Scott River Chinook Salmon Update

The Scott River Chinook salmon, a key contributor to the overall Klamath River salmon run, are in major trouble.  In a November post, I had a “mixed” prognosis for this year’s fall run.  Well the numbers are now in – a record low, bleak run of 117 spawners observed (Figure 1) at the weir downstream of Fort Jones.

Figure 1. Scott River fall run salmon escapement 1978-2020. Source: CDFW unpublished data.

The poor run can be directly attributed to lack of fall river flow, a fact that I had addressed in a 2017 post.  Salmon simply cannot ascend the lower Scott River into Scott Valley spawning grounds from the Klamath River because of lack of streamflow.  Some may spawn in the steep canyon below the Valley (and counting weir), but poor spawning habitat and low flows in the canyon offer little solace for the salmon.

Poor fall flows (Figure 2) can be directly attributed to fall groundwater extraction and surface water diversions for hay-pasture irrigation.  The State Water Board should stop crop irrigation after October 1.  This irrigation practice has been getting worse over the past several decades, aided by improved well extraction and sprinkler technology and greater demand and higher revenues.  Present water use permits allow irrigation into December, which ranchers have been taking advantage of to get an extra crop of hay (with the help of climate change).

Unlike 2020 (Figure 2), water use in past drought years tapered off earlier and flows increased during October (Figures 3-5).  This allowed fall-run salmon access to the Valley.  In contrast, recent wet and normal years see a combination of precipitation and reduced water use, which enhances fall flows (Figures 6 and 7).

In conclusion, the State Board should limit fall water irrigation in Scott Valley to save the salmon.  The Sustainable Groundwater Management Act (SGMA), passed in September 2014, requires local agencies to develop Groundwater Sustainability Plans (GSP) that will assess and project future groundwater conditions, and provide management and monitoring activities.  The Scott River basin is a priority basin.  Siskiyou County is required to develop and submit a GSP for the Scott River basin by January 31, 2022.  A preliminary plan recently developed by the advisory group suggests reducing irrigation acreage (Figure 8) to increase streamflow (Figure 9).  That would help, but what salmon need is a cutoff of irrigation by October 1.  An option for further augmentation is to employ unused groundwater extraction wells in the fall to add water to the river  for short periods.  Stored water in the tailings ponds (red area in Figure 8) could also be gravity-fed or pumped into the river at critical times.

Figure 2. Scott River flow fall 2020. Water year 2000 was a drought year.

Figure 3. Scott River flow fall 2000 and winter-spring 2001. Water year 2001 was a drought year.

Figure 4. Scott River flow fall 2013 and winter-spring 2014. Water year 2014 was a dry year.

Figure 5. Scott River flow fall 2014 and winter-spring 2015. Water year 2015 was a normal year.

Figure 6. Scott River flow fall 2016 and winter-spring 2017. Water year 2017 was a wet year.

Figure 7. Scott River flow fall 2017 and winter-spring 2018. Water year 2018 was a below normal water year.

Figure 8. Baseline (present) and preliminary action alternative for Scott Valley irrigation. Source: preliminary plan.


Figure 9. Analysis of preliminary action alternative. Source: preliminary plan.

 

 

Yuba River Salmon 2020

In a 2017 post and a 2018 post, I related the status of Yuba River Chinook salmon runs. The 2017 spawning escapement estimate was a record low. The 2018 and 2019 runs were not much better (Figure 1). While the record low 2017 can be blamed predominately on the 2013-2015 drought, the poor 2018 and 2019 runs cannot. Water year 2016 was a normal water year and 2017 was a wet year.

The likely culprit in the decline in Yuba escapement is the continuing persistent decline of wild spawners and increase in hatchery strays (greater than 90% of the run), leading to the erosion of the locally adapted Yuba River salmon population. This was the diagnosis for the overall Feather River population by Willmes et al., 2018.

Figure 1. Yuba River fall run salmon escapement 1953-2019.

A further look at the composition of the hatchery strays in the Yuba escapement surveys provides added clues about the cause of the recent decline in overall escapement to the Yuba River. In 2016 (Figure 2), nearly half the tag returns were strays from the Battle Creek hatchery, while the other half were a combination of spring-run and fall-run strays from the Feather River hatchery, along with a smattering of strays from the hatcheries on the American and Mokelumne rivers. In 2017 (Figure 3), Yuba tag returns featured an even greater proportion of strays from Battle Creek, the American, and the Mokelumne. In 2018 (Figure 4), about half of the tag returns were from the Mokelumne River hatchery, and a third were of Feather River spring-run hatchery origin.

Feather-tagged spring-run show up consistently in the Yuba escapement surveys. This is unusual, because spring-run make up only about 10% of the Feather hatchery smolt production, with fall-run being about 90%. One reason is that spring-run smolts are 100% tagged, while fall-run hatchery smolts are only 25% tagged. Another reason is that all the spring-run smolts are released near Gridley just upstream from the mouth of the Yuba, whereas most of the fall-run smolts are released in the Bay. A third reason is that in most years springtime flows in the Yuba are higher and colder than those in the Feather, and are thus more likely to attract returning adults. Regardless of the reason, the fact that a significant portion of Yuba “fall run” escapement is derived from spring-run hatchery smolts is cause for concern.

Battle Creek hatchery fall-run made up about half the tag returns in 2016 and 2017. Much of the smolt production from the Battle Creek hatchery was trucked to the upper Bay in 2014 and 2015, a strategy prone to increased straying.1 No Battle Creek hatchery smolts were trucked to the Bay in 2016, and none showed in the Yuba in 2018. With over 10 million fall-run smolts produced at the Battle Creek hatchery (federal Coleman Hatchery near Red Bluff), nearly double the Feather hatchery production, it is easy to see why Battle Creek hatchery salmon could dominate the Yuba escapement. Without the Battle Creek, American River, and Mokelumne River hatchery strays in 2017, the record low escapement in the Yuba River would have been far worse. The fact that most of the 2017 spawners were hatchery strays from rivers other than the Feather should also be cause for concern.

