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.

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.

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: https://www.rmpc.org

Figure 3. Percent return of 2017 Mokelumne Hatchery tagged smolt releases. Source: https://www.rmpc.org

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.
  2. http://www.fisheryfoundation.org/Reports/2005-2006%20Western%20Delta%20seine%20survey%20report.pdf
  3. https://calsport.org/news/wp-content/uploads/Overview-Habitat-Restoration-in-Delta-LowRes.pdf

May-September Delta Water Temperature Standard Needed

In a 9/22/20 post, I suggested summer Delta outflow standards. In this post I suggest a spring-summer water temperature standard for the Delta as further protection for salmon and smelt. Water temperatures above 23oC (73oF) are harmful to salmon and smelt, which live and migrate through the north and west Delta throughout the summer. Much of the Delta smelt population that remains is located in these regions especially in dry years.1 Spring-run and winter-run salmon migrate upstream through the area in late spring. Fall-run salmon migrate upriver through the summer.

Harm occurs as stress, higher predation, avoidance reactions, poor growth, and reduced long-term survival and reproduction. At higher temperatures (>23oC) migration blockage and mortality occurs. Such temperatures are commonly reached or exceeded in the north Delta even in wetter, water-abundant years.

High water temperatures occur in the Delta when there are high air temperatures and/or low freshwater inflow and outflow. Such conditions are becoming more frequent with climate change. A good example occurred in water year 2020, which featured low precipitation, low snowpack, and high air temperatures.2 Because water managers cannot control air temperatures or watershed precipitation, they must manage Delta inflows from reservoir releases and outflows through the Delta to improve water temperature control in May-September, especially in drier years.

To protect smelt and salmon, there need to be reasonable water temperature standards in the Delta. The existing water temperature standard in the lower Sacramento River above the Delta is 68oF, but managers of the state and federal water projects pay it almost no heed. There is no existing standard for the Delta. The north Delta water quality standard for the Sacramento channel in wet years should be 70oF (21oC) at Freeport and at Rio Vista. In normal and dry water years, the standard should be 72oF (22oC) at Freeport and at Rio Vista. In critical drought years, the State Water Board needs to require additional Delta inflow and curtail exports as needed to respond to extreme events (e.g., water temperatures greater than 75oF during heat waves). At critical times, a change of only a degree or two will help limit fish stress and mortality.

Higher Delta outflow and lower exports are appropriate prescriptions for maintaining reasonable water temperatures in the Delta (see Figures 1-3 and caption notes). For example, in July and August 2020 (Figures 1-3), increased inflow into the 14,000-16,000 cfs range from 12,000 cfs at Freeport could have held water temperature below 22oC. Note in Figure 3 that increased inflow can be captured by south Delta exports (Figure 3). However, during heat waves under extreme drought conditions, the State Board should also limit exports to retain outflows from the Delta to keep the low salinity zone out of the warmer Delta. Otherwise, exports will reduce the portion of Delta inflows (Freeport flows) that reach Rio Vista.

Such standards are achievable, albeit at significant water supply cost. They are worth the effort. High summer water temperatures, such as those that occurred in wet year 2019 and dry year 2020, must be mitigated. The 23-25oC conditions in summer 2020 (portrayed in Figures 1-3) should not occur, and would not under the suggested Delta water temperature standard. For wet years such as 2019 (Figure 4) and 2017 (Figure 5), water temperatures should be kept at or below 70oF (21oC) by maintaining Freeport near 20,000 cfs as needed.

In summary, Delta water quality standards should be adopted for inflow, outflow, and water temperature to protect salmon and smelt in the warmer months of the year, May-September. Such standards are needed because of recent changes in water project operations and the effects of climate change.

Figure 1. Water temperature and salinity in the west Delta near Rio Vista in spring-summer 2020. Note Delta draining in neap-tide periods generally brings warmer water downstream into the west Delta, except in mid-August event when a heat wave drove water temperatures up into 23-25oC range. This event was accentuated by higher exports and associated high Delta inflows.3

Figure 2. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of dry year 2020. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 3. Sacramento River flow at Freeport (FPT), water temperature at Rio Vista (RVB), and south Delta exports at Tracy (TRP) and Banks (HRO) pumping plants in south Delta from May-Oct 2020.

Figure 4. Water temperature and net river flow (tidally filtered) in the lower Sacramento River at Freeport in the north Delta in spring-summer of wet year 2019. Note that it took flows at or greater than 16,000 cfs to keep temperatures near 70oF (21oC).

Figure 5. Sacramento River flow at Freeport (FPT-Y1) and water temperature at Freeport (FPT-Y2) and Rio Vista (RVB-Y2) from May-Oct 2017.

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.