014, 2015, 2020, and 2021. Red line represents safe target daily average water temperature (53ºF) for winter-run salmon egg incubation.

Lake Shasta and Sacramento River Operations: Lessons Learned – #1, Part 2

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Following an introductory post, this is the second post in a series on the lessons learned by the National Marine Fisheries Service (NMFS) from the 2013-2015 drought that devastated Sacramento River salmon populations.  The first post addressed Lesson #1 and its non-application in the first half of 2020. 

This post addresses how the non-application of Lesson #1 in 2020 evolved into a tug-of-war in the second half of 2020 and has cascaded into non-action so far in 2021. For more detail and links, see CSPA’s March 15, 2021 letter to the State Water Board urging immediate action to protect Sacramento River and Delta fisheries in 2021.  See also the State Water Board’s Sacramento River Temperature web page, though some of the links are not live, at: https://www.waterboards.ca.gov/waterrights/water_issues/programs/drought/sacramento_river/index.html

Water and fisheries managers have known for many years that both the Lake Shasta storage level on April 1 and spring releases from Shasta determine how much cold water will be available in the lower Sacramento River through the summer.  However, in 2020, as discussed in Part 1 of this series, the Bureau of Reclamation (Reclamation) refused to decide on water temperature management options for Shasta Reservoir and the lower Sacramento River before April 1.  Reclamation submitted a draft temperature management plan (TMP) to the State Water Board on April 23 and a final TMP on May 20, neither of which evaluated reduced delivery options whose analysis the State Water Board had requested.

Meanwhile, Reclamation was operating in 2020 in the first year of the new Trump-era Biological Opinions for the long-term operation of the Central Valley Project (CVP) and the State Water Project (SWP).1 The stated purpose of these Opinions was to “maximize deliveries” of water to contractors, and did they ever deliver.  See part of the results in Figure 4 of the previous post: very high deliveries to Sacramento River CVP contractors in April and May, so that water in Lake Shasta was committed before the plan to operate Shasta was complete.

By June 1, 2020, the State Water Board had rejected Reclamation’s TMP.  In its June 1, 2020 letter refusing Reclamation’s May 20 TMP, the State Water Board wrote:

Reclamation has declined to evaluate additional operational scenarios. Reclamation’s position is that scenarios with different operational assumptions would be inconsistent with its contractual obligations, and are therefore beyond Reclamation’s reasonable control. The State Water Board disagrees. To the extent that Reclamation delivers water under its own water rights, Reclamation’s obligation to deliver water to its contractors does not take precedence over its permit obligations.

On July 17, 2020, CSPA and its partners reached a settlement agreement with the State Water Board that dealt in substantial part with Sacramento River temperature management.  The settlement agreement requires the State Board to conduct a transparent Sacramento River Temperature Management process.  The process must address all controllable factors, including deliveries, and ensure adequate staffing, modeling and public review.  The CSPA settlement became part of the dispute between Reclamation and the State Water Board in the following months.

After exchanges of letters between Reclamation and the State Water Board in June and July, and an addendum to the TMP on July 31, the State Water Board gave up on 2020 and in an August 4 letter  tentatively approved the TMP, subject to conditions, two of which stated:

  • Reclamation shall develop a draft protocol by September 30, 2020, that meets the criteria identified by the State Water Board;
  • By September 15, 2020, Reclamation shall provide additional information concerning fall operations, including the volume and timing of releases and deliveries each month through December.

On August 31, the State Water Board sent a follow-up letter clarifying its request of Reclamation:

As part of the State Water Board’s conditional approval of Reclamation’s 2020 Temperature Management Plan (TMP), Reclamation is required to develop an initial draft protocol by September 30, 2020. The State Water Board will hold a public workshop this fall in coordination with Reclamation to receive public comment on the initial draft protocol to inform its completion. Once public comments are received, the Board intends to work with Reclamation to refine and finalize the protocol before the beginning of the next temperature planning and water supply allocation season in February 2021. The Board has requested that the protocol include the elements specified in the settlement agreement with the California Sportfishing Protection Alliance, et al., which the Board recently forwarded to Reclamation. This letter provides additional detail regarding issues that should be addressed as part of the protocol.

None of it happened.  No protocol.  No public workshop.  No public comments.  No disclosure to the State Water Board of the timing and releases of release and deliveries from September through December.  No final protocol by February 2021.  Instead, one final letter from Reclamation on September 30, deflecting the issue to the settlement with CSPA even though the issues in the settlement were issues raised by the State Water Board months before the settlement was completed: “Reclamation does not consider a state court voluntary settlement, to which Reclamation is not a party, as valid, enforceable legal requirements imposed on Reclamation.”

After all the correspondence, Reclamation affirmed on September 30 that it was right the first time: “The process for analyzing conditions and incorporating the best information into water management decisions for temperature management at Shasta Reservoir is outlined in the Shasta Cold Water Pool Management Flow Guidance document which was shared with the State Board staff on April 2, 2020.”

And so it comes full circle.  Faced with adversity last fall, the State Water to date performed as it all too often has: it has done nothing.  The Ides of March have passed, and there is every sign that the State Water Board will for a second straight year allow Reclamation to once again defy Lesson #1: Keswick releases need to be decided by April 15.