Monthly Archives: April 2015

Yuba River Steelhead

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I have fished and studied the Lower Yuba River above Marysville for nearly 20 years. This tailwater fishery below Englebright Dam is one of California’s best wild trout fisheries, rivaling that of the Keswick tailwater on the lower Sacramento River below Redding. Both are nearly as good and as popular as the Deschutes River in north-central Oregon, a tributary of the Columbia River. All three rivers are national treasures above and below their dams. But it is the tailwater fisheries that provide for healthy, fast-growing populations of wild resident trout that thrive on nearly perfect year-round conditions for growth: controlled flows, cool water temperatures, and abundant food. Each river has abundant salmon eggs, fry, and flesh that supplement the highly productive waters from their reservoirs.

The Yuba tailwater Rainbow Trout fishery also benefits from Daguerre Dam, a sediment retention and irrigation diversion dam located about halfway up the 20-miles of lower river from Marysville. This small dam blocks runs of migratory predators and competitors from entering the upper tailwater reach. Striped Bass, American Shad, and Sacramento Pikeminnow are very abundant below Daguerre, especially in spring. Adult Chinook Salmon, Steelhead, and Rainbow Trout readily pass upstream through Daguerre’s two fish ladders, while the others do not. The resident trout thrive in the predator-free reach above Daguerre.

Wild Steelhead, the anadromous form of Rainbow Trout, do not thrive in the Lower Yuba River (nor lower Sacramento), however. Yuba River Steelhead are in the Central Valley Steelhead grouping listed as threatened under the federal Endangered Species Act. The reason is simply that they must pass downstream to the ocean as young and back as adults. The odds of making the journeys are slim, especially for the young. Research has shown that the numbers of young trout drop precipitously below Daguerre, ostensibly from predation1. Steelhead young are adapted to migrating to the ocean during the high winter-spring rain-snowmelt season. With the large Bullards Bar Reservoir holding back the much of the seasonal high flows for summer irrigation, especially in dry years, Steelhead young have a tough time surviving the journey to the ocean.

yuba steelheadThe small numbers of Steelhead I have caught or seen caught, or observed while snorkeling, are most often hatchery fish, likely strays originating from the Feather River Hatchery. In fact, a small percentage of the resident trout above and below Daguerre are hatchery steelhead that did not migrate to the ocean (photo at right). Hatchery smolts released in the lower Feather River near the mouth of the Yuba often move up the Yuba.

So how can we improve the Steelhead population and protect the wild trout fishery in the lower Yuba River?

  1. There need to be habitat improvements: instream wood, riparian vegetation, side channels, and spawning gravel are generally or locally lacking in the lower Yuba, especially below Englebright and Daguerre dams.
  2. Hatchery Steelhead smolts should not be released in the lower Feather River; instead they should be trucked to Sacramento River, then barged to the upper Bay.
  3. Wild fry, fingerling, and smolt Steelhead/Rainbow Trout can be captured as they pass downstream at Daguerre Dam, and then trucked/barged to upper Bay.
  4. Predators should be removed from lower Yuba below Daguerre Dam by operating weir traps during dry springs. Striped Bass can be relocated to San Francisco Bay.
  5. Project operations can reduce stranding. Steelhead (and salmon) fry are stranded in large numbers on floodplains and river bars after infrequent winter-spring storms (see charts below). Upstream dam releases should increase before and after storms to better ramp flows to reduce stranding and other detrimental effects of sudden high flows.
  6. Anglers should be encouraged to keep hatchery trout and steelhead (adipose fin-clipped fish) caught on the lower Yuba.
  7. Wild adult Steelhead should be used in a conservation hatchery component of the Feather River Hatchery to help restore wild Yuba/Feather Steelhead. Wild Steelhead can also be restored to river above Englebright and Bullards Bar dams in a trap-and-haul program as prescribed in federal Recovery Plan for Central Valley Steelhead.

Yuba Near Smartville

Deer Creek near Smartville

Can Winter Run Chinook Salmon be Saved in 2015?

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Various resource agencies are scrambling to protect Winter Run Chinook Salmon this year after last year’s debacle, in which water “saved” in Shasta Reservoir wasn’t cold enough to keep Winter Run eggs and fry alive1. Higher, colder flows are necessary to keep the eggs and fry alive in their spawning and early rearing areas near Redding, but were unavailable last summer because Shasta’s cold-water pool was depleted by the end of August.

