Category Archives: Fish (general)

Smelt Status – Winter 2023 How Low Can You Go?

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In prior posts in December 2022 and November 2021, I described the status of listed delta smelt and of longfin smelt.  More recent information shows little change in the dire outlook for these two native Bay-Delta fish (Figures 1-4).

Delta smelt and longfin smelt populations have declined severely over the past few decades due to poor water management. In the Bay-Delta, where the smelt spend most of their lives, south Delta water exports and warming of the Bay and Delta from reduced inflow and outflow has limited their production.  Temporary urgency change petitions (TUCPs) during multiyear droughts and  subsequent orders by the State Water Board have allowed reduced Delta outflow, leading to higher water temperatures and increased Delta salinity. The State Board is again considering yet another TUCP in winter 2023 that would reduce Delta outflow to allow higher exports.

In this winter 2023, the Low Salinity Zone has again moved further upstream (eastward) into the Delta because of falling freshwater inflow to the Delta after the January storms.  Delta exports have fallen with lower Delta inflows as State Board conditions kick in.  The TUCPs are an obvious and direct threat to these population remnants living in the Low Salinity Zone.  Further allowing these weakened standards to be violated is a direct disregard for these nearly extinct species.  Water management places them at extraordinary risk by (1) bringing them further into the Central-Delta zone of the two large South-Delta water diversions, (2) degrading smelt habitat with lethal water temperature, (3) further degrading their already depleted food supply, and (4) increasing the concentrations of toxic chemicals being relentlessly discharged into the Delta.

The scientific literature, and water and resource management agencies, all recognize these major problems.  Many management and recovery schemes have been developed and implemented over the decades.  However, nothing has stopped water managers’ relentless excessive use and abuse of the Central Valley hydrology.  The salmon, smelt, sturgeon, and steelhead are not just the victims but serve as “canaries in a coal mine”, all dying while the water is continually mined from the system.  Meanwhile, water managers blamed this mass extinction event on on climate change, cynically gaming worsening conditions to extract even more water.

There is more and more talk of employing “ecosystem-based management” that integrates the environment into all phases of decision-making, effectively giving the environment a seat at the table.  But the reality is more like giving the chickens a say in how the foxes manage the depopulation of the hen-house.  There is also talk about providing more flexibility in how and when water is used – allocating environmental water as “functional flows” or “environmental water storage” to optimize the ecosystem benefits of what little water is allocated for the environment.  Placed in he hands of water managers, such efforts simply give them more flexibility to game the system to their advantage.  When they think they can get more water, they just ask for it and usually get it.  One policy group proposes: “Making this work may require establishing assets for the environment—such as water budgets, reservoir storage space, and funding to restore physical habitat—that can be flexibly used to adapt to changing conditions.”  No, a piece of bread and a cup of water on the survivors’ deathbeds are all they get.  Even the water managers get to choose the physical habitat and how its restored, and how much extra water they can take as a result.

It is time to change this pattern of abuse of public trust resources by standing up to abusers in the State’s TUCPs, the Update of the Bay-Delta Water Quality Control Plan, and the public review of the Delta Tunnel Project.  The Tunnel simply adds another straw in the Delta, but further upstream, closer to the mouths of the Feather and American rivers, the main sources of Bay-Delta freshwater inflow.

Figure 1. Bay-Delta fall-midwater-trawl longfin smelt catch index 1967-2022.

Figure 1. Bay-Delta fall-midwater-trawl longfin smelt catch index 1967-2022.

Figure 2. Longfin Smelt Fall Midwater Trawl Index in recent two decades 2001-2022.

Figure 2. Longfin Smelt Fall Midwater Trawl Index in recent two decades 2001-2022.

Figure 3. Log-Log relationship for longfin smelt index year (number shown are brood year “recruits”) vs index two years prior (spawners). Red numbers represent brood years that were the product of dry water years, green numbers = normal water years, and blue = wet water years. Blue dots are six most recent years, 2017-2022: fewer spawners produce fewer recruits.

Figure 3. Log-Log relationship for longfin smelt index year (number shown are brood year “recruits”) vs index two years prior (spawners). Red numbers represent brood years that were the product of dry water years, green numbers = normal water years, and blue = wet water years. Blue dots are six most recent years, 2017-2022: fewer spawners produce fewer recruits.

