Category Archives: Chinook Salmon

A New Paradigm for Sacramento River Basin Salmon Habitat Restoration

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Nearly everyone supports the concept of restoring salmon and their habitats within the existing geographic range of the Central Valley.  But why is it so difficult to implement relatively low-cost, simple actions that would unquestionably benefit salmon?  The following is a recent example of the problem and its ultimate, surprising solution.

In 1986, a colleague (Dick Painter) with the Department of Fish and Game [now Department of Fish and Wildlife (DFW)], through a lot of planning and hard work, created an excellent salmon habitat project in a side channel on the main stem Sacramento River in Redding, California.  Many years later, I named this area “Painter’s Riffle” in recognition of the dedicated biologist.  The modified channel worked well for many years but, inevitably, the habitat quality diminished due to lack of fresh gravel replenishment that would have been historically provided from upstream areas prior to construction of Shasta and Keswick dams.  Nevertheless, the area proved beneficial for 25 years by being hydraulically connected to the main river and provided habitats for the river’s four runs of salmon and steelhead.  This circumstance changed dramatically after the City of Redding widened the Highway 44/299 Bridge spanning the Sacramento River just upstream of Painter’s Riffle.  As is now usual and customary for such in-river projects, DFW required the bridge contractor to lay clean spawning gravels in the riverbed (amounting to 20,000 cubic yards) as a platform to commence work.  The concept being, after the bridge project was complete, high reservoir releases from Shasta Dam would eventually wash those gravels downstream and contribute to new salmon spawning areas.  The strategy worked … somewhat.  The gravel mobilized en masse during March of 2011 when Shasta Reservoir went into flood-control releases and 50,000 cubic feet per second surged into the river below Keswick Dam.  The gravels placed under the highway project flushed downstream, but left 8,000 cubic yards in the channel’s entrance, forever plugging Painter’s Riffle.

In early February 2013, while driving across the new Highway 44/299 Bridge, I looked downstream and could readily see what had happened — Painter’s Riffle had been hydraulically disconnected from the river.  I drove to the site (a City of Redding municipal park) to take some photographs and measurements.   That night, I wrote a Proposal to restore the site to its original ecological function and presented the concept to the City of Redding, obtaining its support.  However, when I met with DFW representatives (including a “Habitat Restoration Coordinator”) to garner the agency’s support, you would have thought I’d wacked a hornet’s nest!  My read on the less-than-enthusiastic response was that any “outsider” involvement and alternative scientific perspectives in their internal plans for salmon restoration were unwelcomed.  This was revealed months after my original Painter’s Riffle proposal when a radically different proposal for the site surfaced and was sanctioned by the fish agencies.  They recommended slicing a 10-foot wide trench through the same side channel and only allowing it to function at flows above 10,000 cfs, instead of my submittal which recommended the channel perform at 3,250 cfs, or the minimum reservoir releases.  In my written response to the agencies’ proposal, I explained that winter-run Chinook salmon redds would become stranded and eggs would perish in the side channel if the fish spawned during normal flows above 10,000 cfs (among many other problems).  After many months of valuable time lost, logical minds prevailed and the agencies’ proposal was quietly removed from consideration.

To gain momentum, the project needed an advocate and was proposed to the Golden Gate Salmon Association’s (GGSA Interview) Task Force which includes the three fish agencies:  DFW, USFWS, & the National Marine Fisheries Service (NMFS).  DFW & NMFS representatives were contemplatively silent, but a USFWS representative asserted he had already looked at the site and the gravels appeared to be too large for suitable salmon spawning (paradoxically, in direct conflict with DFW’s in-river project gravel requirements).  The effort was rapidly dying on the vine and, without badly-needed support, GGSA was forced to put the proposal on the back burner.

Trying a different venue, the project was presented to northern California water districts.  Surprisingly, the Glenn-Colusa Irrigation District (GCID), located nearly 100 river miles downstream of Painter’s Riffle said they would champion the cause (aka, do the on-the-ground work).  At this point, with the winds shifting once again in the salmon’s favor, GGSA went to the U.S. Bureau of Reclamation (USBR) and requested their staff to take the task on as part of GGSA’s Salmon Plan.  They were successful.  Although it was still 2013, the reality of the extensive regulatory permitting hurdles forced USBR staff to eventually concede that it would be impossible to implement the project until the following year, even though low river flows (Shasta Reservoir releases) due to the severe drought would have provided perfect conditions for construction.  Regrettably, the salmon would have to wait until the fall of 2014.

