Category Archives: Fish (general)

Butte Creek Spring Run Status – Fall 2024

Posted on by

The spring-run Chinook salmon in Butte Creek had extremely low spawning runs in 2023 and 2024 (Figure 1).

In part, this was because all Sacramento River Valley salmon populations are collapsing due to the direct and indirect effects of the 2020-2022 drought and related management actions, on top of climate change and catastrophic fires.1 Drought conditions in 2021 and 2022 in the spawning rivers, lower Sacramento River, Delta, Bay, and ocean all contributed to poor juvenile salmon survival.

The poor number of Butte Creek spawners in 2024 is also related to the high pre-spawn mortality of adult salmon in Butte Creek in 2021,2 as a result of drought conditions during the winter-spring upstream migration and summer-fall holding and spawning.

Despite the failures of brood years 2020 and 2021, there is optimism for brood year 2022 and its spawning run in 2025 (Figure 2). Water year 2023 was a wet year, with good young survival conditions for juvenile salmon. Though brood year 2022 had only about 3700 spawners, , the returning adults were able to migrate and spawn with minimal stress in a drought year.

The uncertainty that remains is the survival of brood years 2023 and 2024, because of their potential small number of returning spawners in 2026 and 2027. Water year 2024 was a above-normal water year, but it was not without its stresses.3 Early indicators suggest 2025 could be a dry year. The potential for small runs to lead to strong brood years also leaves room for doubt given that four recent years of poor spawners led to poor recruitment (four dots at lower left in Figure 2).

The poor spawner numbers in 2023 and 2024, coupled with the uncertain forecasts for runs in 2025-2027, represent a serious population threat that calls for strong actions to save the species and rebuilding the spawning stock.

Winter Actions

Winter fry-fingerling emigration down lower Butte Creek past the Parrot-Phelan Diversion Dam and the primary screw trap counting station occurs in earnest beginning in mid-December, with a peak in January. The peak in fry emigration (the main element of juvenile salmon production from Butte Creek) occurs during early winter precipitation events. The fry, often still feeding on their yolk sac, leave the cold turbid creek heading for warmer, low-velocity food-rich floodplain waters of the Butte Basin and the Sutter Bypass, and for the tidewater of the Bay-Delta.

Strong winter growth is essential for good survival (good growth rates, and lower rates of starvation and predation). Strong winter growth promotes early smoltification and entry to the ocean. The main success factors in winter are adequate transport flow, access to and from floodplain habitats in the Butte Basin and Sutter Bypass, and low predation rates.

Spring Actions

Pre-smolt, sub-yearling smolts, and yearling smolts emigrate in modest numbers from Butte Creek in spring. These late migrants contribute to population numbers and genetic diversity. Success of these late migrants depends on high transport rates, low water temperatures, minimal diversion to often excessively warm floodplain habitats, minimal entrainment into unscreened water diversions, and minimum flow-through rates from river to floodplain habitats.

Adult spring-run salmon migrate from the Bay to upper Butte Creek in spring. They require adequate flows and water temperatures often not available in drought years, especially in late spring.

Specific Winter and Spring Actions to Consider:

  1. Minimize water diversions at Parrot-Phelan Diversion Dam (and other creek diversions). In early winter, prioritize flow in Butte Creek over diversions for waterfowl pond flood-up and rice field decomposition (Figure 3), except in high runoff conditions. In spring, maintain flow in Butte Creek at the highest levels possible for attraction and holding except in early spring flood conditions.
  2. Minimize the flow split into Sanborn Slough at bifurcation weir. Do not force more than 30% of Butte Creek flow into Sanborn Slough, which reduces important benefits of floodplain access and inundation.
  3. Minimize diversions in Butte Basin and Sutter Bypass.
  4. Keep Butte Slough Outfall closed except under Butte Creek flood relief conditions; instead, maximize flow through Butte Basin and Sutter Bypass.
  5. In the event of dry-drought conditions, capture juvenile salmon at screw trap locations and Parrot Phelan Screen Bypass, and transport them to the mouth of Butte Creek, Verona, a conservation hatchery, downstream floodplain habitat, or a Bay-Delta location.
  6. Maintain adequate transport flows in the lower Yolo Bypass and lower Sacramento River, and into and out of the Delta in winter, to maximize survival to the Bay and ocean.

