Category Archives: Water Quality

The Importance of Big Springs to the Shasta River

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Big Springs contributes streamflow, cold water, and volcanic nutrients to the middle and lower Shasta River. Although its contribution to the overall volume of the Klamath River is small (Figure 1), the cold, nutrient-rich flows originating from Mount Shasta’s source springs, combined with a gentle gradient, play a key role in making the Shasta River the most productive salmon tributary in the Klamath River watershed.

Streamflow

Big Springs is the major source of water for the Shasta River.  It’s 52ºF clear water supports salmon, steelhead, and trout in the middle and lower Shasta River.  Its 100-120 cfs base inflow makes up the predominant flow of the Shasta River in summer (Figure 2).

Much of the water sourced from springs in the watershed is diverted for agriculture or other human purposes. The primary uses are pasture irrigation, hay production, and livestock watering. Other purposes include bottled water production, domestic use, and city supply.

Water from the upper mainstem—both spring-fed and snowmelt—is stored in Lake Shastina and released gradually throughout the summer via a large canal and ditch system. Big Springs, which serves as the main source of spring water for the middle and lower river, is also diverted or pumped into irrigation systems through several small dams and distribution networks.

Notwithstanding its springs-fed sources, the Shasta River experiences ongoing streamflow shortages, especially during summer and fall in most years. Only exceptionally wet years provide enough water for both ranchers and fish. In dry years, nearly all water is allocated to agriculture, leaving the lower river and its main tributaries—such as Parks Creek, Little Shasta River, and Yreka Creek—almost completely dry. Salmon and steelhead manage to survive during these dry periods only in the middle sections of the Shasta River and in nearby large springs fed by Mt. Shasta’s snow fields or by leakage from Lake Shastina.

Before irrigation begins on April 1, base flows in the Shasta River are about 150 cubic feet per second (cfs). They drop to 10-20 cfs or less by summer (Figures 3 and 4). Flow recovers once irrigation ends after October 1. Most diversions in the mainstem Shasta River happen in the reach 10 to 20 miles downstream from Big Springs, as shown by streamflow data from Montague (Figure 5).

Water Temperature

Reduced flows result in elevated temperatures in the lower river, often above 65ºF. These high temperatures restrict salmonid habitat, survival, and smolt production. Unlike the nearby Scott River, dewatering and stranding aren’t major issues in the middle Shasta River’s spring-fed refuge. Instead, high water temperatures between Grenada and the mouth of the Shasta River at the Klamath River pose the main challenge. Historical temperature records at Yreka show that the lower river becomes almost uninhabitable for salmonids in summer, with temperatures reaching 20–25ºC due to low streamflows and warm agricultural runoff.

Data from the Grenada gage (Figure 6) show acceptable water temperatures (below 20ºC) when streamflows exceed 50 cfs. These levels would at least meet the minimum requirements for migrating adult fall-run Chinook salmon in late summer.

Most salmon and steelhead spawning and rearing occur in the middle stretches of the Shasta River below Big Springs, where cold, spring-fed water creates ideal habitat. However, during dry summers like 2021 (Figures 3 and 4), the amount of cold spring-sourced water that reaches Yreka is minimal due to upstream extraction.

Source of Nutrients

“The unique water quality of the Big Springs complex, and presumably other spring complexes associated with the Shasta River south of the Big Springs Creek-Shasta River confluence, was likely one of the largest contributing factors to high historical abundances and productivity of salmonids in the Shasta River.” (Jeffres, et. al. 2009.)

The Shasta River below the spring complexes is rich in natural sources of nitrogen (N) and phosphorus (P). These elements support high concentrations of aquatic invertebrates. This in turn contributes to the river’s historically high fish production (Jeffres, et. al. 2009).

Agricultural runoff is another source of nutrients. However, agricultural return flows often have elevated water temperatures, which, in combination with animal and plant waste, contribute to point sources of low dissolved oxygen in the stream.  Such conditions degrade salmonid spawning, rearing, and migration habitat.