As anticipated from long-range weather forecasts, the heavy rains never arrived during the winter of 2013-2014, but the meetings, conference calls, and draft environmental documents on the proposed Painter’s Riffle project came on like a deluge.  The scales were now tipping against restoration.  In fact, except for GCID, USBR, and GGSA, it seemed no fish entity would formally support the project.  For example, the USFWS suggested “pre-project monitoring” be conducted at the sealed-off side channel before any gravel was moved, perhaps for many years.  Undefined “concerns” were voiced about effects on threatened and endangered fish, but without remedial recommendations and recognition of the benefits.   With this much resistance, it seemed as though we were proposing to build a new waste-water treatment plant on the river that would spew raw sewage into the middle of prime salmon habitats.  The quagmires of state and federal bureaucracies were sucking the enthusiasm for the restoration effort down into the black hole of oblivion.  Nevertheless, after numerous speed bumps in the process and a seemingly endless series of meetings and conference calls, the log jam broke and key pragmatic agency individuals came on board with the project.

Now, at this late date, with renewed zeal, a Herculean effort was set in motion by USBR and GCID staff who worked overtime to update and finalize the numerous regulatory permits to implement the project in the fall of 2014.  But wait, not so fast!  This simple project almost came to a screeching halt when Endangered Species Act restrictions nearly imposed insurmountable obstacles to conduct the in-river work.  At the 11th hour, several knowledgeable, rational DFW biologists stepped up to the plate and delivered on all fronts with support, cooperation, and assistance resulting in NMFS allowing the work to proceed.

Once NMFS gave its blessing, the field implementation to restore Painter’s Riffle went into overdrive because of advanced planning and the due diligence of highly experienced GCID heavy equipment operators.  Two massive front-end loaders, a D-6 cat bulldozer, and an excavator simultaneously went into close-quarter action.  Their execution was well choreographed with all four earth-moving machines weaving up and down and across Painter’s Riffle.  Each operator knew the movements of others through radio communication, hand signals, or most often, years of experience in skilled operation of the machines.  It was mesmerizing to watch the quick transformation of the river channel:  Video of Equipment in Action

With everything going smoothly and swiftly, Mother Nature had another plan.  One of the largest storms to hit northern California in years (ironically, in a fourth-consecutive drought year) slammed into the area during the two weeks of construction.  With heavy rains and winds pummeling the equipment crew, they relentlessly proceeded nonstop during permitted hours.  And, to be sure, this was no ordinary storm.  The so-called “Atmospheric River” or “Pineapple Express” parked itself on top of Redding for an extended period and localized flooding was reported everywhere.  Caltrans even made an emergency stop at the job site to clear plugged culverts spewing heavy rain runoff in the municipal park.  Although Shasta Reservoir was extremely low due to the three prior years of drought, the downstream re-regulating Keswick Dam suddenly had to increase water releases due to localized flooding concerns in the vicinity of the dam.  River flows at the construction site increased dramatically, jeopardizing the work in progress … but the crew diligently kept on working and completed the project ahead of schedule and below budget.

Ultimately, all involved agencies, groups, and individuals praised the project and the unprecedented collaboration.  The finished product is anticipated to benefit the Sacramento River’s four runs of Chinook salmon and steelhead.  As a result, new salmon restoration projects are planned for implementation this and next year … using more-active stakeholder involvement and “outsiders” perspectives.  Perhaps there is hope for salmon after all:  Video of Completed Project

The completed Painter’s Riffle Project.

The completed Painter’s Riffle Project.

Hatchery Reform – Part 2

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Previously… Part 1: Central Valley Salmon and Steelhead Hatchery Program Reform

Environmental Factors Affecting Smoltification and Early Marine Survival of Anadromous Salmonids. 1980. GARY A. WEDEMEYER, RICHARD L. SAUNDERS, and W. CRAIG CLARKE1.