 

Figure 1.  Butte Creek spring-run salmon population (escapement or spawning run size) from 1975 to 2024.  Red circle highlights dramatic decline in 2023 and 2024.
Figure 2.  Spawner/recruit relationship for Butte Creek spring-run salmon with three-year lag between spawners and recruits.  Numbers shown in chart are return years (recruits).  Blue is a wet year two years prior to spawning run when salmon were rearing and migrating to the ocean.  Green are normal water years.  Red are dry and critically dry years.  Year labeled 25 is expected return run in 2025.  Purple line is potential range of runs in 2026 and 2027 depending on success of brood years 2023 and 2024.
Figure 3.  Water diversion rate at Parrot-Phelan Diversion Dam fall 2023 to fall 2024 (water year 2024).

White Sturgeon Recruitment to San Francisco Bay-Estuary in 2024

Posted on by

In a June 2024 post, I hypothesized factors controlling the white sturgeon population in San Francisco Bay-Estuary.  I concluded the major factor controlling the adult stock size was periodic recruitment of juvenile sturgeon from successful spring spawning and early rearing in the lower Sacramento River.  Successful recruitment only occurs in the wettest years, when there are higher streamflows and cooler water temperatures.

Recruitment of young white sturgeon in significant numbers has only occurred in three years since 2010:  2011, 2017, and 2023.  Recruitment in 2024, an above normal water year, is likely to be poor.  Production of young sturgeon is likely of function of attraction of spawners from San Francisco Bay (to high winter-spring river flows – good in 2024), good spawning conditions (streamflow and water temperatures – good in 2024), and good early rearing and transport conditions in the lower Sacramento River and the north and central Delta (streamflow and water temperatures – poor in 2024). 

The adult spawning stock size may not be as important as spawning conditions, given strong recruitment in wet year 2023 under a very low stock abundance (observed Bay die-off in summer of critical drought year 2022).

There are a number of measures that hold promise to protect and enhance adult stock numbers, recruitment, and survival of white sturgeon.

Spawning Conditions

Flows in the lower Sacramento River (Wilkins gage) should be 8,000 to 10,000 cfs or higher in spring.

Flow in the lower Sacramento River (Wilkins Slough) should be at least 8,000-10,000 cfs.

Early Rearing and Juvenile Transport

Sacramento River inflows to the Delta should be at least 20,000 cfs in spring.

Flow from the lower Sacramento River into the Delta (Freeport) should be at least 20,000 cfs in spring and early summer (April-July).

Delta Conditions

The net flow in the lower Sacramento River channel downstream of the entrance to Georgianna Slough should be at least 10,000 cfs in spring and early summer (April-July).  This will require total Delta diversions, including local agricultural diversions and exports by the State Water Project (SWP) and Central Valley Project (CVP), to be limited to approximately 10,000 cfs. 

Flow in the lower Sacramento River in the Delta below Georgianna Slough should be at least 10,000 cfs in spring and early summer (April-July).

White sturgeon recruitment is best assessed at fish salvage facilities at the water project south Delta export pumps.  Young sturgeon produced in the lower Sacramento River reach the Delta in early summer as shown here in 2023.  Note the high export levels of 20,000 acre-feet per day (approximately 10,000 cfs; in this figure, SWP exports are shown behind CVP exports).

Bay Conditions

Delta outflow to the Bay should be at least 10,000 cfs from spring to early fall (April-October).

Delta outflow to the Bay (DTO) and Rio Vista water temperature May-Oct, 2021-2024.  Recommended Delta Outflow is a minimum 10,000 cfs (purple line).

