Category Archives: Steelhead

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.

Open the Delta Cross Channel

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The Delta Cross Channel (DCC) (Figure 1) is closed in spring to minimize the diversion of juvenile salmon from the Sacramento River into the central Delta. However, opening the DCC in May and June will help reduce the detrimental effects of drought on Delta Smelt and Delta water quality.

With San Joaquin River inflows to the Delta at extreme lows and the DCC closed, fresh water flow to the south Delta export pumps comes primarily from the Sacramento River via Threemile Slough (TSL) and Georgiana Slough (GGS) (Figure 2). Net flows from both these sloughs are south toward the state and federal pumping plants via Old and Middle Rivers. Delta Smelt enter the central Delta via Threemile Slough. Salmon, sturgeon, steelhead, and striped bass young enter the central Delta via Georgiana Slough as well as Threemile Slough. Opening the DCC will change Delta net flow patterns and contribute to net downstream flows in the lower San Joaquin River in the central Delta (Figure 2), thus benefitting all the fish entering the central Delta including those migrating downstream from the San Joaquin and its tributaries. With the DCC open, less salt will intrude into the central Delta with the more positive net flows of the lower San Joaquin River. Less of the Low Salinity Zone and its concentrations of pelagic fishes including smelt will flow or be tidally pumped upstream into the central Delta. More of south Delta exports will come directly from the Sacramento River via the DCC, rather than through Threemile Slough or Georgiana Slough, or fromthe Low Salinity Zone.

Yes, the late spring migrations of young wild salmon and steelhead, as well as larval Striped Bass and sturgeon from their spring spawns will enter the Central Delta via the DCC, but fewer will enter via Threemile and Georgiana sloughs. Those that do enter the central Delta will benefit from higher net positive downstream flows in the lower San Joaquin River channel to the Bay. Opening the gates only in daytime may provide many of the above benefits while minimizing impacts (Perry et. Al. 2013, 2015).

Perry, R. W., P. L. Brandes, J. R. Burau, P. T. Sandstrom & J. R. Skalski. 2015.
Effect of Tides, River Flow, and Gate Operations on Entrainment of Juvenile Salmon into the Interior Sacramento–San Joaquin River Delta
Transactions of the American Fisheries Society. Volume 144, Issue 3, 2015, pages 445- 455.

Perry, R. W., P. L. Brandes, J. R. Burau, A. P. Klimley, B. MacFarlane, C. Michel, and J. R. Skalski. 2013. Sensitivity of survival to migration routes used by juvenile Chinook Salmon to negotiate the Sacramento–San Joaquin River Delta. Environmental Biology of Fishes 96:381–392.

Figure 1. Location of Delta Cross Channel gate.

Figure 1. Location of Delta Cross Channel gate.

Central Delta net flow changes from opening Delta Cross Channel

Figure 2. Central Delta net flow changes from opening Delta Cross Channel (DLC in map). Blue arrows are increased net flows. Red arrows signify decrease in net flows. Blue dots indicate CDWR CDEC flow gages. (Base Map Source: CDEC)

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

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/

Mokelumne River Steelhead Management

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The Mokelumne Hatchery releases approximately 100-200 thousand hatchery steelhead to the lower Mokelumne each winter, yet runs remain small with several hundred fish or less.  Why is that?  The answer is pretty straightforward:  the smolts released have little chance to reach the ocean and those that do have little chance finding the Mokelumne on their return as adults.

The figure below depicts the primary causal mechanism.  With the Delta Cross Channel closed in winter and spring, the smolts and adults must migrate via the lower San Joaquin River.  The problem is that flows in the San Joaquin below the Mokelumne forks are negative in drier years because of Delta exports.  The negative flows are shown as the red arrow at Prisoners Point.

Mokelumne Steelhead Migration

Wild and hatchery smolts reaching the San Joaquin follow the river “downstream” to the South Delta export pumps.  Many of the approximately 1800 hatchery smolts “salvaged” since February at the export pumping plants are likely Mokelumne hatchery smolts released in February near Lodi.

Likewise, adult steelhead migrating upstream from the Bay into the Delta in winter and spring cannot find the Mokelumne because its water signature in drier years has been taken almost entirely to the South Delta export pumps.

Solutions:

  1. Hatchery smolts can be barged from the Mokelumne Forks to the upper Bay. Some trucking to the Bay has been attempted in past years.
  2. Wild smolts can be collected at Woodbridge Dam traps in drier years and transported to the upper Bay.
  3. Adults returning in winter and spring should be provided olfactory attraction by insuring minimum positive daily average downstream flows in the lower San Joaquin at Prisoners Point and Jersey Point at least for a portion of each month in winter and spring.
  4. In the long term, spring operations at the Delta export pumps need to be reduced so that outmigrating salmon and steelhead from the San Joaquin basin as well as the Mokelumne follow water from their natal rivers to the Bay, not to the pumps.