“There is reason to suspect that in many cases apparently healthy hatchery fish, though large and silvery, are not actually functional smolts and their limited contribution to the fishery, even when stocked into the same rivers from which their parents were taken, results from their being unprepared to go to sea. This failure to produce good quality smolts probably arises from an incomplete understanding of exactly what constitutes a smolt, as well as from a lack of understanding of the environmental influences that affect the parr-smolt transformation and which may lead, as a long term consequence, to reduced ocean survival.”

This paper is over thirty years old (1980), yet it still rings true. It is most certainly a complicated subject that is an on-going concern in hatchery science and management. There remains room for improvement if funding is available for hatchery program upgrades.

“In the absence of complicating factors such as altered river and estuarine ecology, smolt releases should be timed to coincide as nearly as possible with the historical seaward migration of naturally produced fish in the recipient stream, if genetic strains are similar. At headwater production sites, much earlier release may be called for… The desired result is that hatchery reared smolts which are genetically similar to wild smolts enter the sea at or near the same time.”

It has been apparent for many decades that Central Valley Fall Run and Spring Run Chinook have a classic “ocean-type” life-history pattern, wherein young spawned in the fall head to the ocean early in their first year rather than as yearlings. Even within the ocean-type, Central Valley Fall Run have two types: one has fry rearing in the estuary (Bay-Delta) and the other in rivers. Of these two types, Valley hatcheries have chosen to manage for the latter. Hatcheries pump out smolts by the millions in April and May, on top of a smaller number of “wild” river-smolts. I believe the “river-smolt” type has been the minority contributor at least since all the dams were built. There simply is not enough river habitat, and what there is has been severely degraded by dams, water management, and physical habitat damage (e.g., levees and land use). The majority contributor is the Bay-Delta or “estuary-smolt” type. Fry that move to the estuary in December-January grow quickly and enter the ocean as smolts in March, a month or more before the river-type. This is a huge advantage for the estuary-type. The hatchery programs could focus more effort on this type by out-planting fry to the estuary or lower river floodplains immediately above the estuary (e.g., Yolo Bypass). Experimental out-planting of hatchery fry to rice fields in the Yolo Bypass has proven promising2. There are also many natural habitats in the lower river floodplains and Bay-Delta that could accommodate out-planting.

This post is part of a 4 part series on hatchery reform, check back into the California Fisheries Blog over the next week for Parts 3 and 4.

Central Valley Salmon and Steelhead Hatchery Program Reform

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Dr. Peter Moyle of the University of California, Davis commented last year commented on California salmon and steelhead hatchery reform at the California Fish and Game Commission’s Workshop on Strategic Improvement in California’s Anadromous Hatcheries, held in Sacramento on February 4, 20141.

Dr. Moyle remarked that hatcheries fail to meet their primary dual purposes of sustaining commercial and sport fisheries and assisting in recovery of wild (naturally spawning) salmon and steelhead. Hatchery strategies have led to the complete dominance (90%) of hatchery salmon and steelhead in most rivers, which will ultimately lead to “periodic shut-downs of the fisheries and extinction of most runs, even those supported by hatcheries.” He concluded that a much more radical reshaping of hatchery policy is needed.

He recommends two types of hatcheries: conservation hatcheries that focus on recovery of wild populations, and production hatcheries that focus on sustaining commercial and sport fisheries. He suggests abandoning wild salmon and steelhead management in favor of production hatcheries for some runs (e.g., Fall Run Chinook salmon).

Only the federal Sacramento River hatcheries near Redding operate in the recommended manner. The federal Livingston Stone Hatchery is a model conservation hatchery for endangered Winter Run Chinook Salmon. The Coleman National Fish Hatchery on Battle Creek is a production hatchery for Fall Run, Late Fall Run, and Spring Run Chinook, as well as steelhead. Only wild Late Fall Run, Spring Run, and Winter Run Chinook and steelhead are allowed to pass Coleman’s diversion dam to spawn in upper Battle Creek. Upper Battle Creek thus serves as a wild fish conservation hatchery.