Minimize Sturgeon Adult Harvest and Pre-Adult Fishing Mortality

Sturgeon sport fishing should be limited to the Bay only, with catch-and-release regulations, with the following further considerations:

  1. Fishing for sturgeon should be closed in the east Bay or north Bay if daily maximum water temperatures are expected to exceed 65ºF (18ºC) in any open water portion gage locations in either Bay portions (possible from late spring through early fall).
  2. CDFW could allow limited harvest through short-term regulations, limited by slot (length range) and number.  (Note that slot harvest in 2024 would allow a small harvest of broodyear 2011 white sturgeon, the most recent abundant broodyear in the adult population).

Under such restrictions, the effects of sport fishing on the sturgeon population would be minimal.

In addition, sturgeon collected at south Delta export salvage facilities should be transported to an appropriate location in the Bay for release (presently, they are released in the Delta).   

Population abundance and recruitment of white sturgeon are mainly a function of annual Central Valley hydrology (river flow), with abundant juvenile production occurring only in the wettest years.  Past harvest has only involved a small percentage of the adult population, while watershed hydrology has orders of magnitude greater effect on recruitment and eventual adult population abundance.

Allowing a limited fishery could also help in continuing to assess the health of the population.  Sport fishers should be asked to contribute important information on the sturgeon they catch.

Park Fire – Spring-Run Salmon’s Worst Nightmare

Posted on by

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.

Increasing River, Delta, and Bay Summer Freshwater Flows Proves Viable Action

Posted on by

In Above Normal water year 2024, an increase in summer freshwater flows released from reservoirs to the Bay-Delta estuary has proven a viable action to reduce threats to Central Valley fishes.  Water management actions in early July heat waves alleviated extreme water temperatures that threaten the native fishes in rivers and the Bay-Delta.  These actions can be described as adaptive management experiments to test their potential performance for the update of the State Board’s Bay-Delta Plan. 

Actions

  • Increasing lower Sacramento River flow from 5000 cfs to near 8000 cfs has helped lower Wilkins Slough gage (WLK) water temperatures from 70-72oF to the water quality standard of 68oF (Figure 1), despite record-high air temperatures (Figure 2).
  • Increasing Delta inflow at Freeport (FPT) from 14,000 cfs to 20,000-22,000 cfs (a combination of increased Wilkins Slough, Feather River, and American River flows) has lowered Freeport water temperatures in the north Delta from 72oF to 70oF (Figure 1).
  • A rise in Delta outflow from 8,000 cfs to 12,000 cfs has helped reduce Rio Vista (RVB) water temperatures at the Delta’s exit to the Bay from 75-76oF during the early July heat wave to 72oF after the heat wave (Figure 2).

Benefits

The actions may not seem that dramatic, but they are very important to the river, Delta, and Bay environments and to the salmon, smelt, steelhead, sturgeon, and other native Central Valley fishes that depend on these habitats.  Water temperatures in the 72-75oF range are highly stressful or lethal to these native fishes.  Such temperatures favor non-native predatory and competing fishes.  Water temperatures of 68-72oF are at the upper favorable limits for the native fish and are necessary to maintain viable growth, survival, and reproduction.  These temperatures also help ensure that dissolved oxygen is adequate and that algae blooms do not reach excessive levels.  In other words, they promote a healthier ecosystem.  Water temperatures near or above 75oF, which occurred in the Delta of drought years 2021 and 2022 (Figure 3) under extreme low flows (Figure 4), are deadly to native Delta fishes.

Conclusion

Although water managers in 2024 probably did not have these bold actions in mind to save fish (flows were increased to allow maximum summer water diversions from the Delta), their fortuitous implementation clearly highlights early summer flow measures that should be included in the update of the Bay-Delta Plan.  Two additional actions I would recommend are higher flows in the San Joaquin River to provide some minimal benefit to the San Joaquin’s native fish community, and reductions in water exports.

Figure 1.   DTO = Delta Outflow to the Bay, FPT = Sacramento River Freeport gage, WLK = gage below Wilkins Slough on lower Sacramento River upstream of the Delta, RVB = Rio Vista Bridge in Sacramento River channel northwest Delta, near entrance to eastern Bay.

