Welcome to the California Fisheries Blog

The California Sportfishing Protection Alliance is pleased to host the California Fisheries Blog. The focus will be on pelagic and anadromous fisheries. We will also cover environmental topics related to fisheries such as water supply, water quality, hatcheries, harvest, and habitats. Geographical coverage will be from the ocean to headwaters, including watersheds, streams, rivers, lakes, bays, ocean, and estuaries. Please note that posts on the blog represent the work and opinions of their authors, and do not necessarily reflect CSPA positions or policy.

Klamath River Salmon – the Wrong Advice!

Posted on October 14, 2019 by Tom Cannon

In a June 2019 article in the LA Times , also posted in Maven’s Notebook, JACQUES LESLIE suggests that “hatcheries don’t belong in this picture” once the planned removal of four dams on the Klamath River is complete. Based on my decades of work in the Klamath watershed, this post suggests a different approach. A conservation hatchery could accelerate and improve the outcome of the recovery of Klamath River salmon. I respond below to a few statements in the article.

“Allowing hatchery salmon to mix with struggling native salmon after removing the dams is like rescuing a dying man only to slowly poison him.”

Native salmon are nearly extinct or already extinct over much of the Klamath River watershed. A small population of spring-run Chinook remains only in the Salmon River, and is about to be listed as endangered. Small declining runs of listed Coho salmon remain in several tributaries. Modest runs of wild fall-run Chinook continue in the Scott and Shasta Rivers, but they are not native to the upper watershed above the mainstem dams slated for removal. Remaining salmon in the Klamath River are the progeny of hatchery salmon or of interbred hatchery and wild salmon. Remaining wild Klamath River steelhead are also not native to the upper watershed, and many of them spawn in tributaries downstream of Iron Gate Dam, the lowest Klamath River dam. Wherever they come from, salmon and steelhead that re-populate the upper watershed will not be native to the upper watershed, at least not initially.

“Salmon hatcheries don’t belong in this picture. They are relics of an outdated worldview that maintains that technology can conquer and control nature. They curtail salmon runs on the river, and instead of diverse stocks of fish that possess varied abilities enabling them to return to spawn — and die — at spots all along the river where they were born, hatchery fish’s birthplace is a single place: the hatchery. The identical life histories of these fish make them more susceptible to disease and predators than their native relatives.”

The modern view of hatcheries, and of conservation hatcheries in particular, is that they (and “technology”) can work with nature rather than controlling it. One problem is that the life histories of salmon that have survived the dams are not lined up with the likely best life histories for the 400 miles of migration, spawning and rearing habitat of the upper Klamath watershed that will soon become accessible. Existing life histories of Klamath salmon are lined up with the habitat that was left to them, largely in the few remaining large Klamath tributaries that enter the mainstem downstream of Iron Gate Dam. Managers of a conservation hatchery can select from the few remaining fish that have the most desirable life histories. Outplanting these hatchery-bred juveniles in the upper watershed and similar strategies can provide source stock for wild populations that can then better adapt to the habitats of the upper Klamath watershed.

“In fact, maintaining the salmon hatcheries amount to a federal subsidy for commercial and recreational fishing, a subsidy that is supposed to be justified by the fishery’s economic benefits.”

Hatcheries are mitigation for a loss to society and culture, not a “subsidy.” Those who benefit from the loss commit to paying for the loss. It is absolutely true that the mitigation has created its own set of problems. That does not absolve the beneficiaries of responsibility, and it should not disallow the opportunity to improve or accelerate the transition to the robust self-sustaining wild fisheries that every responsible stakeholder seeks.

“The salmon hatcheries on the Klamath should be phased out as quickly as possible. Even if the post-dam comeback of wild salmon is slow, river managers should resist pressure to continue or even expand hatchery operations.”

The hatcheries as they now exist should be phased out if the need to mitigate ends. Sad thing is that the hydro dams will leave a legacy of degraded habitat and species diversity loss. It remains to be seen how far habitat restoration can go. Conversion of the hatcheries to species conservation would help the recovery effort.