The state hatcheries on the Feather, American, Mokelumne, and Merced rivers operate as production hatcheries, mitigating for the blockage of these major Central Valley salmon tributaries by dams. These hatcheries focus on Fall Run Chinook and steelhead, although the Feather River Fish Hatchery also supports Spring Run Chinook.

Only undammed Sacramento Valley tributaries Deer, Mill, Big Chico, Antelope, and Butte creeks support reliable native runs of wild Spring Run Chinook. Native-wild Spring Run are sustainable in these streams because habitats are accessible at higher elevations where over-summering habitat with deep, cool-water holding pools exists.

One way to improve production of wild fish is to develop conservation hatcheries that combine trap-and-haul programs with over-summering habitats above the dams, as recommended in the Central Valley Salmon Recovery Plan2. This would require a capture-sorting effort, as is presently done at Coleman Hatchery on Battle Creek. Wild fish would be trucked above the dams. Juvenile fish produced above the dams would be trapped and trucked downstream for release below the dams. Conservation hatchery components could be established initially at the four state hatcheries to get the program started with appropriate “wild” genetic stocks.

Wild populations of Winter Run and Spring Run could be established above Shasta Reservoir on the Sacramento River. Spring Run could be established on some combination of the upper Feather, Yuba, American, Mokelumne, Tuolumne and Merced rivers. Wild steelhead could be established above the dams in any of these rivers.

Meanwhile, production hatcheries of salmon and steelhead could continue below the dams. Marking production fish would allow separation of wild and hatchery fish, as well as mark-selective fishery harvest to preserve wild fish until such time wild stocks are sustainable. Trucking/barging of production smolts to Bay would reduce predation and competition with wild fish while increasing populations of production fish for harvest.

Dr. Moyle also recommended establishing wild salmon sanctuaries, as is currently being established on upper Battle Creek. The areas above the dams are good candidates for such sanctuaries. Undammed Valley Spring Run rivers are also good candidates. Isolated tailwaters on the lower Yuba, Mokelumne, and San Joaquin rivers may also be candidates.

More on hatchery reform options can be found at: http://cahatcheryreview.com/summary-conclusions/.

Bay-Delta Fisheries Devastated by Weakened Protections

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Water quality standards under the jurisdiction of the State Water Resources Control Board provide bare minimal protections to the State’s major ecosystems in Critically Dry years. But with the extended drought in seven of the past nine years, protections have been weakened to the point where ecosystems and fisheries dependent on them have been devastated. Yes, rice acreage is down 25%1, but fish production is down 95%, with some species lost forever. Salmon numbers have been maintained by hatcheries and trucking hatchery production to the Bay, but not without a huge mortgage on future wild populations. Hatchery salmon already make up over 90% of ocean and river fisheries. Delta Smelt, Longfin Smelt, Steelhead, Green and White sturgeon, Striped Bass, and wild Chinook Salmon populations have declined another 90% in the past four years, after losing 90% in each in the past several decades. Farm production will return, but some fish will not. The ecosystem will return, but with a much different makeup of new food web plankton species from Asia, greater proportions of non-native sport and pan fish, and a greater assortment of the invasive aquatic plants that already fill waterways. The Delta will be featured more often on the Bass Masters Classic.

And what about the Bay? Only a few hundred thousand acre-feet of water of the millions released from reservoirs this summer will reach the Bay. Water quality and marine fish and shellfish will soon show signs of decline. The Bay-Delta is a major nursery for anchovies, herring, and Dungeness crab. Anchovy stocks are already collapsing2. Sea lions are starving and dying.

How hard would it be to at least maintain the antiquated minimum protections adopted in 1995 Bay-Delta Standards? The Bay is “allocated” a base of about 5 million acre-feet of water each year in the form of a base Delta outflow of 7,100 cfs. This standard for critically dry years is the first to suffer from State Board drought orders. The Board has reduced outflows requirements to 3000-4000 cfs (Figure 1). Such low outflows are in reality closer to zero (see earlier blog3). The amount of water “short” from the critical year base in the important February – June period is approximately 300,000 acre-feet. This amounts to less than 5% of the total 10 million acre-feet of reservoir releases into the Central Valley in 2014 and expected in 2015. The amount is less than 10% of the 5 million acre-feet presently in storage in Central Valley reservoirs. The water could be restored to the Bay by reducing water contractor allocations and/or reservoir storage.