Conclusion

Big Springs and other springs in the Shasta River system supply cold, high-quality water that supports salmon and steelhead populations. Maintaining an adequate amount of spring-fed water throughout summer is vital. Any assessment of river flow needed for salmon and steelhead should consider the source and quality of streamflow, as well as the location of springs in relation to specific reaches of the river. Flow, water temperature, and proximity to springs are all important.

Figure 1. Lower Klamath River with late May of wet year 2017 streamflows in red. Note Shasta River streamflow was only 140 cfs near Yreka, California. Data source: CDEC.

Figure 2. Selected Shasta River hydrology in late May of wet year 2017. Roughly 150 cfs of the 300 cfs total basin inflow was diverted for agriculture, with remainder reaching the Klamath River. Red numbers are larger diversions. The “X’s” denote major springs. Big Springs alone provides near 100 cfs. Of the 100 cfs entering Lake Shastina (Dwinnell Reservoir) from Parks Creek and the upper Shasta River and its tributaries, only 16 cfs was released to the lower river below the dam. Red numbers and arrows indicate larger agricultural diversions. Up to 15 cfs is normally diverted to the upper Shasta River from the north fork of the Sacramento River, west of Mount Shasta.

Figure 3. Streamflow during peak Chinook salmon spawning season in the lower Shasta River near Yreka CA in September and October of drought year 2021. Yellow markers show average for the day over 84 years of gage record.

Figure 4. Streamflow in the lower Shasta River near Yreka CA from April 2018 through June 2021. Yellow markers show average for the day over 84 years of gage record. Note the low streamflow in dry summer 2020 and spring-summer of drought year 2021.

Figure 5. Streamflow in the lower Shasta River near Montague CA from April 2019 through June 2021. Note the low streamflow (<30 cfs) in spring-summer of dry year 2020 and spring of drought year 2021.

Figure 6. Water temperature (hourly) in the lower Shasta River below Big Springs near Grenada CA July 2019 to June 2021. Source: CDEC.

Bibliography

Jeffres, C. A., R.A. Dahlgren, M.L. Deas, J.D. Kiernan, A.M. King, R.A. Lusardi, J.M. Mount, P.B. Moyle, A.L. Nichols, S.E. Null, S.K. Tanaka, A.D. Willis. 2009. Baseline Assessment of Physical and Biological Conditions Within Waterways on Big Springs Ranch, Siskiyou County, California. Report prepared for: California State Water Resources Control Board. https://watershed.ucdavis.edu/sites/g/files/dgvnsk8531/files/products/2021-11/Jeffres-et-al-SWRCB-2009.pdf

Shasta River Watershed Stewardship Report. 2018. Shasta Valley Resource Conservation District 215 Executive Court, Suite A, Yreka, CA 96097. Version 1.2 April 2018. https://ifrmp.org/wp-content/uploads/2021/10/SVRCD_2018_0548_Shasta_Watershed_Stewardship_Report.pdf#:~:text=Shasta%20River%20Watershed%20strongly%20influences%20groundwater%20chemistry%2C%20which%20is&text=Big%20Springs%2C%20Shasta%20River%20at%20the%20Montague%E2%80%90Grenada%20Bridge%2C%20and%20Shasta%20River

Butte Creek Spring-Run Salmon – May 2026 Update

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Central Valley Spring-run Chinook Salmon. Central Valley spring-run Chinook salmon typically return from the ocean and enter the Sacramento River system from February through June. Spawning occurs in Sacramento River tributaries from mid-September through early October with genetically distinct populations known from Clear, Mill, Deer, and Butte Creeks. Central Valley spring-run Chinook salmon also spawn in the Feather and Yuba rivers. Juveniles emigrate soon after emergence as young-of-year, or remain in or near their natal streams and emigrate as yearlings. Yearlings typically emigrate with the first flow increases in the fall and early winter. Similar to winter-run, Central Valley spring-run Chinook salmon populations have suffered significant declines in size. They are state and federally listed as threatened. CDFW

Butte Creek is a moderately sized tributary of the Sacramento River, located in California’s Central Valley near Chico, CA (Figure 1). It supports a core population of the threatened spring-run Chinook salmon native to the Central Valley and Sacramento River. Over the past decade, the Butte Creek watershed has experienced some of the largest Sierra fires of recent record.1 Prior to this period, the spring-run salmon in Butte Creek had represented a successful recovery within one of the Central Valley’s few remaining undammed streams.

