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 Source: CDFW unpublished data.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:

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:

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:

Mokelumne River Hatchery 2017 Releases

In previous posts over the past two years, I remarked on the progressive management of the Mokelumne River Hatchery, a mitigation hatchery operated by the California Department of Fish and Wildlife in partnership with the East Bay Municipal Utility District. Hatchery production over the past several decades has led to the recovery of Mokelumne River fall-run Chinook salmon (Figure 1 and 2). There were remarkable returns to the Mokelumne in 2017, despite the 2013-2015 drought. Returns from 2016 hatchery releases in 2018 were also good.

The hatchery’s annual 6 million smolt releases in 2017 (Table 1) survived well under the hatchery’s management practices (Figure 1). Returns of adults two years later to the river and hatchery below Camanche Dam in 2019 totaled 10,000 to 20,000 as in other recent years (Figures 1 and 2).

Overall, a good 2019 escapement was expected because 2017 was a wet year. However, in-river numbers (Figure 2) in 2019 were not as high as might be expected.. Hatchery return patterns were similar to those from the 2016 releases returning in 2018. Again, the best returns were from releases of hatchery fish to the coast near the Golden Gate and from Half Moon Bay just south of San Francisco (Figure 3). Returns ranged from near zero to 2.5 percent (Figure 3). The half-million smolts released to the river had near zero returns to fisheries and river/hatchery, while the one million releases to the coast in May had good returns of 1.3 to 2.5 percent. Late May releases (900,000) from the east Bay at Sherman Island also had good returns of 1.5 to 1.8 percent. Earlier May and late April releases to coast, east Bay, and river (nearly 4 million) had returns less than 1 percent.

Since 2017 was a wet year with high spring Delta outflow than drier 2016 (Figure 4), a better return would be expected from the 2017 hatchery releases to the Mokelumne River and even the eastern Bay. The river also had much higher flows in spring 2017 (Figure 5), which should have benefitted in-river hatchery releases. Late May releases proved much more successful in wet year 2017 than late April or early May releases, even to the coast, providing further evidence of better performance of later release of older, larger hatchery smolts. But the continued poor returns from in-river releases even in wet year 2017 remains a problem.

Meanwhile, straying of fish produced in the Mokelumne remains an issue. Up to half or more of returning adults stray to other Central Valley rivers and hatcheries. Maintaining genetic integrity and “wild” spawners in spawning reaches of individual Central Valley rivers would require marking or genetic tests of all hatchery fish, as well as measures to keep hatchery-origin and stray adults from individual spawning grounds. Maintaining genetic integrity and minimal “domestication” of the hatchery stocks would require selective brood stock management in the hatcheries.

Figure 1. Returns to Mokelumne Hatchery 1964-2019.

Figure 2. In-river spawning grounds counts 1952-2019.

Table 1. Summary of Mokelumne Hatchery smolt releases in spring 2017. Source:

Figure 3. Percent return of 2017 Mokelumne Hatchery tagged smolt releases. Source:

Figure 4. Delta outflow spring 2016 and 2017.

Figure 5. River flow at Woodbridge Dam 2016-2017.


The Delta as Salmon Nursery

The Delta is an important nursery area for Central Valley Salmon. This fact continues to be ignored or under-appreciated. The phenomenon is fully consistent with the general science on salmon in their southern range in the eastern Pacific. Nearly all California Chinook salmon are “ocean-type,” meaning that juveniles reach the ocean in their first six months after rearing for extended periods in estuaries. To grow, young salmon fry need to rear in winter in warm productive areas of floodplains and tidal estuaries (Bay and Delta). Flood control infrastructure limits floodplain habitat except in wetter years. Water management, mainly reservoir storage, limits transport of fry to the Bay except in wetter years.

That leaves the Delta as the key nursery area in non-wet years. Thus, the state of the Delta in non-wet years largely determines the success of Central Valley salmon. Salmon smolt production to the ocean is one to several orders of magnitude lower in drier years, which is the fundamental cause of salmon run declines over the past several decades during periods of drought (Figure 1).

Getting salmon fry to the Delta, successfully rearing them in the Delta, and then getting them to the Bay and Ocean are keys to their success. Peaks between droughts, and even small runs during droughts, are driven by trucking smolts from the hatcheries to the Bay and Ocean, bypassing the Delta survival sink. Without hatchery contributions, the underlying pattern for wild-natural salmon would show drastic declines during and after droughts. Improving Delta-derived smolt production is the key to improving the wild component of Central Valley salmon.

For nearly four decades, I have been promoting Delta salmon habitat improvements.1 I have also helped show the importance of winter rearing of salmon fry in the Delta.2 I have also conducted a comprehensive review of Delta salmon rearing habitats and restoration.3 In other posts in this blog, I have offered much discussion on the role of the Delta in salmon production and survival.

The State Water Resources Control Board is in a multi-year process of updating decades-old water quality standards. Focusing on salmon as a key public trust resource is the way to go. The new standards need to assure that fry get to the Delta, do well in the Delta, and then get to and through the Bay to the Ocean.

Figure 1. Over the past several decades the Central Valley fall-run Chinook salmon has declined sharply during and shortly after three major periods of drought: 1987-1992, 2007-2009, and 2013-2016. Source: CDFW Grandtab.


  1. Cannon , T. C. 1982. The importance of the Sacramento-San Joaquin estuary as a nursery area of young Chinook salmon. Unpublished NMFS report.

Feather River Fall-Run Salmon Update – 2019 Spawning Run

Feather River spring-run and fall-run salmon are the backbone of the California salmon fisheries, making up 20-40% of the total catch and spawning runs. In a review of Feather River fall-run Chinook salmon in September 2019, I described their status through the 2018 run and expressed optimism for the 2019 run. My assessment proved overly optimistic, as the 2019 run numbers came in lower than expected. The lower-than-expected returns appear to be the consequence of the 2017 Oroville Dam spillway failures.

The 2019 spawning run (escapement), though improved over the previous four drought-influenced years, was smaller than those of the previous wet-year-influenced periods 2000-2002 and 2012-2014 (Figures 1 and 2). The run of 80,000 adult salmon in 2019 should have been 25-50% higher, because 2017 was a wet year. The 2019 run, the offspring of brood-year 2016 was raised in the river and hatchery in winter 2017 during the events of the February 2017 spillway failures (Figure 3). The 2019 run showed lower hatchery and wild river smolt production due to the the direct and indirect consequences of the spillway failures. Suspended sediment (turbidity) levels during the spillway failures in the river and the hatchery reached highly stressful if not lethal levels (Figures 4 and 5). These levels were elevated through the winter and spring of 2017 due to the dredging of spillway debris from the river immediately below the failed spillway (Figure 6). Lower Feather River flows during the winter and spring were highly erratic (Figure 7) due to efforts to repair the spillway and dredge the debris from the river below the spillway. Rapid flow reductions from the dam led to well-documented stranding of young salmon in the lower Feather River floodplain.1

The prognosis for the 2020 run is mixed. Spawner numbers in 2017 were fair (80,000; Figure 1). Water year 2018 was below-normal, generally leading to poor spawning, rearing, and emigration survival. Hatchery smolt releases in 2018 were increased several million over 2017 releases, which should bode well for the 2020 run. Wild spawning and rearing in fall of 2017 and winter-spring of 2018 still had to contend with the ramifications of the 2017 spillway failures, although some restoration did occur in summer 2017.2

Figure 1. Feather River fall run Chinook salmon escapement (river and hatchery counts 1964-2019.

Figure 2. Feather River Fall-Run Chinook salmon spawner-recruit relationship. Recruits are escapement for that year. Spawners are recruits from three years earlier. Red represents drought conditions during brood year rearing. For example: 2015 represents winter-spring of 2015 when brood year 2014 was rearing and migrating in lower Feather River downstream to the Bay. Blue designates wet year rearing and migrating conditions. Green represents normal years. Note 2017 represents the 2019 escapement from young reared and emigrated in winter-spring conditions in 2017, a wet year.

Figure 3. Oroville Dam main spillway failure in February 2017. Oroville Dam was constructed during 1961-68 period.

Figure 4. Turbidity (NTUs) measured below spillway in lower Feather River in Oroville, February 9-10, 2017.

Figure 5. Photo of emergency spillway use on February 11, 2017.

Figure 6. Turbidity measured in Feather River near spillway recovery efforts in winter 2017. Spikes in turbidity occurred during ongoing dredging and debris removal activities.

Figure 7. Streamflows in lower Feather River at Gridley and lower Sacramento River below mouth of Feather River at Verona, and turbidity at Verona in winter-spring 2017. CDEC data.

  1. White, J.S.S., K. Lentz, and J. Kindopp. 2017. Stranding of Chinook Salmon (Oncorhynchus tshawytscha) and Steelhead (Oncorhynchus mykiss) in the lower Feather River, 2017. Final Report. Department of Water Resources, Division of Environmental Services, Oroville, CA.
  2. ,