The Delta had one plankton bloom that came and went this spring4. Plankton blooms are needed to drive the Bay-Delta food chain. Without freshwater flow to the Bay there will be no blooms and little food through the summer for Bay-Delta fishes. Water quality will suffer as well. The prognosis for the Bay-Delta and other California ecosystems is grim. California fisheries will suffer for decades to come.

Figure 1. Delta outflow as calculated by the California Department of Water Resources for Feb-May, 2015. Top red line represents 7100 cfs minimum standard. Lower red line represents typical weakened level of protection.

Debate on Salmon Trucking Heating Up

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A recent FISHBIO blog post1 reported on the CalNev American Fisheries Society annual meeting, where AFS members considered the subject of “off-site” release of hatchery salmon smolts. The general perception is that releases away from hatcheries and the natal river leads to high stray rates, with some estimates of stray rates as high as 90%. The blog post discusses the problems caused by straying to non-natal rivers. The blog post states a concern that the practice of off-site releases will lead to reduced population fitness and genetic diversity, and that reproductive success will be half of wild-origin fish:

“Such losses in biocomplexity are dangerous because of the many threats salmon face in the highly altered Central Valley, and the potential inability of this species to persist if faced with a major environmental disaster, which the current drought in California may foreshadow. Yet despite recommendations from the California Hatchery Scientific Review Group, who warned about increases in straying rates due to off-site releases as early as 2010, managers from across the state have responded to drought conditions by trucking salmon from hatcheries to release sites in the Delta and Bay.”

While FISHBIO’s concerns about straying and genetics are well-founded, it is a little late for the Central Valley Fall Run Chinook. Studies have shown that populations across the Valley are homogeneous, with little or no genetic diversity, and consist mainly of hatchery fish and some natural offspring of hatchery fish. There really are no viable “wild” Fall Run Chinook populations left in the Central Valley. Even runs on rivers with no hatcheries (e.g. Yuba and Cosumnes rivers) are made up almost entirely of hatchery strays.

In making the decision to truck hatchery smolts to the Bay-Delta, Federal and State fisheries managers have recognized the harsh reality that having some salmon is better than having none. No one wants to go back to the bleak escapement years of 2007 to 2009, when less than 100,000 adult salmon per year returned to the Central Valley (compare with 870,000 in 2000 and 200,000-400,000 fish per year since 2009). Recent improvements were in large part due to the smolt trucking program in which 50-80% of Central Valley hatchery smolts were trucked to the Delta or Bay.

Can we have our cake and eat it too? Are there measures we can undertake to improve diversity and reduce straying? Yes, there are many, but they come with costs and with no guarantees.

The hatcheries can be more selective in the genetic material (parents) they use in producing smolts. Hatchery managers can barge smolts to the Bay to reduce straying (during barging, the smolts are suspended from barges in net pens, and thus imprinted on their natal waters during their trip downstream). Hatcheries can mark all hatchery fish to clearly differentiate between wild fish and hatchery fish (generally, hatcheries currently mark only 25% of hatchery juveniles). The Fish and Game Commission could establish mark-selective sport fisheries that allow sport harvest only of hatchery fish. The fisheries agencies could develop Wild Fall Run sanctuaries on some tributaries.

Ultimately, long-standing aspects of Delta operations must change to allow more juvenile salmon to get out of the system and more adult salmon to find their way back to natal streams. Delta exports during the spring are particularly devastating to juvenile outmigrants from the San Joaquin tributaries, including the Mokelumne, because these juveniles are drawn to the south Delta pumps. Low Delta outflow, particularly during spring, magnifies the effects of exports. Opening the Delta Cross Channel during spring may actually improve survival of San Joaquin and Mokelumne juveniles, but only when combined with high Delta outflow. Closure of the Delta Cross Channel gates during the fall, either by design or through fortuitous operational decisions, has reduced straying of Mokelumne River salmon adults to the American River, allowing multiple small pulse flows from the Mokelumne in the fall to help improve adult returns.