The five charts included below tell the story of what happened last year. In summary, these are the main reasons why the Bureau of Reclamation ran out of cold water in Shasta Reservoir…

  • First, approximately 200,000 acre-feet (AF) of cold-water pool storage was released to senior water rights contractors in May. (Amount calculated from Figure 1 and Table 1).
  • Second, approximately 500,000 AF of cold-water pool storage was released in June and July that could be argued was needed for maintaining river temperature control below Redding. However, I would argue that given the precarious state of the Shasta cold-water pool in June and July, federal and state agencies should have released less (to maintain 58°F at Clear Creek instead of the chosen target temperature of 56°F) to sustain Shasta’s cold-water pool. My guess is they could have saved 2000 cfs or about 240,000 AF of total storage in June and July. This water would have come out of the Sacramento River Settlement Contractors’ 560 TAF deliveries for June-July (Table 1).
  • Third, somewhat less cold-water pool water could have been saved in early weeks of August.

If the Bureau of Reclamation had saved this 440,000 AF from May-July (about a third of deliveries), there would have been no extreme mortalities of Winter Run Chinook Salmon in the late August-October period from low flows and high water temperatures. Contractors could have made up some of their loss in the late August-October period when higher colder flows would have been released from Shasta for fish. If Sacramento River contractors were unable to use this water late in season, the water could have been used to maintain Delta water quality standards or left as carryover storage in Shasta Reservoir.

In summary, cold-water pool releases from Shasta Reservoir from May through August of 2014 were too great to support the cold water resource, resulting in the loss of much of the year’s production of Winter Run eggs and fry to low flow, warm water conditions. In similar conditions in 2015, releases for contractor irrigation deliveries should be reduced in order to sustain Shasta’s cold-water pool through the summer. Such protections should be the cornerstone of the Drought Operations Plan being developed by the agencies. NMFS and DFW should not approve the Plan without this element to protect Winter Run.

Figure 1

Figure 1. Mainstem flow of the Sacramento River below Redding, May-Sept 2014. Flows generally reflect releases from Shasta Reservoir. (Source: USGS Mobile Data Site)

Figure 2

Figure 2. Mainstem Sacramento River flows at Wilkins Slough gage below most of the contractor diversions. (Source: USGS Mobile Data Site)

Figure 3

Figure 3. Power-Point slide of risk to Winter Run adults, eggs, and fry as a function of water temperature in Shasta Reservoir releases (as measured Keswick Reservoir releases – KWK).2

Figure 3

Figure 4. Power-Point slide of risk to Winter Run eggs as a function of water temperature in Shasta Reservoir releases (as measured Keswick Reservoir releases – KWK) and temperature in the river below the mouth of Clear Creek near Redding.3

Table 1

Table 1. Water deliveries from Reclamation to Sacramento River contractors in 2014.
(Source: http://www.usbr.gov/mp/cvo/vungvari/table_28_2014.pdf)

  1. See, for instance, https://cdfgnews.wordpress.com/2015/01/26/agencies-taking-measures-to-protect-winter-run-chinook-preparing-to-release-approximately-600000-fish/ ↩
  2. Source: NOAA’s National Marine Fisheries Service’s (NMFS) Update to the State Water Resources Control Board by Garwin Yip, February 18, 2015 ↩
  3. Source: NOAA’s National Marine Fisheries Service’s (NMFS) Update to the State Water Resources Control Board by Garwin Yip, February 18, 2015 ↩

Central Valley Hatchery Steelhead Program Misdirected

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Approximately 1.3 million yearling Steelhead smolts are released each year in rivers below our three state and one federal Central Valley Steelhead hatcheries. The hatcheries include Coleman Hatchery (federal) on Battle Creek near Redding, Feather River Hatchery (state) near Oroville, Nimbus Hatchery (state) on American River near Folsom, and Mokelumne River Hatchery (state) near Lodi. The smolts are generally released as yearlings in February at about 4 to-the-pound and 6-10 inches in length. In some drought years (e.g., 2014), Nimbus Steelhead are also released to the American River as several-month-old fingerlings in June because hatchery source water from Lake Natoma is too warm to carry the fish through summer until the normal February release date.

The problem with releasing over a million hatchery Steelhead smolts into the rivers in the spring is that wild Spring-Run and Fall-Run Chinook salmon fry emerge or have recently-emerged from redds at this time. The one-inch salmon fry are ready-made prey for the hatchery Steelhead smolts. Figure 1 shows the partial stomach contents (six salmon fry) of a hatchery Steelhead smolt caught in early March in the lower American River.

Figure 1.

Figure 1. Partial stomach contents of an American River hatchery steelhead smolt (head at right) captured in early March 2015 near Sunrise Bridge. There were partial remains of twenty salmon fry in various stages of digestion in the stomach.

