2017 Klamath Chinook Run – “Disaster or Catastrophe?”

Posted on April 10, 2017 by Tom Cannon

The Klamath River Chinook salmon fall run is expected to be a record low in 2017.¹ Predictions are near or below the record low run in 1992. These record low runs followed extended droughts from 2013 to 2015 and 1990 to 1992, respectively.

A very low run in 2016 prompted the Yurok Tribal Council to cancel its commercial fishing season to protect future fish populations. The 2016 salmon allocation was the second lowest on record, and failed to provide each tribal member a salmon. The Tribe did not serve fish at the annual Klamath Salmon Festival for the first time in the event’s 54-year history. In January 2017, the federal government issued a disaster declaration for the 2016 Yurok Tribe fishery.²

An April 6, 2017 article in the Eureka Times Standard stated:

Tribal fishery scientists such as Michael Belchik of the Yurok Tribe stated the low return of spawners is the result of several severe years of drought conditions and river management practices, which caused the waters to warm and become hot beds for toxic algae and deadly parasites. In 2014 and 2015, up to 90 percent of juvenile Chinook salmon on the Klamath River are estimated to have died from an intestinal parasite, believed to be a major cause for this year’s low run, as were poor ocean conditions…. “All these things together conspire to create a real catastrophe for fisheries,” Karuk Tribe Natural Resources Policy Advisor Craig Tucker said.
Organizations see dam removal and changes to the federal government’s management of the river as being key solutions to the underlying causes of this year’s low salmon return.” “The solution for this problem is to remove the Klamath dams now,” Pacific Coast Federation of Fishermen’s Association Executive Director Noah Oppenheim said.

A Yubanet article described the expected ancillary effect on the whole California coastal fishery:

The disaster stems from a crash of Klamath salmon stocks, but in order to protect the few Klamath fish that are in the ocean, fisheries regulators have little choice but to close or nearly close the economically valuable commercial and sport fishing seasons along the length of the Northern California and Oregon coastlines. This will impact tribal and non-tribal families alike.

CDFW stated: “Chinook that will be harvested in ocean fisheries in 2017 hatched two to four years ago, and were deeply affected by poor river conditions driven by California’s recent drought.”

A UC Davis study placed some of the blame on hatcheries. “My results suggest that hatcheries’ harm to wild salmonids spans the entire Klamath River basin. For fall Chinook salmon, the decline is concurrent with increases in hatchery returns – a trend that could lead to a homogenous population of hatchery-reared Chinook”.

Having been involved in the Klamath River for 40 years, I provide some of my own insights in this post. In follow-up posts, I will take a closer look at the Scott and Shasta rivers, the two main salmon tributaries of the upper Klamath that contribute substantially to the overall upper Klamath salmon run.

A summary of the overall Klamath salmon run escapement numbers or spawner estimates for the past 40 years is shown in Figure 1. The spawning numbers in 2016 were low, yet this drop came only two and four years after near record runs. Contributions for all six upper Klamath subcomponents in 2016 were down substantially from 2014. Predictions of a poor run in 2017 come from the low number of two-year-old “jack” salmon in the 2016 spawning run.

The question is: why did the strong run in 2014 produce the expected record low run in 2017? And why did the strong run in 2012 produce the weak run in 2015? And on the flip-side, why were the runs in 2012 and 2014 so strong, especially given they occurred during the recent multiyear drought?

A close look at the spawner-recruit relationship (Figure 2), how recruits are related to the number of spawners three years earlier, provides further insight into factors controlling long-term recruitment.