In conclusion, the escapement of fall-run salmon to the Yuba River has declined over the past five years, approaching record-low levels. Spawners are now predominately hatchery strays from smolts released in the Bay and along the coast. Natural “wild” Yuba River smolt production is virtually nonexistent. This is a crying shame for what is widely regarded as one of the best non-hatchery salmon rivers in the Central Valley. I have spent many days on the Yuba River over the past two decades. I observed the big runs at the turn of the century and in 2013 and 2014. The river’s pools turned purple with adult salmon. Dead and dying salmon filled the backwaters, feeding eagles and buzzards. The odor was prevalent. Spawning salmon and redds were everywhere. Such occurrences are now rare. Our Yuba River needs so many fixes, a subject for another post.

Figure 2. Composition of tag returns from Yuba River spawners in 2016. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. MeRF = Merced River fall run. Data source: rmis.org.

Figure 3. Composition of tag returns from Yuba River spawners in 2017. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. BCF = Battle Creek fall run. Data source: rmis.org.

Figure 4. Composition of tag returns from Yuba River spawners in 2018. FRS = Feather River spring run. MRF = Mokelumne River fall run. FRF = Feather River fall run. ARF = American River fall run. Data source: rmis.org.

Klamath’s Shasta and Scott Rivers – Update Fall 2020

In a November 2019 post, I gave updates through 2018 on the status of fall-run salmon in the Scott and Shasta rivers, major tributaries of the Klamath. I described how continuing improvements in river management paid off for the Shasta River’s fall Chinook run. I also described how lack of protections in water management left the Scott run in poor condition.

In this post, I update fall-run Chinook spawning escapement through 2019, with some insight into the 2020 runs. I also provide data on the runs in the Salmon River, the Scott and Shasta’s sister Klamath tributary. The 2019 salmon runs should have benefitted from water-abundant 2017, but may have been handicapped by poor numbers of returning spawners in 2016.

The runs of fall-run Chinook in all three of these major Klamath River tributaries improved in 2019 compared to the runs in 2016 that were severely affected by drought and fire.1 However, runs in all three rivers in 2019 fell short of the 2017 and 2018 runs (Figure 1). Good water conditions in all three rivers in 2017 (Figure 2)2 should have led to improvements in runs over 2017, which were a product of 2014-2015 drought and 2014 fires. They also should have been better than the runs in 2018, whose runs were spawned in drought year 2015 and reared in dry year 2016.

The fact that there was not greater improvement in the 2019 runs is likely the consequence of low numbers of spawners in the fall of 2016. The low number of spawners in 2016 resulted from the continuing effect of the devastating 2014 fires on the watersheds (especially the Salmon River), ongoing poor water management (especially in Scott and Shasta rivers), and poor water conditions in the dry falls of 2017 and 2018 (limiting 2019 the returns of 2-year-old “jacks and jills”).

The prognosis for 2020 is mixed. This results on the upside from improved numbers of spawners in 2017 and a wet water year in 2019. On the downside, the relatively poor water conditions in fall 2017 and the dry conditions in 2018 and 2020 are likely to depress the numbers of adults that return in 2020. Initial counts from Shasta and Scott rivers3 however indicate poor runs not unlike 2004 or 2016. Overall, the decline in spawners produced from strong runs (2014 and 2017) in the Klamath’s main wild salmon tributaries, as well as drought, fire, and continuing poor water management, do not bode well for the future of Klamath salmon.

Figure 1. Shasta, Scott, and Salmon River escapement of fall-run Chinook salmon 1978-2019. Source; CDFW data.

Figure 2. Salmon River streamflow 2013-2020 with long-term average.

 

Klamath’s Scott River Salmon and Steelhead in Trouble

Scott River – April 2020

The Scott River is a major contributor to Klamath River salmon and steelhead runs.1 The fry of fall-run Chinook and Coho salmon that spawned in the Scott system this past fall-winter are now leaving their gravel beds. Steelhead are completing their spawning run. These salmon and steelhead are in for a tough year because flows are low (Figure 1), precipitation has been minimal (Figure 2), and the snowpack is well below average (Figure 3).

The state of California needs to step up to protect these iconic and socio-economically important wild salmon and steelhead runs and the critical habitats that support them. The State Water Resources Control Board, supported by the California Department of Fish and Wildlife, needs to maintain adequate flows in the Scott River through the fall. If the state does nothing, the river will dry up by summer, and most of the young fish will die.

The State Water Board and CDFW must control and carefully monitor surface diversions and groundwater extractions for pasture and hay irrigation. Otherwise, the river and all its aquatic life will die, and domestic-use water will dry up.

Coho salmon are a state and federally listed endangered species protected by law. Water rights issued and managed by the State Water Board require protection of these natural resources. Fish habitat is protected by state laws; state agencies need to enforce these laws. Local entities such as water districts, resource conservation districts, water and land trusts, tribes, communities, and landowners need to pitch in.

Figure 1. Streamflow in the Scott River September 2019 to April 2020, plotted next to 70-year average (log scale).

Figure 2. Monthly average precipitation in inches at Callahan, CA over past two decades. Note near zero precipitation in Feb 2020. Source: CDEC.

Figure 3. Snow survey data summary for Scott River and Shasta River watersheds in 2020. Source: CDEC.

Klamath River Salmon – the Wrong Advice!

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.