While many hatchery Steelhead likely migrate from the rivers towards the Bay-Delta soon after release, many also stay in the rivers. This is especially true in the American River, where they may be released early as fingerlings prior to summer and are thus likely to take up residence in the river. Many Feather hatchery smolts take up residence in the lower Yuba River. Smolts released in rivers also are more prone to becoming permanent river residents in drought years when there are fewer pulses of flow to stimulate emigration to the sea, especially in the Feather, American, and Mokelumne Rivers. Salmon fry may become prey of the hatchery Steelhead smolts for a few days to a month or more.

Releasing hatchery Steelhead into the lower rivers in such large numbers also impacts wild Steelhead that are present in much smaller numbers. The hatchery smolts compete with the wild smolts. Hatchery smolts attract large numbers of predatory birds and fish (e.g., Striped Bass). Hatchery smolts also feed on wild Steelhead fry that emerge from redds from April to June.

What can be done to help solve the problem?

  1. Hatchery Steelhead smolts should be trucked to the lower Sacramento River rather than being released in their natal rivers.
  2. The trucked hatchery smolts should be placed in barges, then barged from the Sacramento River to low salinity waters of the Bay to reduce the probability of their immediately returning to their natal rivers (and to maximize their survival to the ocean). Barging is necessary to minimize subsequent adult straying to non-natal rivers, a problem if smolts are trucked all the way to the Bay.
  3. Fingerlings should also not be released into natal rivers below the hatcheries. They too should be trucked then barged to the upper Bay.
  4. Pre-smolts could be released in early winter to natural floodplain habitats or even to specially designed flooded rice fields to grow to smolt size.

These actions, if taken, will both reduce predation on wild salmon and Steelhead fry and markedly increase survival of hatchery Steelhead to the Ocean and subsequent escapement of adult Steelhead to the rivers. Record low numbers of Steelhead returned to Central Valley rivers in winter 2015. More on this subject will come in later posts.

For more details on the Steelhead hatchery programs see the following website: http://cahatcheryreview.com/summary-conclusions/

The Delta Plan – where is the water habitat?

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The Delta Stewardship Council’s Jessica Davenport, Program Manager, Ecosystem Restoration and Land Use, released an issue paper in August of last year entitled “Restoring Habitat with Science and Society in Mind”. 1

“The Delta Plan shall include measures that promote all of the following characteristics of a healthy Delta ecosystem:

  1. Viable populations of native resident and migratory species.
  2. Functional corridors for migratory species.
  3. Diverse and biologically appropriate habitats and ecosystem processes.
  4. Reduced threats and stresses on the Delta ecosystem.
  5. Conditions conducive to meeting or exceeding the goals in existing species recovery plans and state and federal goals with respect to doubling salmon populations.”

The Delta Plan,2 much like the Governor’s Bay Delta Conservation Plan (BDCP),3 has no measures that would promote a healthy Bay-Delta ecosystem. The plans virtually ignore water habitat: the characteristics of the water in the hundreds of miles and tens of thousands of acres of open water in the Bay-Delta. The plans fail to even define the components of a healthy ecosystem or how they relate to water habitat:

  • “viable populations” – what constitutes viable?
  • “functional corridors” – what is functional?
  • “appropriate habitats and ecosystem processes” – what is appropriate?
  • “threats and stresses” – what threats and stresses?
  • “conditions conducive to doubling salmon populations” – what conditions?

The plans simply focus on “restoration” of thousands of acres of edge habitat on marginal lands in Suisun Marsh and the Delta, virtually ignoring the “real problem” and its fixes. The “restoration” that is promoted will take decades to implement and will do little to promote a healthy ecosystem, at least in the short term.

The “real problem” is water management in the Central Valley and Bay-Delta. The “real problem” is our insatiable demand for water while virtually ignoring the beneficial uses and public trust requirements of the Central Valley and Bay-Delta ecosystems. There are water quality standards and endangered species biological opinions that provide minimal protections for resident and migratory native fish species. Yet the first thing that regulators do in droughts is relax these protections to provide more water for agriculture. As a consequence, the fish populations and their habitats suffer irreversibly in drier years, and especially in extended periods of drought. The result is fish populations on the verge of extinction, poor Bay-Delta water quality, salt in Delta water diversions, salmon smolts having to be trucked hundreds of miles from hatcheries to the Bay, and no freshwater inflow to the San Francisco Bay estuary.

Water is the ecosystem process ignored in the BDCP and Delta Plan. The characteristics of the water habitat in time and space are the missing element in the plans. The fish habitat that is most important is the water in Delta channels and bays, not the acreage of tidal marsh. Adding tidal marsh habitat will not fix the water habitat or provide a healthy ecosystem

The BDCP justified taking more water via the “tunnels” by offering thousands of habitat acres in return. The Delta Plan promotes these same land acreage solutions.