The spawner-recruit relationship is weak at best, reflecting the fact that estimates might be poor and/or that other factors are more important than just the number of spawners. The 1995 recovery after the record low 1992 run provides compelling evidence that survival and recovery can be strong even from the weakest of runs (with strong hatchery support – see hatchery component for 1995 in Figure 1). Unfortunately, 2017 appears to suggest that strong runs can produce very weak returns three years later if other factors such as drought are dominant.
The population crashes (2016, 2004, 1992) occurred after multi-year droughts (Figure 3). Multiyear effects compound changes to sediment, pathogens, and water quality, the suggested causes of these crashes.
Population expansions (2012-2014, 2007-2009, 2000-2003, 1995-1997, 1985-1988) occur after a series of wetter years.
There may be some underlying effect of floods, as indicated by the poor run in 1999, a consequence of the New Year 1997 flood that washed out the fall 1996 spawn.
The poor run in 2016 and the expected record low run in 2017, in addition to the effects of the 2013-2015 drought, may have been affected by poor ocean conditions, as was believed to be the case in the poorer than expected 2004-2006 runs.
Several factors potentially affect production or survival per spawner: conditions during the spawning run (flows, water temperature, disease, upstream passage hinderances, etc), first year rearing and emigration conditions (flows, water temperature, predators, prey, disease, toxins, etc), and ocean conditions. It is likely that flows throughout the water year (Figure 4) have some effect on survival of the affected or subsequent brood years.
The contribution of the Shasta River appears to have increased in recent years, likely as a result of the Nature Conservancy’s efforts at Big Springs (more on this in an upcoming post).

Overall, the droughts of 1990-1992 and 2013-2015 (Figure 3) were likely the single most important factors in the upper Klamath Chinook salmon population dynamics. The role of the Irongate Hatchery contributions seems relatively stable and a likely important contributor to recoveries after drought. I was unable to determine the contribution of hatchery salmon to the other components of the run, but it is likely a large factor in the Bogus Creek and upper Klamath elements. It is possibly a lesser factor in the Salmon, Scott, and Shasta river elements, which speaks to the importance of these potentially “wild” runs.

In closing, some thoughts on potential solutions:

Knowing a good run was occurring in drought year 2014, managers could have done more to protect the spawners, eggs-embryos, and subsequent rearing-emigrating juveniles with better flows and water quality. Perhaps the recent federal court decision may help ensure future protections. In poor water supply years like 1990-1992 and 2013-2015 (Figures 3 and 4), water managers simply must provide protections for salmon.
Future removal of the four dams may help reduce the adverse multiyear effect of droughts on disease and water quality and may provide additional spawning and rearing habitat.
Much more could be done to increase run components from the Scott and Shasta rivers (more on this in upcoming posts).
The hatchery program is long overdue for reform and upgrade. The program should shift from production to conservation of fall-run and spring-run Chinook, Coho and steelhead.
These and other suggestions are discussed in a prior post.

Figure 1. Chinook salmon escapement estimates to the upper Klamath River including Irongate Hatchery, Bogus Creek, Scott River, Salmon River, Shasta River, and Klamath River mainstem below Irongate Dam. The preliminary prognosis for fall 2017 total escapement is 11,000. Source: http://www.pcouncil.org/salmon/background/ document-library/#EnvironmentalAssessmentsalLib

Figure 2. Spawner-Recruit relationship for upper Klamath River fall-run Chinook salmon population. The number is the transformed (log10X – 3.5) escapement estimate for the fall of that year as shown in Figure 1. The color represents winter-spring hydrology conditions in the Klamath River two years earlier when this brood year was rearing in river habitats. Red is dry, green is intermediate, and blue is wet (from Figure 3). Circle color represents late summer water year conditions in numbered year. For example: year 92 represents the recruits in fall 1992 from brood-year 1989 spawn that reared in 1990 winter-spring (red dry year); the red circle represents dry conditions in late summer of that water year (1992). Note that the spawning run for 2002, the year the large die-off of adult salmon occurred in the lower river due to low flow and high water temperatures, likely contributed to the poor returns (recruits) in 2004 and 2005.

Figure 3. Average annual discharge by water year (10/1-9/30) of Klamath River as measured at Link River near Klamath Falls, Oregon. Data source: https://waterdata.usgs.gov/nwis/ annual?site_no=11507500&agency_cd=USGS&por_11507500_113138= 545477,00060,113138,1962,2017&year_type= W&referred_module=sw&format=rdb

Figure 4. Monthly average flow (cfs) in Klamath River below Irongate Dam in selected years. Year 2011 was a wetter year. Year 1992 was a critically dry year. Years 2002, 2005, and 2013 were dry years. Year 2016 was an intermediate water year. Source: www.waterdata.usgs.gov.

