Author Archives: Tom Cannon

Fundamental Needs of Central Valley Fishes – Part 1b: River Flows – Winter Flows

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In the coming months and years, regulatory processes involving water rights, water quality, and endangered species will determine the future of Central Valley fishes.

To protect and enhance these fish populations, these processes will need to address four fundamental needs:

  1. River Flows
  2. River Water Temperatures – holding, spawning incubation, juvenile rearing and migration.
  3. Delta Outflow, Salinity, and Water Temperature
  4. Valley Flood Bypasses

In the previous Part 1a post, I discussed river flows during fall.  In this post, I discuss river flows during winter.

Winter Flows

Winter is the season of high river natural flows.  Even in drought years, Sacramento River flows measurably spike during storms that provide stormwater runoff from numerous undammed tributaries and local sources (Figure 1).  On the mainstem Sacramento River and those of its tributaries that also feature rim dams, most of the stormwater inflow is captured and stored for spring-fall water supply.  On the San Joaquin River, all the major tributaries and mainstem have large storage reservoirs that capture Sierra and upper Valley runoff, so there is limited controlled winter runoff (Figure 2).

Winter flows are needed to attract adult winter-run and spring-run salmon, smelt, steelhead, and sturgeon to upriver spawning grounds.  Winter flows also carry young salmon and steelhead to the Delta, Bay, and ocean by providing velocity, water temperature, and turbidity conditions that speed migration and deter predation by birds and fish.  Winter flows stimulate food production and availability.  Winter flows and associated high water levels provide access to off channel and floodplain rearing areas that provide refuge and food.  Winter flows clean substrate and wash gravels, and thus improve spawning conditions.  High winter flows wash sediment, nutrients, and organic material into the estuary that stimulate Bay-Delta productivity.

On the Sacramento River, winter flows carry juvenile winter-run, spring-run, late-fall-run, and fall-run salmon through up to 200 miles of rivers and the Delta to the Bay and ocean.  Much of the route is leveed and channelized, with little cover/refuge and abundant predators.  Higher flows provide turbidity and lower water temperatures that deter predation.

In the San Joaquin River watershed downstream of the rim dams, flows are minimal in the absence of flood flows and dam spills.  Thus, de facto drought conditions persist downstream of San Joaquin watershed dams in all but the wettest years.  Recruitment into the salmon populations is confined to San Joaquin offspring produced in wet years, augmented by hatcher strays, since there is minimal juvenile survival to the ocean in other years because of low flows.

In the non-flood years where reservoirs capture most reservoir inflow during the winter, supplemental releases from Central Valley reservoirs should be considered to piggy-back on and enhance natural flow pulses to benefit salmon and other native fish.  Such action would most benefit salmon populations below rim dams.  Such releases can be prescribed as a portion of the natural or unimpaired inflow to the reservoirs.

Figure 1. Daily average Delta inflow from the Sacramento River 2012-2016 as measured at Freeport. Red circles denote winter-spring flow pulses that support important ecological processes such as salmon migration. Water years 2012-2015 were drought years; 2016 was a below-normal water year.

Figure 1. Daily average Delta inflow from the Sacramento River 2012-2016 as measured at Freeport. Red circles denote winter-spring flow pulses that support important ecological processes such as salmon migration. Water years 2012-2015 were drought years; 2016 was a below-normal water year.

Figure 2. Delta inflow from the San Joaquin River 2012-2016 as measured at Vernalis. Prescribed fall and spring flow releases from reservoirs for salmon migrations dominate the hydrograph in these drought years. Winter flow pulses were lacking with the exception of 2016. Water years 2012-2016 were drought years in the San Joaquin watershed.

Figure 2. Delta inflow from the San Joaquin River 2012-2016 as measured at Vernalis. Prescribed fall and spring flow releases from reservoirs for salmon migrations dominate the hydrograph in these drought years. Winter flow pulses were lacking with the exception of 2016. Water years 2012-2016 were drought years in the San Joaquin watershed.

Fundamental Needs of Central Valley Fishes – Part 1a: River Flows – First Pulse of Fall Rains

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In the coming months and years, regulatory processes involving water rights, water quality, and endangered species will determine the future of Central Valley fishes.