How can we really restore the Delta as habitat for smelt, salmon, steelhead, sturgeon, and other native fishes? We have to focus on Delta inflows, outflows, tides, and exports: hydrology, salinity, water temperature, and primary productivity patterns in the water habitat. The real habitat of the Delta is the three-dimensional characteristics of water in time and space. What should the water habitat be for Delta smelt when they hatch in the spring to insure good survival? How do we sustain the smelt in summer? Can they actually survive if all the Delta inflow is exported in August under relaxed standards? What happens to all the wild salmon smolts coming out of Central Valley rivers? What kind of water habitat do they need to pass through the Delta? They do not get a truck ride to and around the Delta. What is a “functional migration corridor” for them?

So instead of focusing on acreage, we should focus on the real habitat, water and all of its characteristics in time and space in the Delta, rivers, and the Bay. That way, we can promote the real ecosystem process that provides for a healthy Bay-Delta ecosystem.

The Delta Science Plan4 is just more talk and smoke and mirrors. What the Delta needs is more water and better water habitat. We do not need a new vision.

http://calsport.org/fisheriesblog/wp-content/uploads/2015/04/Box-1.-Delta-Science-Plan.png

Mark-Selective Chinook Fishery in Puget Sound

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Puget Sound is a large inland marine water body in Washington State that supports runs of five Pacific salmon, steelhead, and multiple marine fish species. Chinook salmon are a very popular recreational and (in the past) commercial species in Puget Sound. To support the naturally spawning Chinook salmon runs, numerous hatcheries were built in throughout the Pacific coast area.

As a result of the Endangered Species Act, the Chinook salmon fisheries were very restricted or completely closed to protect wild (“naturally spawning”) fish. This included closure for all (both hatchery and wild) Chinook salmon.

Through various planning efforts by sports fishermen, Native American tribes, Washington Department of Fisheries and Wildlife (WDFW) and others, a mark-selective approach for providing some fishing opportunities for Chinook salmon was developed. The approach involved marking of hatchery fish by removal of the adipose fin (a small fin near the tail) to identify hatchery fish from wild ones. Once removed, the fin does not normally regrow, and therefore, if caught by a fisherman, the fish can be identified as a hatchery fish and retained (if it meets other restrictions such as size limit, season, etc.). Wild fish (with the adipose fin) can then be readily identified and released. In addition, a certain percentage of hatchery fish may have a small “coded-wire tag” inserted into their heads. This provides additional information about the fish such as which hatchery it was reared in. WDFW has also added rules that wild salmon cannot be brought aboard a vessel (i.e., inside the gunwale) to assist in releasing the wild fish unharmed.

Each year, the WDFW and Native American tribes (co-managers of the fisheries in Washington State) set quotas on the number of marked Chinook salmon that may be taken in Puget Sound (which is divided into several subareas to assist in management for various runs of Chinook salmon. For example, one subarea may be dominated by a run to a specific hatchery. Depending on the projections for adult returns to that hatchery, a quota for take is established and considered in the overall quota for that subarea).

The quotas for each subarea are monitored through dockside sampling. They are also supported by WDFW staff that fish for Chinook salmon with methods similar to those used by private and charter sport fishing groups. This “on the water” sampling provides key information about take, wild/hatchery fish ratios, and fishing effort. The information is used to support the overall development of quotas.

Seasons and quotas are set early in the year so that some planning by fishermen (e.g., vacations, days off, etc.) can be made. However, if the quota is reached early, the season may be closed early.

Overall, the mark-selective approach has re-opened fishing opportunities. These have been very popular with fishermen, as noted by the large groups that are currently observed on the water. This has also helped support economically important aspects such as charter fishing, tackle shops, boat sales, etc.

The WDFW has provided very detailed information about the mark-selective Chinook salmon fishery in Puget Sound (and elsewhere in Washington State) in multiple publications and press releases (see wdfw.wa.gov/publications). These publications provide information on the overall program, sampling techniques, quota development, and other pertinent aspects of the mark-selective approach.

Several issues have arisen about the approach, which are of interest. These include costs associated with marking millions of hatchery fish and monitoring programs, incomplete or non-marking of hatchery fish, mortality associated with capture and release of wild fish, and other aspects of the program. However, overall, this approach has helped to provide fishing opportunities that would not be possible under the no-take restrictions that were originally imposed by the Endangered Species Act.

Hatchery Chinook salmon

Hatchery Chinook salmon taken in a Puget Sound mark-selective fishery. Photo by the author.