Bringing Back the Klamath Salmon

Posted on November 7, 2016 by Tom Cannon

Restored tributary spring creek of Scott River, Klamath River tributary, with abundant juvenile Coho salmon. (See YouTube video for underwater view of countless juvenile Coho salmon rearing in this creek.)

A recent post on the KCET website by Alastair Bland spoke of efforts to save salmon on the Klamath River. I add my perspective in this post.

I have been involved in the Klamath salmon restoration on and off for nearly 30 years. In my experience, the runs of salmon and steelhead keep declining because not enough gets done and because there is lack of progressive management. The Klamath is a big watershed (Figure 1). I tried to sit in the middle of one element of the process a few years ago on the Scott and Shasta Rivers, the Klamath’s two main upstream salmon tributaries below Iron Gate Dam. I found there were not just two sides involved in conflict, but really five: tribes, government agencies, ranchers-landowners, a power company, and environmentalists. There were even sides within sides. The four tribes often did not agree or work together. The four fish agencies often could not agree. The two states did not always agree, and individual state agencies disagree, resulting in conflicting water rights, water use, and water quality regulations. Counties and cities disagree. Neighboring Resource Conservation Districts differ in approaches. Many citizens want a new state carved from the two states. Some landowners love salmon and beavers, and others do not. Then there are the big watershed owners: private timber companies, US Forest Service, and Bureau of Land Management that manage forest watersheds differently under a wide variety of regulations and approaches that often do not protect salmon. I watched county sheriffs try to lead landowners in policy and enforcement, with a willingness to enforce vague trespassing rules on rivers and creeks. I watched as State Water Resources Control Board members toured watersheds and met with tribes and local leaders in an effort to resolve conflicts in over-appropriated watersheds. I watched as CDFW staff tried to enforce stream channel degradation and water diversion regulations on private and public lands.

While some progress gets made, it is too slow to save the native fish. Coho and spring-run Chinook are hanging on but slowly going extinct. Fall-run Chinook are supported by hatcheries but still declining. The iconic Klamath and Trinity Steelhead are silently and slowly fading away.

For decades, the various sides have waged war over water, dams, and property rights. The watersheds and fish have suffered as “Rome” burned. Some folks have worked hard to save what is left (e.g., Blue Creek watershed). Over the decades many battles have been waged and much compromised. Lawsuits abound. Commercial and sport fishing get constrained more and more each year. Fewer California residents make the trip north to fish the Klamath each year.

There remain many intractable problems that may never be resolved. The upper watershed in Oregon, mainly around Klamath Lake and the Sprague River, suffers greatly from agricultural development and attendant water quality issues that are unlikely to go away. Much watershed damage has already occurred from timber cutting, urban and agricultural development, roads, fires, and floods. Global warming will continue to reduce rainfall and essential over-summer snowpack throughout the Klamath watershed.

Despite the grim outlook, I have found there are a host of potential actions that can help even before we get to the long-awaited four-dam removal. We need to stop the bleeding, save the patient, and start recovery. Many of the treatments and tools are already available. Some are willingly provided by Mother Nature (e.g., water and beavers). There are many diverse efforts and treatments already underway on a small scale that can be expanded and coordinated. Lessons learned can be better shared.

To get the process moving faster, I offer the following recommendations:

Move toward making the Klamath tributaries, the Salmon, Scott, and Shasta rivers, salmon sanctuaries like Blue Creek on the lower Klamath, an effort being coordinated by the Yurok Tribe. Allow the Karuk Tribe to coordinate on the Salmon River (give them a grant to do this). On the Scott and Shasta Rivers, allow ranchers to coordinate. The Nature Conservancy is already involved in the Shasta River, as Western Rivers Conservancy is in the Blue Creek Sanctuary.
Re-adjudicate water rights and water quality standards on the Scott and Shasta rivers. I know these are “fighting words”, but it must be done now. At least start this process, starting with the State’s new groundwater regulations. Vital portions of both rivers sit dry much of the year from surface diversions and groundwater extraction. Hundreds of thousands of young salmon and steelhead literally dry up every spring and summer, including tens of thousands of endangered Coho salmon. State laws prohibit this, as do State Board regulations, yet it continues on a large scale. Make the State enforce the laws.
List Klamath spring-run Chinook as a federal and state endangered fish. They have become extinct from the Scott and Shasta rivers in my lifetime. They hold on in the Salmon River. They need and deserve full protection of the state and federal endangered species acts.
Fully implement federal and state recovery plans for salmon and steelhead. Get funding.
Re-introduce Coho and spring-run Chinook salmon to tributaries where populations are or are near extinction, including tributaries above dams.
Rehabilitate hatchery programs on the Klamath and Trinity rivers. Develop conservation hatchery elements within these existing programs to promote wild genetic strains of salmon and steelhead in the tributaries.
Reconnect the upper Shasta River to allow salmon and steelhead access. This process was started by the Nature Conservancy and tribes, but is long delayed and unfunded.
Fully fund and implement a salmon and steelhead rescue program for young stranded in tributary spawning rivers.
Improve access of spawning salmon and steelhead to historic spawning grounds blocked or hindered by irrigation dams, road crossings, or low streamflow.
Ensure the ongoing development of the Klamath-Trinity Coho Salmon Biological Opinion for operation of the Shasta-Trinity Division of the federal Central Valley Project adequately protects and helps restore the endangered Coho salmon.
Require the California Resources Agency to take a leadership role in making the Klamath a priority.

Figure 1. Klamath watershed. (Source DOI.)

For more on the Klamath recovery see the following:

Shasta Success?

Posted on November 1, 2016 by Tom Cannon

It would appear that this year’s management of Shasta Reservoir’s cold-water pool by federal and state agencies responsible for Sacramento River salmon has been at least partially successful in meeting objectives. Unlike the last two drought years (2014 and 2015), adequate cold-water storage and releases from Shasta were sustained through summer 2016 to protect winter-run salmon eggs and embryos in gravel beds. Water temperatures were generally kept within safe margins, and water levels were sustained to limit stranding of eggs and embryos. It remains to be determined whether spawning and rearing conditions were adequate to reach target survival estimates for winter-run salmon smolts.

Shasta Cold-Water Pool

Operation of the lower gates of Shasta Dam’s Temperature Control Device (TCD) allowed access of Shasta Reservoir’s deeper colder water through October (Figure 1). The temperature of the water released from the dam has been sustained at an average 52°F in September and October. In September and October of 2014 and 2015 averages were 57/61°F and 54/57°F, respectively.

Water Temperature

On June 17, the control point for 2016 Sacramento River water temperatures was set at 56°F at Balls Ferry (25 miles below Keswick Dam near Redding). Normally the regular control point is at Bend Bridge (41 miles below Keswick) as prescribed by NMFS and the State Water Board, but the change was allowed to conserve Shasta’s cold-water pool. Water temperatures at Bend Bridge were above 56°F for most of the April-August period, even exceeding the safe adult salmon holding and spawning level of 59°F from mid-April through early June (Figure 2). Although temperatures in 2016 exceeded objectives, they showed a marked improvement over summer 2014 (Figure 3), when depletion of the cold-water pool led to poor survival of the 2014 spawn.

Streamflow and Water Level changes

Streamflow and water level changes in 2014 led to stranding of salmon redds in 2014 (Figure 4). Water level dropped 3 feet over the summer in 2014, including nearly 2 feet in August when most of the winter run eggs and embryos were still in the redds. In contrast, water levels in 2016 changed little until September when levels dropped only 1.5 feet (Figure 5). Most winter run salmon fry leave the redds by early October.

Figure 1. Latest operation of TCD.

Figure 2. Water temperature at Bend Bridge in 2016. Yellow is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 3. Water temperature at Bend Bridge in 2014. Yellow line is safe level for adult holding and spawning. Red is normal target prescribed by NMFS and State Board.

Figure 4. Stranded salmon redd in early fall 2014 after Shasta releases were curtailed when cold-water pool was depleted. (CDFW photo)

Figure 5. Water level at Bend Bridge in summer 2014.

Figure 6. Water level at Bend Bridge in summer 2016.

American River Salmon and Steelhead – Update

Posted on October 14, 2016 by Tom Cannon

In a September post I opined about the state of the American River salmon and steelhead. I am more inclined now to scream. This beautiful river running through the state’s capital city, Sacramento, one of the Central Valley’s top three producers of salmon and steelhead, is now the most abused. Water temperatures and flows have reached critical limits because of high summer releases from Folsom Reservoir, leaving this year’s salmon run in the lower American River in jeopardy.