I last updated the status of the Butte Creek spring-run salmon in a November 2024 post.  The spawning runs in spring-summers of 2023 and 2024 had been devastatingly low after suffering in the most recent three-year drought (2020-2022).  Some recovery in the spawning population in 2025 and 2026 brings a measure of optimism.

Problems with Recruitment

Low runs in 2023 and 2024 (Figure 2) suggest that brood years 2023 (BY23) and 2024 (BY24) will make limited contributions to runs between 2025 and 2028. Fewer eggs and any poor survival rates (e.g., from the 2024 fires or Thiamine deficiencies) will restrict recruitment of age 2-4 spawners from both brood years, limiting their contributions (recruitment into) to the future runs.

Initial survey findings show that the runs in 2025 and 2026 had fewer contributions from BY23 and BY24. Instead, most of the fish came from BY21 and BY22 spawners, whose offspring thrived during the wet years of 2023 to 2025 and gained advantages from fishery closures in those same years. Preliminary information on the 2026 run (not shown in Figure 2) indicates a low run, with only modest numbers of age-4 BY22 spawners, and lacking the normally predominant age-2 (BY 24) and age-3 spawners (BY 23).

The Cause

The cause of depressed recruitment in 2023 and 2024 was most likely poor spawning and early survival conditions during drought water years 2020-2022 that affected brood years 2020-2024.  The poor 2023 run was likely the consequence of poor survival of their source spawning adults (prespawn mortality in 2019-2021), eggs laid (2019-2021), and juveniles reared (2020-2022) of BY19-BY21 affected by the drought conditions of fall 2019 through winter-spring 2022.  For example, conditions in 2020 were very poor from low flows and high water temperatures from spring to fall (Figure 3).  The failure of PG&E’s Butte Canal in 2023 may have also been a factor.

The cause of the poor 2024 run is more complicated, because the number spawners in 2021 was high.  Drought conditions in fall 2021 and spring 2022 likely contributed to poor reproductive success and low smolt production (Figure 4).  However, the 2023 and 2024 ocean fisheries were closed, which should have more than doubled the normal run size.  The 2024 massive Park Fire may have contributed to the poor run, with lower summer-fall flows and higher water temperatures (Figure 5) and high pre-spawn mortality.

Other factors related to escapement (run size) include ocean conditions (e.g., the warm water blob and Thiamine deficiency), fishery harvest (or lack thereof), conditions in the lower Sacramento River and Bay- Delta.  All factors acting together in combination is yet another factor, with each factor potentially contributing to the other factors.

Conditions in the lower Sacramento River and Bay-Delta are changing for the worse.  For example, 2026 has been a relatively wet year, but poor snowpack and low March precipitation has led to stressful river and Bay-Delta habitat conditions in March during the peak of the adult spring-run salmon migration from the ocean.  Delta inflow was too low and water temperatures too high from mid-March to early April in 2026, almost as poor as drought year 2022 (Figures 6 and 7).  This problem led the Bureau of Reclamation to release a pulse flow from Shasta Dam in early April 2026 to help migrating salmon in the Sacramento River and its tributaries.

Solutions

The improvement of reliably robust runs of spring-run Chinook salmon is bound up in ongoing debates on how to manage Butte Creek salmon and their habitat.  Resource enhancement funds are scarce.  There is significant mitigation funding available from the PG&E 2023 flume failure that could play an important role.  More on solutions in upcoming posts.

Figure 1. Current distribution of spring-run Chinook salmon as reported by CDFG, 1998.

Figure 2. Butte Creek spring-run salmon escapement estimates by surviey 2001-2025. Source: CDFW.

Figure 3. Butte Creek water temperature and streamflow at USGS BCK-gage near Chico Feb-Oct 2020. Water temperatures above 18-20C are stressful to migrating and holding adult salmon.

Figure 4. Butte Creek water temperature and streamflow at USGS BCK-gage near Chico Aug 2021 to Jun 2022. Water temperatures above 18-20C are stressful to migrating juvenile salmon and holding adult salmon.