Figure 4. Catch of Delta smelt in 20-mm Survey in late March 2022. Seven were captured in the north Delta just upstream of where adult hatchery smelt were released in December 2021.

Figure 4. Catch of Delta smelt in 20-mm Survey in late March 2022. Seven were captured in the north Delta just upstream of where adult hatchery smelt were released in December 2021.

 

 

Missing an Opportunity Downstream of Shasta Lake Late Fall – Early Winter Pulse Flow for Salmon Needed

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Juvenile winter-run, spring-run, fall-run, and late-fall-run salmon need a flow boost in the fall and winter to help them emigrate 300 miles down the Sacramento River from their spawning area below Shasta Lake to and through the Bay-Delta.1 Yet while winter storms have now caused massive runoff downstream, the spawning reach of Sacramento River remains at its minimum flow. Even small pulse releases from Shasta and Keswick reservoirs during storms would start hundreds of thousands of juvenile salmon on their way to the ocean.

Historically, more than 50% of salmon spawning in the lower Sacramento River took place downstream of Clear Creek (Figure 1). That distribution has now changed, with over 90% of the spawning upstream of the mouth of Clear Creek in the 20 miles of river downstream of Keswick Dam. This change is a consequence of water management that confines suitable spawning habitat in summer and fall to the uppermost river reach.

Many juvenile salmon begin their migration to the ocean when the first fall rains create a pulse in streamflow. These fish include winter-run and late-fall-run smolts, and fall-run and spring-run fry. The first fall rain-induced flow pulse has been long recognized as an important functional flow event for all four salmon runs. For many decades, the fall pulse was recognized as an important feature needed in salmon management to ensure good survival of smolts to the ocean.

The fall pulse has often been forestalled in recent decades both by droughts and by water management. When the fall pulse comes, it comes only from upper river tributaries. But the natural salmon production cycle in the upper 20 miles of the spawning reach misses out on the flow benefit of fall rains. All runoff is captured in Shasta Reservoir. While downstream reaches receive tributary rainfall-induced streamflow (Figure 2), the upper river receives no pulse from Shasta Reservoir despite significant inflows (Figure 3). This factor alone is a key factor limiting natural production of the four salmon runs in the upper Sacramento River.

Lack of flow from Shasta also limits the effectiveness of the overall flow pulse (Figures 4 and 5) that carries the juvenile salmon downstream to the estuary. The upper Sacramento River, McCloud River, and Pit River flow into Shasta Lake. These major spring-fed rivers are the largest contributors of natural flows to the Sacramento River watershed, especially in drier years. They have not provided any the mainstem streamflow to the Bay-Delta estuary as yet this year. This pattern is generally true in all but the wettest water years.

Shasta Lake gained about 40,000 acre-feet in the first fall storm (Figure 6). A pulse flow of 5000 cfs for three days (an increase of approximately 2000 cfs for 72 hours) would have amounted to approximately 12,000 acre-feet, or roughly 30% of the water gained and (0.8% of the total storage). Considering that much of the first storm fell as snow, water managers could have reasonably have executed such a short pulse..

The second storm has delivered Shasta Reservoir another 100,000+ acre-feet. With a wet forecast for January, it is now time to release a least a short pulse from Shasta to move juvenile salmon downstream to where they can surf the tributary inflow to the Sacramento River downstream to the Delta. It is not too late. Before the storm that began December 29, most of the juvenile salmon remained upstream of Red Bluff or downstream in the river above the Delta,2 as few had shown in Sacramento seines and trawls (data not shown).

CDFW map

Figure 1. Upper Sacramento River and historic salmon spawning distribution by percent by region. River-mile shown in parentheses. (Data source: CDFW)

Graph of 2022 Sacramento flows

Figure 2. Fall river flows at seven locations from Keswick Dam RM-300 (KWK), Bend RM-250 (BND), Hamilton City RM 200 (HMC), Colusa RM-144 (COL), Wilkins Slough RM-140 (WLK), Verona RM-80 (VON), and Freeport RM-50 (FPT) in the Delta.