After nearly filling this past spring, Folsom Reservoir was drained of an unprecedented 550,000 acre-ft of water (and most of its cold-water pool) over the summer (Figure 1) in support of cities and farms in central and southern California. Fall flows from Folsom Lake to the 20 miles of the lower American River have been cut to drought levels (Figure 2) to conserve what minimal storage is left and to have some cool water for late fall salmon spawning.

The lower American River is now host to tens of thousands of adult Chinook salmon that have migrated into the river to spawn. These salmon are now “holding” for their eggs to mature and for water temperature to fall below 60°F so that their spawned eggs can survive. Scientific research has led the National Marine Fisheries Service, the Environmental Protection Agency, the California Department of Fish and Wildlife, and the State Water Resources Control Board to recommend “holding” water temperature be less than 60°F to ensure the health of the holding, pre-spawn salmon and the viability of their eggs.

At a time when nearly all the Central Valley spawning rivers are near 60°F or below, the lower American remains warmer (Figure 3), with daily average water temperatures of 65°F.

While fishing the lower American River on October 12, an adult female salmon swam up to me “gasping” for air. Other than a raw lamprey scar, she appeared healthy. I tried to revive her by holding her steady in a slight current, but she eventually died. It took less than an hour for the carcass to be covered by silt and become unrecognizable. I wondered how many more like her were on the bottom of the river.

I can only assume that fisheries agencies are desperately trying to manage the river to save as many salmon as possible given the warm, low water levels in Folsom Lake and the limited options that now remain available to them. The main problem is this past summer’s draining of Folsom’s cold-water pool. In future years, the Bureau of Reclamation and the fisheries agencies need to fully implement the requirements of the CVP/SWP biological opinions as copied verbatim in my September post, linked above.

Figure 1. Folsom Lake storage in acre-ft in 2016. Maximum is 975,000 acre-ft. (Note: flood control limits in spring often keep the reservoir from filling.)

Figure 2. Flows from Folsom Lake to lower American River in 2016. Note the average of about 5000 cfs per day (10,000 acre-ft per day) released from early May to mid-August (roughly 1 million acre-ft from storage and reservoir inflow).

Figure 3. Summer to early fall water temperatures in the lower American River in 2016. Yellow line is target maximum-allowed standard. Red line is recommended maximum-allowed holding temperature limit for adult Chinook salmon.

2015 Winter-Run Salmon Progress Report – Lessons Learned and Not Learned

Posted on October 10, 2016 by Tom Cannon

The Sacramento River Temperature Task Group’s report on water year 2015¹ released at the end of last year prematurely proclaimed successful operations for 2015 under its Temperature Control Plan (TCP). If the Group had waited a few more months, it would have reported utter failure, with the poorest survival and production of winter-run salmon yet recorded.² Below, I excerpt from the Report, and offer some observations.

In summary, water year 2015 has been one of the driest years in decades and it followed three consecutive dry years throughout the state. Shasta Reservoir was projected to have end of year storage of 1.1 MAF in the May 90% forecast. Due to such low storage in Shasta Reservoir, Reclamation utilized Trinity River water to conserve Shasta Reservoir storage. The amount of water brought over from Trinity River through the Spring Creek Tunnel into Keswick Reservoir was a great benefit to the temperature operations on the Sacramento River. In all, Reclamation achieved meeting the TCP at Clear Creek (see Chart 1) of 57°F not to exceed 58°F through October 1, 2015, as indicated in the Temperature Management Plan, when 90% of the redds were emerging.

Comment: The Trinity water brought into Keswick Reservoir was 58-59°F, warmer than even the downstream criteria, resulting in more of the Shasta cold-water pool being used to cool it. The problem was recognized by the parties, as it resulted in demands to replace the existing Whiskeytown temperature curtain to cool the Trinity water before it was released into Keswick Reservoir. Achieving the 2015 goal of not exceeding 58°F turned out ineffective as well. Less than normal amounts of Trinity water have been brought into Keswick so far in 2016.