Figure 2.  Average daily air temperatures at Red Bluff (KRDD) in Sacramento Valley, Modesto (KMOD) in San Joaquin Valley, and Rio Vista Bridge (RVB) in west Delta May-July 2024.  Note Delta air temperatures are generally 5-15oF lower in the Delta than the valleys.  Also note the record or near-record air temperatures in early July.

Figure 3.  Average daily water temperatures in the north Delta channel of the Sacramento River at Freeport May-July 2021-2024 and average of years for decade 2001-2010.

Figure 4.  Average daily (tidally filtered) streamflow in the north Delta channel of the Sacramento River at Freeport, May-July 2021-2024 and average of years for decade 2001-2010.

Salmon and Sturgeon Bay Summer Season 2024

Posted on by

Starting with the Strawberry Moon

The Strawberry Moon, sometimes called the planting moon, is the June full moon (e.g., June 21, 2024). June is the end the juvenile salmon and sturgeon emigration season from the Central Valley to the Bay.  The Strawberry Moon June 2024 super tides drained the warm river and Delta waters into the Bay driving the remainder of the brood year 2023 salmon and sturgeon with it toward the Bay.

In a wet year, the young salmon and sturgeon are pushing through the Delta throughout June.  But 2024 was just an average water year, with the seasonal salmon and sturgeon emigration to the Bay ending with lower streamflow and higher water temperatures from the rivers through the Delta and then entering the Bay.  At this point, we cannot yet determine if the seasonal event was successful – we just do not know.  Regardless, we now must look toward the Bay to ensure that fish die-offs from warm water, low DO, and toxic algae blooms do not occur again.

What is important now is maintaining the Bay through the summer by ensuring toxic algae blooms and warm water do not stress the salmon and sturgeon present in the Bay.  With water temperatures in the eastern parts of the Bay already high (22oC/72oF) at the beginning of summer, it seems the Bay is destined for another bad summer of toxic algae blooms and dying adult sturgeon. 

What can be done to help keep the Bay cool this summer?  There are three actions that when taken together and in sequence can help keep the Bay cooler:  Keeping the rivers cooler keeps the Delta cooler.  Keeping the Delta cooler keeps the Bay cooler.  There are also some Bay actions that can sustain cooler water temperatures.

  1. Keeping Lower Rivers Cooler

First, how to keep the lower Sacramento and San Joaquin rivers entering the Delta cooler.  Higher streamflows speed the water along in the hot Valley keeping the rivers from absorbing heat.  We are only talking about 5oF or so, but it is an important five degrees. That is accomplished by maintaining adequate (legally prescribed) streamflows with reservoir releases, especially during summer heat waves that are getting hotter and more frequent with each decade (i.e., climate change). 

Figure 1.  Drought year 2022 spring-summer streamflow and water temperatures at Wilkins Slough (RM 120) upstream of the Delta.  Red line shows the target of 68ºF/20ºC needed to protect fish and keep the Delta cool.

Figure 2.  Wet year 2023 spring-summer streamflow and water temperatures at Wilkins Slough (RM 120) upstream of the Delta.  Red line shows the target of 68ºF/20ºC needed to protect fish and keep the Delta cool.

  • The Sacramento River in the North Delta

Next is the Sacramento River channel in the north Delta’s Freeport to Emmaton reach, with Rio Vista in the center.  This reach tends to emulate the input at Freeport, although it tends to warm when flow falls below 20,000 cfs (the inflow from Freeport, Cache Slough, and the San Joaquin River), as it too tends to warm as it slows down and sloshes back and forth with the tides in the summer sun.  Delta diversions[1] can (and often do) take 12,000-13,000 cfs out of the 20,000 cfs Delta inflow (65% is the prescribed limit).