Figure 6. Flow in the Sacramento River at Freeport at the entrance to the north Delta in spring 2022-2026. Red line is recommended minimum Freeport flow. Source: CDEC.

Figure 7. Water temperature(F) in the Sacramento River at Freeport in the north Delta in spring 2022-2026. Red line is recommended maximum Freeport water temperature for spring salmon migrations. Source: CDEC.

Bay-Delta Conditions – Early Spring 2026

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Figure 1. Sacramento River system and major water gaging locations in red.

Figure 1. Sacramento River system and major water gaging locations in red.

Dry and Warm Beginning in March

The end of winter 2026 brought dry conditions to the lower Sacramento River and Bay-Delta (Figure 1). What had been wet-year-type conditions in early March at Wilkins Slough (WLK) and Freeport (FPT), and high Delta outflows (DTO), had become dramatically drier by late March (Figures 2 and 3). The lower flows and dry warmer weather brought warm water temperatures stressful (>65ºF) to many of the Delta’s native juvenile fish (smelt, salmon, steelhead, and sturgeon) that concentrate in the lower Sacramento River and the Bay-Delta in early spring.

Reservoirs were holding back what remained of the winter snowmelt (Figure 4), putting unnecessary stress on this year’s fish reproduction. Minimum flows should have been 10,000 cfs at Wilkins Slough, 20,000 cfs at Freeport (below inputs from the Feather and American Rivers), and 10,000 cfs Delta outflow (see Figure 1 for locations).

Delta exports were moderate but falling from 8000 cfs to 5000 cfs during March (Figure 5). With falling Delta inflows and dry and warming conditions, central and southern Delta water temperatures also increased to stressful levels (reaching 70ºF, Figure 5). The moderate exports decreased outflow and increased Delta water temperatures.

Many of the naturally produced juvenile salmon had passed into the Delta by early March (Figure 6) and began showing up in Delta export salvage (Figure 7).  Millions of Sacramento River hatchery salmon were released in late March and began showing up in Delta export salvage facilities (Figure 8).  These fish also suffered from the low flows and related stress-level water temperatures.

Wet and Cool April

Wet and cool weather returned to the Central Valley in April.  Reclamation also released a flow pulse from Shasta Reservoir into the Sacramento River to help salmon migrations (Figure 9).  Benefits of the flow pulse came late to the problem but will likely provide benefits further into the spring.

Figure 2. Sacramento River daily average streamjlow and water temperatures, and Delta outflow to the Bayin early spring 2026. Orange, green, and blue lines are recommended minimum daily-average flows for Freeport, Wilkins Slough, and Delta outflow. Red line is the sress-level for water temperature at Wilkins Slough and Freeport for juvenile Delta native fish.

Figure 2. Sacramento River daily average streamjlow and water temperatures, and Delta outflow to the Bayin early spring 2026. Orange, green, and blue lines are recommended minimum daily-average flows for Freeport, Wilkins Slough, and Delta outflow. Red line is the sress-level for water temperature at Wilkins Slough and Freeport for juvenile Delta native fish.

Figure 3. Delta outflow and Sacramento River channel flow below rhe Delta Cross Channel (GES) along with west Delta water temperatures at Antioch (ANH), Rio Vista (RVB), and Emmaton (EMM) in early spring 2026.

Figure 3. Delta outflow and Sacramento River channel flow below rhe Delta Cross Channel (GES) along with west Delta water temperatures at Antioch (ANH), Rio Vista (RVB), and Emmaton (EMM) in early spring 2026.

Figure 4. Streamflow and water temperature from the lower Feather River at Gridley (GRL) and American River at Fair Oaks (AFO) in early spring 2026.

Figure 4. Streamflow and water temperature from the lower Feather River at Gridley (GRL) and American River at Fair Oaks (AFO) in early spring 2026.

Figure 5. Delta exports from state Harvey Banks and federal Tracy pumping plants, San Joaquin River Delta inflow at Mossdale, and water temperatures at the three locations in early spring 2026.

Figure 5. Delta exports from state Harvey Banks and federal Tracy pumping plants, San Joaquin River Delta inflow at Mossdale, and water temperatures at the three locations in early spring 2026.

Figure 6. Catch of juvenile salmon in Knights Landing screw trap along with river flow, water temperature, and turbidity from August 2025 to April 2026.

Figure 6. Catch of juvenile salmon in Knights Landing screw trap along with river flow, water temperature, and turbidity from August 2025 to April 2026.

Figure 7. Export rates and juvenile salmon daily salvage at south Delta export pumping planrs in winter and early spring 2026.

Figure 7. Export rates and juvenile salmon daily salvage at south Delta export pumping planrs in winter and early spring 2026.

Figure 8. Marked hatchery salmon Delta pumping plant salvage and export rates from November 2025 to April 2026. Also shown is net flow in south Delta Old and Middle River channels (OMR) near export facilities.

Figure 8. Marked hatchery salmon Delta pumping plant salvage and export rates from November 2025 to April 2026. Also shown is net flow in south Delta Old and Middle River channels (OMR) near export facilities.

Figure 9. Shasta/Keswick Dam release rates into the Sacramento River near Redding CA in late winter and early spring 2026. Also shown is daily average rate for previous 62 years.

Figure 9. Shasta/Keswick Dam release rates into the Sacramento River near Redding CA in late winter and early spring 2026. Also shown is daily average rate for previous 62 years.

American River Salmon Update – Spawning Season, November 2025

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In a 10/19/2023 post and a 11/21/2024 post, I discussed how the lack of access to Folsom Reservoir’s deep cold-water pool results in delayed natural and hatchery spawning of American River fall-run salmon.  Delays, and spawning in warmer water, cause reductions in spawning success, smolt production, recruitment into harvestable fishery stocks, and spawning escapement (run size) to the American River.  Lower salmon contributions from the American River significantly reduce California coastal and river salmon fishery stocks.  Poor production in the American River contributed to the closure of California salmon fisheries in 2023-2025.

During the 2020-2022 drought, Reclamation released water from the lower-level power bypass (sacrificing hydropower production) to provide the cold water (<55ºF) salmon needed for spawning in the ten-mile spawning reach from Nimbus Dam (near Fair Oaks gage) to the William Pond gage (Figure 1).  This is the prime spawning reach for salmon in the lower American River.  However, in the fall of the wetter years 2023-2025, Reclamation did not use the power bypass to release cold water (Figures 2 and 3), despite higher storage levels than during the drought (Figure 4).  The lack of cold water delayed natural spawning and hatchery egg taking, to the detriment of egg viability, fry production, and smolts reaching the ocean.

Ultimately, the number of adult salmon returning to the American River to spawn (escapement) is the important measure of success.  There are many factors that may contribute to the number of returns.  Recent returns are up (Figure 5).  The 2023 and 2024 returns were good despite having been the product of the 2020-2022 drought reproduction (Figurer 6).  Closed fisheries in 2023 and 2024 contributed to higher escapements.

I also believe efforts to improve fall water temperatures below Folsom during the drought improved both the wild and hatchery components of escapement.  I remain concerned that a return to warmer fall water temperatures will hinder future escapement.

I am also concerned with apparent efforts to sustain higher fall 2025 reservoir levels (see Figure 4) by reducing tailwater stream flow rates (Figure 7).  Such low flows reduce the quantity and quality of salmon spawning habitat.  Many critical spawning side channels become dewatered at such low flows1.  Main channel velocities, substrate, and depths are also compromised at low flow rates.

Reclamation  also reduced funding for the salmon hatchery and for river habitat projects in 2025, and will likely do the same in subsequent years.  This strategy will not help to recover American River salmon stocks to levels that once again can contribute toward commercial and recreational salmon fisheries.

Figure 1. Map of three CDEC gaging stations on the lower American River.

Figure 2. Average daily water temperatures in Nov-Dec period at William Pond gage 2021-2025. Red line (55ºF) denotes upper safe level for Chinook spawning.

Figure 3. Average daily water temperatures in November period at Fair Oaks gage 2021-2025. Red line (55ºF) denotes upper safe level for Chinook spawning.

Figure 4. Late summer and fall Folsom Reservoir water storage (acre-feet) 2021-2025.

Figure 5. Adult salmon escapement estimates for the American River 1975-2024. Source: Grand Tab.