Despite the SRTTG best projection and modeling efforts to manage Sacramento River water temperature for winter-run spawning and egg incubation in water year (WY) 2014, winter-run brood year (BY) 2014 was considered a year class failure. One hundred percent of BY 2014 redds were exposed to temps above 56°F daily average temperature (DAT) at the Sacramento River above Clear Creek California Data Exchange Center monitoring station temperature compliance point (CCR) at some time period during WY 2014. Of significant concern were those eggs, alevin, and fry exposed to the elevated DAT above 56°F (and as high as 62.3°F) throughout September and October when the cold water pool out of Shasta Reservoir was depleted.

Comment: So the Task Group met the monthly average but allowed the daily average temperature to exceed 58°F in summer 2015 (Charts 2 and 3). The Report suggests improvement compared to 2014 conditions, but 2015 was also above 56°F. On 10% of the days in summer 2015, hourly water temperature exceeded 60°F at the CCR gage at Bonnyview Bridge in Redding during warm afternoons. On 60% of the days, water temperature reached or exceeded 59°F, the tolerance limit for salmon eggs and embryos. ³

Temperature monitoring results of 70 loggers indicated slight variation and stratification in temperature between in-river, backwater, and deep pools, but in general all winter-run salmon eggs and alevins were exposed to poor water quality due to warm water temperatures.

Comment: If they knew this, why did they allow it?

The plan called for real-time operations that targeted 57° at the Clear Creek compliance location not to exceed 58°F with minimized flows. By targeting 57°F not to exceed 58°F, where the majority of the redds were above Hwy 44, we were able to extend the use of the cold water pool.

Comment: By targeting the Clear Creek compliance location, the Task Group pretty much assured that adult winter-run salmon would seek out cooler waters near Redding, essentially confining their spawning to the uppermost 10 miles of their historic 60 mile spawning reach. The Group extended the cold-water pool by creating low survival conditions in the spawning reach. Reclamation was able to bring in warmer Trinity water for water supply (at the expense of Shasta’s cold-water pool) and did not have to sacrifice hydropower or peaking hydropower using Shasta Dam’s warm-water bypass (an operation which most likely would have been required if the target had been the appropriate 56°F). Reclamation was also able to meet its water supply commitment of 75% allocation to the Sacramento River settlement contractors in the fourth year of drought. So far in 2016, Reclamation has met its commitment of 100% allocation to the settlement contractors.

Perhaps more perplexing is what was left out of the report: water temperature and flow conditions in the salmon-migration and sturgeon-spawning reach in over 100 miles of the Sacramento River below Red Bluff. There was no mention of the Basin Plan’s targets for this reach of the river where water temperatures were too high (>22°C, 72°F) to allow adult salmon migration, while creating lethal conditions (>20°C, 68°F) for juvenile sturgeon⁴ (Chart 4). There was a complete disregard for the winter-run salmon objective of 56°C at Red Bluff in the Basin Plan, Water Right Order 90-05, and the NMFS BO: all 150 days from May through September failed to meet the objective (Chart 5). So far in 2016, the objective has yet to be met, despite the fact that Shasta was nearly full at the beginning of May.

Hopefully, the Winter Run 2016 report will be more comprehensive and complete than the Report for 2015. The 2016 Report should include not only the consequences for spawning habitat near Redding, but should also analyze the condition of rearing and migratory habitat below Redding through the fall and winter. The report should also cover consequences to the other salmon, including the ten million federal hatchery salmon smolts released near Redding.

Chart 1. Map of 60 miles spawning reach below Keswick Dam on Sacramento River. Various temperature compliance points are noted. The NMFS BO specifies Bend Bridge with relaxation allowed in drier years. In 2015 the compliance point was above Hwy 44 bridge. Clear Creek 58F DAT was the compliance point in spring 2016. Balls Ferry 56°F is present compliance point in summer 2016.

Chart 2. Summary of 2015 spring-summer monthly average temperature at Clear Creek compliance point.

Chart 3. Summer 2015 spring-summer water temperatures at compliance locations. Note the red line is one degree above the target 56°F they noted.

Chart 4. Water temperature and river flow at Wilkins Slough at RM 125 on the Sacramento River May-September 2015. Historical average flow shown by green triangles.

Chart 5. All 150 days from May through September were higher than the 56°F Basin Plan objective for Red Bluff.

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