Input water temperatures at Freeport in June of 2023 and 2024, with streamflow of 15,000 cfs, were generally 70oF or higher (Figure 3).  In 2023, inflows of 20,000-40,000 cfs brought water temperatures in the 62-66oF range with slightly higher water temperatures during heat waves.  When streamflow at Freeport fell below 20,000 cfs in summer 2023, water temperatures reached 70oF or higher, especially during heat waves, when water temperatures spiked 2-4oF.  Maintaining 20,000 cfs inflow at Freeport generally would bring water temperatures below 70oF.[2]

Figure 3.  Wet year 2023 and above normal year 2024 spring-summer streamflow and water temperatures of the Sacramento River at Freeport (RM 90) at entrance to the Delta. 

Downstream of Freeport in the central portion of the Sacramento River north-Delta channel at Rio Vista Bridge, water temperature patterns are similar to Freeport although slightly warmer and more erratic (Figures 4 and 5).  Rio Vista is subject to inputs of warmer water from Cache Slough and the San Joaquin River and thus tends to be slightly warmer than Freeport.  Net river flows at Rio Vista are also lower, as Delta water diversions can markedly reduce the Delta inflows by this location.  Operation of the Delta Cross Channel also complicates the flow splits upstream of Rio Vista.  Cooler Delta air compared to the Sacramento Valley is also a factor.  However, the main factors appear to be water temperatures and inflows from upstream (Freeport).  Keeping Freeport streamflows cooler should keep Rio Vista water cooler, especially during summer heat waves like the three in July 2023.

Figure 4.  Water temperatures at the Rio Vista Bridge in the north Delta 2019-2024.  Red line is recommended 72ºF limit.

Figure 5.  Water temperature (daily average) at Rio Vista Bridge in north Delta from May-September 2023 – a wet year.  Also shown are Rio Vista Bridge (Delta) and Red Bluff (Sacramento Valley) daily average air temperatures.

  • The Bay

Summer Bay water temperatures are a function of inputs from the Delta and ocean, and of local air temperatures and tidal circulation.  At the Benicia Bridge between the east Bay (Suisun Bay) and the north Bay (San Pablo Bay), the influence of freshwater inflows is not unlike that in the rivers and Delta.  In wet years like 2023, high freshwater inflows in June kept salinity and water temperature lower (<20oC/68oF) (Figure 6).  Warm water generally comes in from the Delta, especially during the twice monthly tidal-cycle draining of Delta water into the Bay (Figure 7).  A one-foot stage drop from the 500,000-acre Delta into the Bay is 500,000 acre-ft of warm Delta water that over several days can have a measurable effect on the Bay.  The late June 2024 full super moon is already heating the Bay with warm river and Delta water (Figure 7).  A cooler Delta would make for a cooler Bay.

Figure 6.  Hourly water temperatures and salinity (EC) at Benecia Bridge in west Suisun Bay June 2022-June 2024.  Red boxes denote June periods in each year.

Figure 7.  Hourly water temperature (degrees C) and salinity (EC) in east Suisun Bay in late June 2024 after full moon.  Note warm fresher water from upstream (Delta) on ebb tides.

Conclusions and Recommendations

Poor water conditions in the Sacramento River, Delta, and Bay this summer will have negative effects on salmon, sturgeon, and other native fish populations.  Unless there is action to mitigate these effects, the summer fish die-offs that occurred in summers of 2021-2023 in the Bay are likely to occur again this summer.  The following actions can reduce these negative effects:

  • Maintain the water quality standard of 68oF (daily-average) in the lower Sacramento River at the Wilkins Slough gage.  This will require raising river flow from the planned 4000-5000 cfs level to 6000-8000 cfs level or higher (during heat waves).
  • Maintain an average daily Delta freshwater inflow of 20,000 cfs at the Freeport gage.
  • Increase the freshwater inflow above 20,000 cfs and/or reduce Delta water diversions as necessary during heat waves to maintain a daily-average 68oF at the Freeport gage and maximum hourly 72oF at the Rio Vista gage.
  • Consider operational changes to the False River weir, Delta Cross Channel gates, and Montezuma Slough gates, which may also help reduce localized adverse effects.

[1] South Delta exports, smaller regional diversions, Delta agriculture, etc.

[2] Based on review and analyses of many years of data at Freeport and other locations.