Graph of Shasta River Flows

Figure 3. Shasta Reservoir inflow and outflow in December 2022. (Data source: CDEC)

Graph of fry/smolt

Figure 4. Screw-trap catch of fry spring-run and fall-run salmon with environmental data in fall 2022 at three locations in lower Sacramento River.

Graph of Juvenile Chinook

Figure 5. Screw-trap catch of winter-run fry-smolt salmon with environmental data in fall 2022 at three locations in lower Sacramento River.

Graph of Shasta storage levels

Figure 6. Shasta Reservoir storage level in Nov-Dec 2022.

Central Valley Hatchery Salmon Production Is Being Wasted A Tale of Two Hatchery Salmon Smolt Release Groups

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There are two common strategies for releasing juvenile salmon from  state and federal salmon hatcheries in the Central Valley.  One strategy is the release of hatchery salmon smolts at or near the hatchery where they are produced.  The other strategy is trucking the smolts from the hatchery and releasing them into the Bay.  There is much controversy and argument over the relative merits of the strategies.  There can be little argument that release into the Bay generates far more adult salmon than release near the hatcheries.

Consider what occurred with two American River release groups after their release in May 2018 and return as adults in 2020.  Release group #061465 was 669,000 fall-run smolts (3-4 inches long) that were transported 20 miles downstream from the American River (Nimbus) Hatchery and released into the mouth of the American River under the Jibboom Street Bridge.  Release group #061467 was 650,000 fall-run smolts transported approximately 100 miles downstream to net pens at the Wickland Oil Terminal for release into eastern San Pablo Bay, about 20 miles from the Golden Gate Bridge and the Pacific Ocean.

The estimated percent survival based on tag recoveries was 0.04% for group #061465 (released near the hatchery).  The estimated percent survival was 2.20% for group #061467 (released in San Pablo Bay).  The returns by locations are shown in Figures 1 and 2.  These relative results are common.

Figure 1. Returns for tag group #061465.

Figure 2. Returns from tag group #061467.

 

The Demise of Sacramento River Spring-Run, Fall-Run, and Late-Fall-Run Chinook Salmon

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We all know the story of the demise of Sacramento River winter-run Chinook salmon below Shasta Dam over the past several decades (Figure 1).1 But what has happened to the other three Chinook runs: the spring, fall, and late-fall runs? They too have declined (Figure 2-4). Just 50 years ago, 300-500 thousand Chinook salmon ascended the Sacramento River to spawn. This was decades after most of the big Central Valley dams were built. Today, less than 10,000 Chinook salmon return to spawn near Redding. Most of these are Battle Creek and Livingston Stone hatchery fish, plus strays from Feather, American, Mokelumne, and Merced hatcheries. Wild, native Chinook are becoming increasingly rare with each decade.

There are many factors that have led to the demise of Sacramento River Chinook salmon. No doubt, the two major droughts (76-77 and 87-92) had major roles. There was bad management and lack of regulatory protection on many levels. Today, the details of a post mortem are of less value than recognizing the problem and doing something about it.

Much has been tried and accomplished (three of the four runs substantially improved around the turn of the century). A decade of effort and wet years achieved much. However, the three major droughts since (07-09, 13-15, and 20-22) have undone much of those gains and more.

What needs to be done now to bring the salmon back from the brink of extinction is the following:

  1. Recognize and acknowledge the problem (we haven’t)
  2. Develop a single integrated, comprehensive plan to solve it (there isn’t one)
  3. Overhaul the massive salmon hatchery program (we spend huge sums raising and releasing over 30 million salmon smolts each year – the price per pound is astounding – most never reach the ocean)
  4. Overhaul our salmon fisheries program managed by the Pacific Fisheries Management Council (it’s not working – the stocks are in a constant state of over-fishing – and the fishery is not the most important problem – shutting fishery gates after fish have escaped the corral doesn’t solve the problem)
  5. Overhaul the Central Valley water supply management system (it’s taking all the water for humans and leaving none for the salmon – don’t let folks blind you, it’s true)
  6. Overhaul the Central Valley water quality management system (drought “emergencies” routinely bring weakening of standards, wiping out annual salmon runs)
  7. Rebuild salmon habitat from the ground up (much is gone and what is left is degrading fast, as past and present efforts at watershed restoration literally burn away each year).
  8. Implement the comprehensive plan with prioritized short- and long-term goals, objectives, and actions.