Figure 6. American River spawner/recruit relationship – { log10(escapement) -3.5]. Number is year of escapement (recruits). Color denotes water year type two years prior. Red is dry, green is normal, and blue is wet. Note escapement in 2023 and 2024 are red, denoting spawning and rearing occurred two years earlier in dry water years.

Figure 7. Streamflow (daily average) in the American River at Fair Oaks gage Aug-Nov period 2021-2025.

Reclamation plans to take more water from the Delta

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A December 3, 2025 article in the LA Times warns of the federal government’s plan to take more water from the Delta. This is not something new – they have maximized exports much of this year and last year (Figure 1).  The State of California has also been doing this, but to a lesser extent (Figure 2).  Together, the two projects can export up to 22,000 acre-ft per day (8,000 acre-ft/day at Tracy, 14,000 acre-ft/day at Banks).  In a wet (2023) or above-normal year (2024 and 2025) exports can exceed 6-million acre-feet out of a potential maximum export pumping capacity of 8 million acre-feet.

The projects were able to exceed expectations in above-normal water year 2025 by eliminating the Fall-X2 Action that over the past decade required higher Delta outflows and lower exports in the September-October period to protect Delta smelt in the Bay-Delta.  In September 2025, the projects were able to export 674,000 acre-feet by dropping the Fall-X2 Action, compared to 536,000 acre-feet in September 2024 when the Fall-X2 Action was implemented.

The increased September exports in 2025 had significant environment effects that impacted salmon, smelt, and other Bay-Delta native fishes.

  • First, Delta outflow to the Bay was reduced in half (about 300,000 acre-feet, Figure 3) through a combination of the higher exports and lower reservoir releases (Delta inflow, Figure 4). That led to higher temperatures of water entering the Bay and the low salinity zone (LSZ) moving upstream from the Bay into the west Delta channel near Rio Vista (Figures 5 and 6).  These effects are detrimental to salmon at the peak of their fall migration into the Bay from the ocean and to the low salinity zone, which is designated critical habitat for smelt.
  • Second, lower Delta inflow from the Sacramento River (Figure 4) led to higher water temperatures in the north Delta at Rio Vista (Figure 6) and Freeport (Figure 7).
  • Third, reduced flows in the lower Sacramento River (Wilkins Slough, Figure 8) led to higher water temperatures (Figure 9), detrimental to salmon during their spawning migration to the upper Sacramento River and its tributaries.

In drier years (below-normal, dry, and critical), there are no Fall-X2 Actions, but there are many other restrictions on river flows, exports, and reservoir storage use to protect fish and their habitat as well as future water supplies.  In the past, Delta exports in drier years have been limited to only 3 to 5 million acre-feet per year.  We have yet to see the federal government’s plan to export more water in such years.  We can only guess as to what drastic changes to expect and the environmental damage that could ensue with the new federal export plan.  Higher spring exports in 2025 (see Figure 1) is one such change.

Figure 1. Federal exports from the south Delta via the Tracy Pumping Plant (TRP) in 2024 and 2025

Figure 2. State exports from the south Delta via the Harvey Banks Pumping Plant (HRO) in 2024 and 2025.

Figure 3. Delta Outflow to the Bay in Aug-Sept period of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 4. Streamflow in the north Delta at the Freeport gage May-Dec 2024 and 2025. The Fall-X2 Action was implemented in September 2024 but not in September 2025 nor in October 2024 or 2025.

Figure 5. Salinity and water temperature in the west Delta near Rio Vista from August 2023 through September 2025 with emphasis on Sep-Oct period. Red lines denote water temperature (20C) above which there is significant stress on migrating adult fall-run salmon. The Fall-X2 Action was not implemented in October 2024 or September 2025.

Figure 6. Water temperature in the Sacramento River channel at the Rio Vista Bridge gage Aug-Sep 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 7. Water temperature in the Sacramento River channel at the Freeport gage in September 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 8. Streamflow in the lower Sacramento River at the Wilkins Slough gage in September of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.

Figure 9. Water temperature in the lower Sacramento River at the Wilkins Slough gage in September of 2024 and 2025. The Fall-X2 Action was not implemented in September 2025.