To protect and enhance these fish populations, these processes will need to address four fundamental needs:

  1. River Flows
  2. River Water Temperatures
  3. Delta Outflow, Salinity, and Water Temperature
  4. Valley Flood Bypasses

In this post, I summarize a portion of the issues relating to River Flows: Fall Rains. Part 1b will cover winter river flows.

River Flows – Fall Rains

In most years, the first substantial fall rainfall stimulates many important ecological processes such as salmon and smelt spawning runs and salmon and steelhead smolt migrations to the ocean.  Figure 1 below shows the effects of 2016’s late October rains,  and Figure 2 below shows the effects of 2015’s December rains, in the lower Sacramento River flows at Wilkins Slough near Yuba City below Colusa.  Most of these flow pulses came from storm runoff from un-dammed upper Sacramento Valley tributaries such as Cow, Cottonwood, and Battle Creeks.  Such flow pulses stimulate the migrations of young salmon toward the ocean.  Figure 3 below documents these migrations in the form of  rotary screw trap collections at Knights Landing in the lower Sacramento River.

Under current operations, flows from the major reservoirs are generally held to the minimum requirement in the fall season in order to increase reservoir storage (Figure 4).1  What is needed are flow pulses (spills) from the major Valley reservoirs to the major rivers below dams, to stimulate the migration of the juvenile salmon spawned immediately downstream of these dams.  Just downstream of Whiskeytown Reservoir on Clear Creek, Shasta and Keswick reservoirs on the upper Sacramento River, Oroville Reservoir on the Feather River, and Folsom and Nimbus reservoirs on the American River are vitally important salmon-producing reaches whose flow is completely controlled by the operation of the dams.  Water releases timed to the natural flow pulses would stimulate migration from these important salmon-producing reaches, providing even more flow and stimulus for young salmon from all the Valley rivers to pass successfully through the Delta and Bay to the ocean.

Meanwhile, downstream in the Delta, the CVP and SWP export facilities generally ramp up exports during the initial storm pulse (Figure 5 below shows an example from 2016).  Because of the importance of the initial storm pulse, the CVP and SWP should limit exports during the initial pulse, not only to help salmon get through the Delta and Bay, but also to minimize the diversion of young salmon to the south Delta.

Figure 1. Lower Sacramento River flow at Wilkins Slough in fall 2016.

Figure 1. Lower Sacramento River flow at Wilkins Slough in fall 2016.

Figure 2. Lower Sacramento River flow at Wilkins Slough in late fall 2015.

Figure 2. Lower Sacramento River flow at Wilkins Slough in late fall 2015.

Figure 3. Catch of juvenile salmon in Knights Landing rotary screw traps 2001-2004 vs. flow in lower Sacramento River at Wilkins Slough.

Figure 3. Catch of juvenile salmon in Knights Landing rotary screw traps 2001-2004 vs. flow in lower Sacramento River at Wilkins Slough.

Figure 4. Release of water from Shasta/Keswick to upper Sacramento River near Redding, fall 2016.

Figure 4. Release of water from Shasta/Keswick to upper Sacramento River near Redding, fall 2016.

Figure 5. Export of water from south Delta by State Water Project, fall 2016.

Figure 5. Export of water from south Delta by State Water Project, fall 2016.

  1. For additional discussion of the negative effects of this practice, see previous post. ↩

American River Salmon Hatchery Begins Taking Salmon

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California Department of Fish and Wildlife has announced that it opened the American River Nimbus Hatchery ladder on Nov 2.  At the same time, the feds have managed to cool down the river to allow salmon in the river to also begin spawning (Figure 1).  The Bureau of Reclamation cooled the river by opening lower level outlets of Folsom Dam for a portion of the day beginning in late October (Figures 2 and 3).  This allowed the release of  colder water from deep in the reservoir into the Nimbus regulating reservoir directly downstream of Folsom Reservoir.  There, the cold water mixed with warmer reservoir waters before discharge to the lower American River.

The real story here is that the feds had to wait until November to cool water both in the river, and in the Nimbus Fish Hatchery just downstream of Nimbus Dam.  The supply of cold water in Folsom Reservoir is limited this fall because of excessive releases of stored water to the Delta this past summer (see prior post).  The summer shrinkage of Folsom’s cold-water pool subjected the salmon that entered the lower American River in September and October to a month or more of stress from warm water.  That stress will likely reduce survival of pre-spawn and spawning salmon, diminish their success in spawning, and make many of eggs and embryos spawned in the river unviable.