In conclusion, a conservation hatchery program could help to restore populations of coho, spring-run Chinook, fall-run Chinook, and steelhead to the areas of the watershed to which dam removal will restore access. Recovery efforts for native green and white sturgeon, bull trout, redband trout, and suckers could also benefit from modern conservation hatchery programs. Conservation hatcheries can also preserve the genetic diversity of these native fishes for the future when and if habitat is restored or altered by climate change.

Twists and Turns of 2019 Fall X2

Posted on October 2, 2019 by Tom Cannon

The California Department of Fish and Wildlife (CDFW), in a September 24, 2019 letter from Director Charlton Bonham, asked the US Bureau of Reclamation (Reclamation) to immediately implement “Fall X2” flows. Fall X2 increases Delta outflow from August 15 through October of wetter water years to protect Delta smelt. Fall X2 is a condition in the federal 2008 Smelt Biological Opinion for the Long-term Operation of the Central Valley Project (CVP) and the State Water Project (SWP).

Reclamation had issued a perfunctory Environmental Assessment in August 2019 to purportedly analyze the effects of eliminating Fall X2 in 2019. Reclamation claimed authority to unilaterally rescind the condition because the Biological Opinion has provisions for “adaptive management” of the condition.¹ In response to Bonham’s letter, Reclamation, on October 1, backed away from rescinding Fall X2.

Over the past week, X2, the focused location of the 2 parts per thousand (ppt) salinity level in the Bay-Delta, had moved upstream several kilometers from its prescribed km 74 location.² Salinity increased (Figure 1) because Delta outflow declined (Figure 2). X2 had moved nearly half way to the km 81 location to which Reclamation had proposed to operate in 2019. The lower Delta outflow appeared in part to be in response to reduced releases from Reclamation’s Folsom Reservoir to the lower American River on September 25-26 (Figure 3), which in turn showed up as reduced Delta inflow at Freeport on the Sacramento River below the mouth of the American River (Figure 4). The state increased Oroville Reservoir releases by 2,000 cfs over the past week to make up for falling Shasta releases into the lower Sacramento River.

In response to its decision to implement Fall X2 after all, Reclamation increased flow releases from Folsom Reservoir into the lower American River on September 30, thus keeping Delta inflows as measured at Freeport above 18,500 cfs. The state decreased south Delta exports by 3000 cfs (50%) on 28 and 29 September. X2 is again at km 74.

Figure 1. Salinity (EC) at Mallrd Slough near Chipps Island in Suisun Bay (about km 74) 2-30 September, 2019. X2 (about 3800 EC) was again at this location by Sep 30.

Figure 2. Measured daily average Delta outflow near Pittsburg in Suisun Bay 17-25 September 2019. After low outflows on 25-26 September the subsequent rise through 30 September was in large part due to cessation of monthly spring tides in addition to increased Oroville and Folsom reservoir releases.

Figure 3. Daily flows in the lower American River – Aug1 to Sep 30, 2019.

Figure 4. Daily average Sacramento River flow at Freeport in north Delta during September 2019.

See “Reclamation’s Proposed Delta Smelt Fall Habitat Action In 2019” at http://calsport.org/fisheriesblog/?p=2813. Reclamation is also trying to permanently eliminate Fall X2 in a new Biological Opinion. See description in http://calsport.org/news/a-fresh-disaster-for-fish-bureau-of-reclamations-new-plan-for-long-term-operations-of-the-cvp-and-swp-water-export-business/ ↩
74 kilometers from the Golden Gate. ↩

Feather River Fall-Run Status through 2018

Posted on September 28, 2019 by Tom Cannon

In my last post on the status of Feather River fall run salmon in May 2017, I analyzed recruitment through the fall-run in 2016 that included survival of brood years through 2013. In a recent May 2019 post, I discussed the survival of hatchery brood year releases through 2013. After near record low escapement/recruitment in 2008 and 2009, there was a strong recovery from 2010-2014, followed by lower runs in 2015 and 2016 (brood years 2012 and 2013), the product of the 2012-2016 drought. Brood years 2012 and 2013 suffered from poor juvenile river survival of hatchery and wild salmon in critical drought years 2013 and 2014. Overall production was sustained by Bay and coastal hatchery smolt releases (trucking and pen releases).

In this post, I update the status of the run through 2018 with the addition of escapement estimates for the 2017 and 2018 runs. I also provide information on returns of hatchery brood year 2014. In addition, I provide a prognosis for the fall 2019 run.

2017 and 2018 Escapement

Poor river escapement in 2017 (Figure 1) likely reflects poor survival of naturally spawned salmon from fall through spring of critical drought water year 2015. The strong hatchery escapement in 2017 (Figure 2) reflects higher survival of brood-year 2014 hatchery releases. Escapement improved in 2018 with higher river and hatchery contributions from brood year 2015.

Brood Year 2014 Hatchery Survival

Survival estimates based on hatchery coded-wire-tag returns for brood year 2014 (released in spring of critical drought year 2015) were high (3-5%) for coastal releases, good (1-2%) for Bay releases, and poor for river releases (Figure 3). Approximately 6 million smolts were released, of which 4.2 million were released to San Pablo Bay net pens. Of the remainder, 1.6 million were released to the Feather River, 10,356 at Tiburon near the Golden Gate,¹ and 331,000 to Half Moon Bay on the coast south of San Francisco.

Prognosis for Brood Year 2016 (Fall 2019 Run)

River flows and Delta outflow conditions were much better in winter-spring 2017, a wet water year, than in 2015, a critical drought year (Figure 4). Hatchery brood year 2016 releases totaled nearly 5 million smolts, with 750,000 released in the Bay, 264,000 to the Golden Gate at Tiburon, and 3.5 million to the Feather River (Figure 5). River natural and hatchery release survival should be good given the wet year conditions. Hatchery Bay release survival should be good given high outflows. All indications look good. “Finally there are larger numbers of big king salmon showing in the upper river on the Sacramento River. … Over on the Feather River flows are great and water temperatures have finally dropped to excellent levels to catch the fresh king salmon migrating towards the Feather River hatchery. More salmon have come through this week than the entire month of August.”²

Figure 1. River spawner estimates 1953-2018.

Figure 2. Hatchery spawner estimates 1964-2018.

Figure 3. Feather River hatchery smolt release survival to adults from 2008-2014 brood years based on coded-wire-tag returns. Data Source: https://www.rmis.org/.

Figure 4. Delta outflow winter-spring 2015-2017.

Figure 5. Brood year 2016 Feather River Hatchery smolt releases spring 2017. Source: https://www.rmis.org/.

I described the 2013 Tiburon release in a previous post. ↩
https://sacramentofishing.com/2019/09/08/sacramento-river-fishing-report-8/ ↩

Reclamation’s Proposed Delta Smelt Fall Habitat Action In 2019

Posted on September 18, 2019 by Tom Cannon

The US Bureau of Reclamation (Reclamation) is proposing a “Delta Smelt Fall Habitat Action” that would eliminate the requirement to increase outflow from the Delta in the late summer of this wet water year.¹ The “Fall X2” flow increase that Reclamation has placed on the chopping block is a major provision in the 2008 Delta smelt biological opinion (BiOp). Reclamation describes the substitute proposed Action in a summary its webpage:

The Proposed Fall Habitat Action (Proposed Action) for Delta Smelt habitat in Water Year (WY) 2019 will achieve the Action 4 objective. Action 4 of the 2008 BO requires adaptive management to ensure that the implementation addresses the uncertainties about the efficiency of the action. Action 4 also states that as new information is developed and as circumstances warrant, changes by the Service to the Fall X2 action itself may be necessary. The Proposed Action is a plan to adaptively manage and modify its operation of the CVP/SWP under RPA Action 4.²

In brief, the “circumstances” that “warrant” this “adaptive management” are that getting rid of Fall X2 will allow Reclamation to export more water from the Delta this fall.

In August 2019, Reclamation issued an Environmental Assessment (EA) of the Proposed Fall Habitat Action. Though the Action will unravel a major component of the 2008 Biological Opinion for smelt, the comment period was 15 days. CSPA submitted comments; some of them are restated below, in response to citations from the “Effects Analysis,”³ an appendix to the Environmental Assessment.

The Effects Analysis quotes the BiOp to portray the Proposed Action as a scientific investigation, stating:

“[T]here is a high degree of uncertainty about the quantitative relationship between the size of the Action described above and the expected increment in Delta Smelt recruitment or production.” (p. 1).

Comment: After 2011, it has been nearly impossible to measure population response to changes in management because the smelt population has become so low. Likewise, a negative response cannot be detected at the present population level. The only certainty to be gained from harming a nearly extinct population even more is that Reclamation will increase exports from the south Delta.

The Effects Analysis selectively calls out results of the first implementation of the Fall X2 requirement in 2011:

“Abiotic habitat did increase in 2011 as predicted from the AMP, but other variables such as zooplankton abundance were too variable to draw a conclusion, and Delta Smelt growth rate comparisons remain incomplete as of 2019.” (p.2)

Comment: Following implementation of Fall X2 flows, smelt abundance increased sharply in the fall 2011 index. A quick look at zooplankton 2011 vs 2010 (Figure 1) also indicates an increase in zooplankton (key smelt food source) in Suisun Bay/Marsh in 2011.

Figure 1. Zooplankton (key Delta smelt food source) in September 2011 and 2010.
Note increased abundance downstream in 2011.

The Effects Analysis tries to explain the lack of response of Delta smelt to the 2017 Fall X2 action as a function of water temperature, concluding that the action was just futile:

In 2017, a Fall X2 adaptive management action was implemented. The results of the 2017 monitoring program were evaluated in the IEP’s 2019 draft FLOAT-MAST, which concluded that summer water temperatures were a major factor in the condition of Delta Smelt in 2017, stating at p.102: Given the long periods in July and August >22C we are confident that water temperature had a major negative effect on Delta Smelt in 2017 and is likely a primary factor in the lack of response of the Delta Smelt population to the high flows. And at p. 104: Dynamic biotic components were somewhat better in 2017; however, the lack of response of the Delta Smelt population suggests that any benefits of changes in the habitat were minimal. (p. 3)

Comment: It is true that recruitment of Delta smelt in 2017 was exceptionally low, despite the Fall X2 action. This is because the number of adult spawners in 2017 was at a record low (Figure 2).

Fall 2017 water temperatures were slightly higher in the west Delta at Jersey Point compared to 2011 (Figure 3). However, fall 2017 water temperatures were not unusually high compared to fall 2011 for Freeport or for Rio Vista in the Sacramento River channel of the Delta (Figure 4). June and July Sacramento River water temperatures were substantially higher in 2017 than in 2011, because June and July Sacramento River flows were much lower in 2017 compared to 2011 (Figure 5).

In general, spring habitat conditions were poorer in 2017 than in 2011: 2017 had lower spring Delta outflows (Figure 6) and much higher south Delta exports (Figure 7).

In sum, the 2017 fall index for Delta smelt was unusually poor because of poor conditions for Delta smelt in the spring and summer. However, the response of longfin smelt to the implementation of Fall X2 in 2017 had a better outcome (Figure 8). Despite poor number of spawners, the 2017 recruitment of longfin smelt per spawner was high.

These data undermine Reclamation’s conclusion that the 2017 Fall X2 action had no benefit.

Figure 2. Log vs Log plot of fall FMWT Index of Delta smelt (recruits) vs previous fall index (spawners). Blue years are wet years. Red years are dry and critical water years. Year types are determined by the California Department of Water Resources for the Sacramento River runoff to the Bay-Delta Estuary (http://cdec.water.ca.gov/cgi-progs/iodir/WSIHIST).

Figure 3. Comparison of Jersey Pt habitat conditions in 2017 versus 2011. Tidally filtered flow data were not available for 2011.

Figure 4. Freeport and Rio Vista water temperatures 2013-2019.

Figure 5. Freeport flow and water temperature summer 2011 and 2017.

Figure 6. Summer Delta outflows in 2011 and 2017.

Figure 7. South Delta federal exports (TRP) and state exports (HRO) in 2011 and 2017.

Figure 8. Longfin smelt spawner-recruit relationship, with improved recruitment in 2011 and 2017. Wet year blue, dry year red. Source: http://calsport.org/fisheriesblog/?p=2513

So, after stating inaccurate and misleading reasons why the Fall X2 action is not effective, the Effects Analysis offers inaccurate and misleading reasons why not implementing Fall X2 and instead fussing with the Suisun Marsh Salinity Control Gates (SMSCG) will be a positive switch.

“Forecast of salinity conditions in the Delta indicate that operating to an X2 of 80 km along with SMSCG operations in September and October would result in suitable salinity conditions (< 11,000 uS/cm) in the western Delta including Suisun Marsh, Grizzly Bay, and Honker Bay during these two months.” (p. 17)

Comment: Operating the SMSCG tide gates, while not implementing Fall X2, will push more Delta outflow into Suisun Marsh, with less outflow reaching eastern Suisun Bay. Both actions would potentially negatively affect Delta smelt compared to implementing the Fall X2 Action per the existing BiOp.

“However, as explained above, this estimate of abiotic habitat index does not account for the habitat created in Suisun Marsh through the operation of the SMSGC, which would increase the index.” (p. 31)

Comment: moving outflow through SMSGC reduces habitat in eastern Suisun Bay, and subsequently traps any Delta smelt in Suisun Marsh once the gates are again closed.

Conclusion: Stock-recruitment models show a strong positive population response for Delta smelt in 2011 (see Figure 2) and longfin smelt in 2017 (see Figure 8). The strong population responses in 2011 and 2017 offer a strong case for implementing the Fall X2 action in 2019. Reclamation’s only justification for eliminating the Fall X2 action in 2019 is to increase water available for export. Biology has nothing to do with it.

Delta Outflow Measurement

Posted on September 11, 2019 by Tom Cannon

Delta outflow has been estimated by state and federal agencies for over 50 years. The Department of Water Resource’s Delta Total Outflow is a daily-average algorithm calculated in cubic feet per second (cfs) for Station DTO, a hypothetical location near Chipps Island in Suisun Bay. The federal Bureau of Reclamation’s Delta Outflow estimate is calculated similarly and presented as a daily average flow in cubic feet per second on Reclamation’s website.

Now a third estimate of Delta Outflow is available from the federal US Geological Survey on one of its websites (https://waterdata.usgs.gov/nwis/inventory?agency_code=USGS&site_no=380245121532301). This site has daily average estimates for a “gage” near Chipps Island since summer of 2016. The estimate is from tidally filtered flow/stage data.

A comparison of the DWR and USGS estimates is shown below in Figures 1 and 2. The two estimates are very similar. A closer comparison during the low-flow summer periods of 2018 (Figure 3) and 2019 (Figure 4) indicates significant differences, or at a minimum a modicum of uncertainty in one or both of the estimates. The average flow in the DWR data for 2018 data is about 10% higher over the period than the USGS data. The role of tides or tidal filtering in the USGS estimate is a likely factor in the difference. Under high seasonal tide periods (termed spring tides), outflows can fall to near zero, with major ramifications to salinity and water over the entire Bay-Delta, especially in the high export summer season.

The state’s current water quality control plan for the Delta includes objectives for Delta outflow (Figure 5). The objectives are stated as a monthly average. The low level of the objectives 3000-8000 cfs should give one pause as to the level of protection that these objectives provide to public trust resources like fish. The Water Resources Control Board is in the process of updating its plan and water quality objectives.

In past posts, I have advocated for daily salinity standards for the Delta rather than bi-weekly or monthly objectives for outflow, flow, export, and salinity. Such daily standards could be readily planned for, managed, monitored, and assessed for effectiveness.