The sooner we implement these actions the better – Sacramento River salmon are facing a “Passenger Pigeon” moment. The longer we wait, the tougher it is going to be and the less chance there is we will succeed.

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1970-2021 In-River Winter Chinook

Figure 1. Sacramento River Winter-Run Chinook

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1969-2021, In-River Spring Chinook

Figure 2. Sacramento River Spring-Run Chinook

Graph of Adult Escapement (fish/year) Mainstem, Keswick Dam to Red Bluff Diversion Dam spawn years 1952-2021, In-Rier Fall Chinook

Figure 3. Sacramento River FallRun Chinook

Graph of Adult Escapement (fish/year) Mainstem, Upstream of RBDD, Sacramento River, spawn years 1971-2021, In-River Late-Fall Chinook

Figure 4. Sacramento River Late-Fall-Run Chinook

 

How did Winter-Run Salmon do in Summer 2022? Not Good.

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First the bad news. The production in 2022 of winter-run salmon fry in the upper Sacramento River near Redding was at record low levels, similar to the disaster years 2014 and 2015, maybe worse (Figure 1).

Next, more bad news (there is no good news). Most of the fry are now in the 100-mile reach below Red Bluff, with only a small proportion to date (November 7) reaching Knights Landing below Chico (Figure 2). Flows (Figure 3) remain too low for good fry survival, with little flow increase following late October and early November rains. Clear water conditions make it easy for the tens of thousands of striped bass and smallmouth bass residing in the 100-mile reach to pick off migrating juvenile salmon. Up till late October, water temperatures above 60ºF kept bass active (also Figure 3). With conditions expected to be similar to last year, one can only expect this year’s production to be similar to last year’s poor production (Figure 4).

Some might say increased hatchery winter run production in 2022 is good news. Higher than normal numbers of hatchery fry are being raised in the Livingston-Stone Fish Hatchery for release next winter. But last winter’s hatchery releases during critical drought conditions did not fare well, as shown by the very small numbers that reached the Delta (Figure 5). To compensate, Interior began increasing egg-taking1 for the hatchery and transporting adults and hatchery smolts to upper reaches of Battle Creek. While these actions are worthwhile, the problem remains that drought year release returns (harvest plus escapement) average about 0.2%, compared to 2% returns in wet years.2

The prognosis for the winter-run salmon from all these sources of recruitment during the 2020-2022 drought to return as adults into fishery catches and the spawning runs is grim.3 The population does recover after wetter year periods (2016-2019, Figure 6), but not without the support of the hatchery. More needs to be done to improve wild and hatchery fry survival and smolt production to safely recover the winter-run salmon population. Flow pulses and enforcement of the state water temperature standards are needed. Vitamin injections, more hatchery egg-taking, and taxi rides alone will not do the job.

Graph showing Run Size from 2007 through 2022

Figure 1. Annual catch of unmarked juvenile winter run salmon in screw traps near Red Bluff as of November 13, 2022. (Source)

Graphs showing Water Temperature and Daily Estimated Passage

Figure 2. Juvenile winter-run salmon catch in Red Bluff and Colusa screw traps in 2022. (Source)

Graph showing flow CFS and Temp

Figure 3. Water temperature and flow rate below Keswick Dam (KWK, RM 300), at Bend near Red Bluff (BND, RM 250), and below Wilkins Slough (WLK, RM 120) in 2022. (Source)

Graph of Cumulative Catch per Brood Year

Figure 4. Annual catch of unmarked juvenile winter run salmon in screw Chipps Island trawls near Pittsburg, CA. Red arrow shows 2021 catch. (Source)

Graph of Observed Chinook Salvage at SWP and CVP Delta Fish Facilities

Figure 5. Salmon salvage at south Delta export facilities in 2021. Salvage of hatchery release groups is color coded. Red arrow shows winter-run hatchery smolt release group and the subsequent capture/salvage of two smolts from the group in late March. (Source)

Graph California Central Valley Population Database Report CDFW GrandTab Adult Escapement

Figure 6. Winter run salmon escapement 1970-2021. (Source)