Figure 1. Water temperature below Nimbus Dam on the lower American River near the Nimbus Hatchery Oct 4 – Nov 2, 2016. Red line denotes safe water temperature for holding and spawning salmon, and salmon egg survival.

Figure 1. Water temperature below Nimbus Dam on the lower American River near the Nimbus Hatchery Oct 4 – Nov 2, 2016. Red line denotes safe water temperature for holding and spawning salmon, and salmon egg survival.

Figure 2. Temperature of the water released from Folsom Dam Oct 21 – Nov 2, 2016. Red circles show the release of water from Folsom’s cold-water pool.

Figure 2. Temperature of the water released from Folsom Dam Oct 21 – Nov 2, 2016. Red circles show the release of water from Folsom’s cold-water pool.

Figure 3. Flow releases from Folsom Dam. Red circles depict flow releases of cold water from lower level outlet of dam Oct 21 – Nov 2, 2016.

Figure 3. Flow releases from Folsom Dam. Red circles depict flow releases of cold water from lower level outlet of dam Oct 21 – Nov 2, 2016.

Does the Central Valley Need a Predator Removal Program?

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The Columbia River Pikeminnow Sport Reward Program just finished another year.  A near-record 200,000 adult pikeminnow were harvested and $1.7 million rewards paid.  The goal of the program is to harvest 10-20% of the population each year to reduce the population about 50%.  Harvest rates in recent years reached as high as 17% as compared to this year’s 11%.

So why after 25 years is the program still harvesting near-record numbers of pikeminnow?  The likely reason is that the program is not based on sound science.  The Columbia pikeminnow population dynamics likely are best described with a standard Ricker-Type Population Model (see chart below), with reduced recruitment of young at high adult population levels because of competition and cannibalism.  The introduction of a light harvest can actual increase recruitment of young by reducing competition and cannibalism, with the increased recruitment replacing the harvest, even providing a constant harvest or yield.  This is how fishery quotas may be sustained year after year, such as in Alaska’s Bristol Bay Sockeye salmon fishery.

This same dynamic likely applies to pikeminnow and some other predators in the Central Valley.  Pikeminnow are likely near their saturation level in the Central Valley.  Any light harvest such as from a sport-reward or removal program would likely have little or no effect.  Increasing harvest on non-native predators like largemouth bass by reducing sport-fishing harvest regulations would likely also have a limited benefit.  However, striped bass, the most popular sport fish in the Delta, has a population that is already seriously depressed by long-term loss of juveniles to water diversions.  Striped bass may respond more directly to increased harvest, further reducing recruitment and further depressing the population.

Thus the species composition of fish that eat other fish could change, satisfying those who vilify stripers and infuriating those who fish for them.  But the potential for reduced overall loss of juvenile salmon or other native species that might follow from “predator removal” is far more complex and questionable than its proponents maintain.

Ricker-type stock-recruitment population dynamics model that likely applies to Columbia River and Sacramento River pikeminnow populations

Ricker-type stock-recruitment population dynamics model that likely applies to Columbia River and Sacramento River pikeminnow populations

Bringing Back the Klamath Salmon

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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.)

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.

image2To get the process moving faster, I offer the following recommendations:

  1. 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.
  2. 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.
  3. 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.
  4. Fully implement federal and state recovery plans for salmon and steelhead. Get funding.
  5. Re-introduce Coho and spring-run Chinook salmon to tributaries where populations are or are near extinction, including tributaries above dams.
  6. 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.
  7. 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.
  8. Fully fund and implement a salmon and steelhead rescue program for young stranded in tributary spawning rivers.
  9. Improve access of spawning salmon and steelhead to historic spawning grounds blocked or hindered by irrigation dams, road crossings, or low streamflow.
  10. 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.
  11. Require the California Resources Agency to take a leadership role in making the Klamath a priority.
Figure 1. Klamath watershed. (Source DOI.)

Figure 1. Klamath watershed. (Source DOI.)

For more on the Klamath recovery see the following: