More on Mark-Selective Steelhead Fisheries

Posted on February 10, 2016 by Don Beyer with Prologue by Tom Cannon

Don Beyer and many others are concerned with the recent movement to limit hatchery production and mark-selective fisheries of Steelhead in the Puget Sound and Columbia River regions in Washington State. At the center of the debate have been proposals to eliminate hatchery programs on rivers with wild Steelhead.¹ Typically, WA Steelhead fisheries focused on winter hatchery fish (adipose fin clipped), with catch-and-release of wild non-clipped fish in winter and spring. In recent years, popular mark-selective and wild catch-and-release fisheries have been shut down on rivers in WA with seemingly healthy populations of wild Steelhead.² Will NMFS extend these strategies to California?

Recent catch of a hatchery Steelhead in the lower American River in Sacramento. (Photo by T. Cannon)

Marking of Hatchery Fish for Selective Fisheries

by Don Beyer

Salmon and steelhead hatcheries have been in existence for decades along the Pacific coast. The purpose of these hatcheries has been to maintain or improve fisheries for sport, commercial, and tribal interests. They are also a key factor in providing mitigation for habitat losses due to water resource projects such as dams, urbanization, land use alterations, and pollution which have negatively impacted wild fish populations.

Hatchery fish are utilized for food consumption by not only humans, but by marine mammals (e.g., Orcas, seals/sea lions, porpoise/dolphins), birds (bald eagles/ospreys/herons), and other fish (e.g., bull trout), many of which are protected under the Endangered Species Act (ESA), Marine Mammal Act, or other similar Federal acts. The sport fishing industry that has developed over decades around fish resulting from hatchery programs also has a very large economic impact involving millions of dollars.

As a result of the ESA and its efforts to protect non-hatchery raised salmon or steelhead, it was difficult for fishermen to distinguish between hatchery and non-hatchery fish and it appeared that harvest would need to be strictly curtailed or eliminated. To resolve this challenge, hatchery fish were required to be clearly “marked” so that they could be differentiated from non-hatchery fish. The most widely adopted approach has been to remove the adipose fin (a small non-functional fin near the tail of the fish) in juvenile fish before they leave the hatchery to migrate to the ocean. In this manner, if a fisherman caught a salmon or steelhead with an intact adipose fin, they were required to carefully release the fish (even if the season was open for that species). This approach (termed “selective fishery”) was to allow fishermen to continue fishing while protecting ESA-listed salmon or steelhead. Without this approach, the sport, commercial, and likely tribal fisheries would have ceased to exist. It took many years in all Pacific coast states, along with the efforts of many people, to get the selective fishery approved and implemented.

Other approaches are also being undertaken to minimize or eliminate interactions of ESA and non-ESA listed fish. For example, in the past, steelhead from Washington state hatcheries were released at the hatchery and often at other locations either upstream, downstream, or even other river systems. To minimize potential interactions with ESA-listed steelhead, this practice has been minimized to releases only at the hatchery. This takes advantage of the exceptional homing abilities of adult hatchery fish to return to their place of origin (i.e., the hatchery), thus reducing the interactions with non-hatchery fish.

Without the adipose-marking of fish, current fisheries would not be able to continue because fish protected under ESA could not be differentiated from hatchery fish. As such, a major food source for humans and other ecosystem components (e.g., those mentioned above) would cease to exist along with the loss of a major industry dependent on hatchery production. Without selective fishing, the only possibility for a return to a harvestable level of fish would be for ESA-listed species to recover to a level of sustainability that includes harvest. This is a long-term undertaking and may not be possible in some areas where the habitat would not sustain recovery. However, in some situations such as the Columbia River system, progress is being made through recovery of habitat, improvements in hydroelectric and hatchery programs, and harvest restrictions. On the latter, the selective fishery approach has allowed a very viable sport, commercial, and tribal harvest to continue.

Shasta Spill Prescription to Benefit Wild Salmon

Posted on January 15, 2016 by Tom Cannon

In recent posts I described the need for spill – releases from reservoir storage to increase the number of young salmon reaching the ocean.¹ Last summer and fall, Sacramento River salmon were forced to spawn nearer Shasta Reservoir because of limited cold water releases to save reservoir storage in the ongoing drought. Instead of the normal 50 miles of cool water, the salmon only had 10 miles. This winter, the young salmon that spawned in the Sacramento River near Shasta and survived now have to contend with minimum Shasta releases, since most of the reservoir inflows are being stored for future water supply. The winter flow pulses that stimulate emigration and carry the young salmon 300 miles to the lower river, Delta, Bay, and ocean are missing from the spawning reach below Shasta (see Keswick Outflow in chart below).

In contrast, millions of Battle Creek hatchery salmon released 30 miles below in the Sacramento River have the advantage of local inflows from un-dammed tributaries (Bend flows in the chart) to carry them to the ocean. (Note: hatchery fish releases are often timed to flow pulses.²) From the chart below you can see that these inflows have actually been higher than releases from Shasta Reservoir.

In the previous posts I had suggested spills (releases) of 5-10 % of reservoir inflows to increase salmon survival in the current drought. So far this winter, a reasonable prescription would have been several days of 500 cfs spill each time reservoir inflow approached or exceeded 10,000 cfs. A 500 cfs spill would represent a 12-15% increase in streamflow to stimulate emigration of young salmon downstream into the higher flow reach of the river. This would certainly qualify as an adaptive management experiment to help improve survival of endangered salmon in the Sacramento River.

Inflow and outflow from Shasta Reservoir in December 2015 and early January 2016. The Bend Bridge gage is on the Sacramento River near Red Bluff, CA, approximately 30 miles below the Keswick Dam gage. Sacramento River flow at Bend Bridge includes the inflow from Cow, Clear, Cottonwood, and Battle creeks.

http://calsport.org/fisheriesblog/?p=558 ↩
Hatchery Winter Run salmon smolts from the Livingston Stone Hatchery are generally released near Redding in the low flow reach below Keswick Dam. They too would benefit if their release was timed with spills. ↩

Scott River – Crisis Update

Posted on December 19, 2015 by Tom Cannon

In a recent post¹ I related that the Scott River, a major salmon producing Klamath tributary in northern California near Yreka and Fort Jones, is again in crisis due to low fall flows in the present drought. I suggested that normal December storms might be too late to save the Fall Run Chinook, but would likely accommodate the later spawning Coho.

Two December storms (Figure 1) have come and helped the salmon. Counts near Fort Jones recently reached near 400 for Chinook and 200 for Coho. Neither number is good, but the Chinook number, though preliminary, is very low, as it should be several thousand or more. Waiting for several months to ascend the river to spawn has likely taken its toll on the Chinook. The storms were also nearly too late for Coho, but these circumstances are fairly normal for Coho.

Graph of December streamflow in Scott River below Fort Jones

Figure 1. December streamflow in Scott River below Fort Jones. (Source: CDEC)

The late storms made things very difficult for Chinook. In a recent newspaper article² on the Scott, it was noted that late runs usually spawn in the lower river, downstream of the good spawning reaches. The lower river spawning grounds are subject to winter storm scouring. In the article, some sources blamed the low fall flows on agricultural groundwater pumping during the summer and fall, which lowered the water table in Scott Valley. Lack of summer snow storage in the adjacent mountain ranges was also a key factor.

But the article and its sources miss what my previous post suggested as a solution to the problem. Groundwater could have been pumped into the river in the Valley in substantial amounts in the fall using some of the irrigators’ idle pumps. A concerted pumping effort in October and November, for one to several weeks, could have gotten the Chinook up from the mouth into the Valley to the perennial flowing spawning tributaries and river reaches. The salmon could have spawned or have been ready to spawn when the rains did come.

The winter rains are already recharging the groundwater basin in the Scott Valley, so the costs of the effort in terms of next year’s water supply would have been minimal. The cost of electricity is minuscule in comparison with the loss of production of one of the Klamath’s most prolific salmon-producing tributaries.

More on Spill

Posted on December 15, 2015 by Tom Cannon

In a recent post I suggested “spill” (targeted reservoir releases) to enhance salmon production in Central Valley rivers. Well, it is now time to employ spill to help Winter Run and Spring Run Chinook salmon in the upper Sacramento River below Shasta near Redding. Waiting for El Niño to help these fish may be too late. Confidence and early indications that El Niño will come this winter should make the necessary commitment for spill now more palatable. Spill releases could have already been made from Shasta Reservoir with these recent storms to support emigration of young salmon from the spawning and rearing reach.

After the salmon spawning, irrigation, and water transfer season ended in October, there have only been minimum flows and no spills to enhance young salmon emigration. Flow from Shasta-Keswick (river mile 302) has remained near the minimum requirement of 4000 cfs (Figure 1).

Recent Storms – December 2015

The recent storms have sharply increased flow in the Sacramento River downstream of the spawning reach at Bend Bridge at river mile 258 (Figure 2) below the input of four large creeks entering the Sacramento River below Redding (Figure 3). Inflow to Shasta Reservoir has nearly quadrupled during the two storms, reaching 8,000-10,000 cfs. A prescriptive “spill” release of 5-10% of inflow (500-1000 cfs) is needed. That would raise Keswick releases to about 5000 cfs, which would help stimulate emigration from the spawning reach into the higher flow reach below the tributaries, and down into and through the Delta.

December 2003 Case Study and Precedent

December 2003 had similar circumstances. Screw trap catch of Winter Run salmon at Knights Landing (RM 90) had a sharp increase coincident with flow increases in December 2003 (Figure 4). Spill in December 2003 (Figure 5) helped increase the river flow.

Concern for Young Salmon in the Delta

Higher freshwater inflows from the storms in 2015 have already pushed the Low Salinity Zone out of the Delta into Suisun Bay. Winter Run and Spring Run salmon (as well as Late Fall smolts and Fall Run fry) are likely now entering the Delta in large numbers (comparable monitoring results from 2003-4 are shown in Figure 6). Spill wouldl help move fish through the Delta and west to the Bay. The Delta Cross Channel remains open, allowing the emigrating salmon to spread into the Central Delta. This increases the need for spill to keep these fish moving west before the DCC is closed and south Delta exports divert freshwater inflow and emigrating salmon away from the Bay and toward the Delta pumps.

Spill is also needed from other reservoirs on the Feather, Yuba, and American Rivers that have also received significant inflow during the recent storms. Spill from these reservoirs is needed to stimulate migration of young salmon from their tailwaters as well as to contribute more to the combined Delta inflow and outflow.

Though it is a hard decision not to store all of the inflow from these first storms of the season in reservoirs, releasing 5-10% as spill would go a long way to help saving the wild endangered salmon that depend on the early winter flows.

Graph of releases from Keswick fall 2015

Figure 1. Flow releases to Sacramento River from Keswick Reservoir fall 2015. Minimum prescribed outflow to Sacramento River is approximately 4000 cfs in drought years like 2015. Keswick Dam is at rivermile 302, nine miles below Shasta Dam.

Figure 2. Flow in the Sacramento River at Bend Bridge (RM 258) 44 miles below Keswick Dam fall 2015. Flow spikes from recent storms come from local tributary creeks upstream of Bend Bridge.

Figure 3. Location of Winter Run spawning and rearing reach (green hatched line) below Keswick Dam (RM 302) near Redding, CA. Four major tributary creek inputs are shown below Redding. The mouths of Cottonwood and Battle Creeks are about RM 270.

Figure 4. Catch index of older juvenile (non-fry) in Knights Landing (RM 90) rotary screw trap Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

Figure 5. Flow releases to Sacramento River from Keswick Reservoir fall 2003. Releases were approximately doubled to 9000 cfs at mid-month, ostensibly to help stimulate young salmon emigration and allow greater Delta exports ¹.

Figure 6. Catch index of older juvenile (non-fry) in trawls and seines in the Sacramento River near Sacramento, Oct 2003-Mar 2004. Source: http://www.science.calwater.ca.gov/pdf/ewa /support_docs_110804/Salmon%20Criteria%20Figures%201_2_Chappell.pdf

High exports in December03-January04 did result in substantial counts of juvenile Winter Run salmon at South Delta Fish Salvage Facilities during the period. ↩

Spill and Salmon Survival

Posted on December 13, 2015 by Tom Cannon

In an earlier post, I suggested “spill” to help recover salmon in the Central Valley. Spill is nomenclature used for reservoir releases. In this case I refer to spill as reservoir releases to help juvenile salmon emigrate from spawning reaches below dams to the ocean. On the Columbia River, “spill” refers to reservoir releases around hydropower turbines usually through spillways. Such spills have been used successfully on the Columbia River to avoid turbine passage that may kill young salmon and to create flows through and below reservoirs to reduce young salmon mortality by shortening their emigration time. On the Sacramento and other Central Valley rivers, “spill” releases can go through hydropower turbines because young salmon start their emigration below the dams. Young salmon have been found to emigrate during flow pulses, with survival directly related to the amount of flow.

More “spill” below the rim dams is needed in the Central Valley to increase survival of naturally produced (wild) salmon and steelhead. Spills help young salmon emigrate from tailwater spawning and rearing reaches below dams to the Delta, Bay, and ocean. Both timing and magnitude are important. Timing relates to when the young salmon are ready to migrate and to natural flow pulses in the Valley. Magnitude is simply how much flow, which relates to precipitation and available reservoir storage supply.

Timing

Most of the Chinook salmon runs emigrate to the San Francisco Bay-Delta as fry soon after hatching. Some migrate as sub-yearling fingerlings and smolts¹ while a few migrate as yearling smolts.

Winter Run Salmon

Winter Run hatch in late summer and early fall in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as fingerlings and pre-smolts to the Delta when the river cools, especially during the first flow pulses in late fall and early winter. In drier years they may not emigrate until February or even March. Generally they move down to the Delta in the first flow pulse in December (Figure 1).

Late Fall Run Salmon

Late Fall Run also hatch in winter in the Sacramento River below Shasta and Keswick reservoirs. They usually emigrate as yearling smolts in late fall or early winter, at the same time as the Winter Run. Unlike Winter Run, they are often fully developed smolts and thus migrate quickly to the ocean.

Spring Run Salmon

Spawned in early fall, Spring Run hatch and migrate as fry and fingerlings with the first pulse of flow in late fall and early winter. Some migrate as presmolts and smolts in spring.

Fall Run Salmon

Spawned in fall, Fall Run hatch and emigrate as fry in winter during flow pulses. Some emigrate as fingerlings and pre-smolts in spring.

Figure 1. Older Juvenile Catch Index for the Knights Landing rotary screw trap October through March 2000-2003. Older juveniles are generally Winter Run and Late Fall Run. (Source: http://www.science.calwater.ca.gov/pdf/ewa/support_docs_110804/ Salmon%20Criteria%20Figures%201_2_Chappell.pdf)

Steelhead

Steelhead spawn in winter and spring and emigrate as smolts after rearing in Valley rivers for one to three years. They migrate to the ocean during winter and spring flow pulses.

Spill Recommendations

To illustrate my recommendations, I focus on 2015 – a drought year with very limited reservoir supply and managed spill potential. Such years would be considered worst case scenarios for applying spill prescriptions. Yet despite limited potential in 2015, there were opportunities with the available supplies and precipitation to provide spill that would have substantially benefited salmon. Below are charts of flows for drought water year 2015 that depict the effects of two storm periods on Delta inflow and outflow. Delta inflow came primarily from runoff in un-dammed tributaries. Figure 2 depicts Delta inflow at Freeport with two distinct pulses of storm flow. These same flow pulses are apparent as Delta outflow to the Bay in Figure 3.

Figure 2. Delta inflow in water year 2015. (Source: CDEC)

Figure 3. Delta outflow in water year 2015. (Source: CDEC)

Below Shasta-Keswick in the lower Sacramento River, there was no winter storm flow (Figure 4). There were only two small managed flow increases of about 1000 cfs for three or four days each (a total of about 15,000 acre-ft), because Shasta held nearly all of its inflow from the two storm periods (Figure 5). Shasta inflow reached over 20,000 cfs for six days in each of the storms (Figure 6). Out of approximately 1,500,000 acre-ft of new storage inflow, Reclamation released only15,000 acre-ft (1%) of storm inflow for salmon.

A spill prescription of just 5% of inflow below Shasta-Keswick in the primary nursery for Winter Run salmon could have provided an increased 3000-4000 cfs of “spill” for seven days, instead of the 1000 cfs increases. Instead of going into the irrigation season at 2.72 million acre-ft, in storage, Shasta would have started at 2.67 million acre-ft. Given the potential benefit of the flow releases, this prescription even for a drought year is more than reasonable.

This example is for the fourth year of drought, when the reservoir began the winter at only 25% of capacity. In wetter years when storage is over 50% capacity, spills of 10% should be considered.

The same circumstances and potential benefits occur below other large Central Valley storage reservoirs, especially Oroville Reservoir on the Feather River and Folsom Reservoir on the American River. Spills of 5% in low storage years and 10% in higher storage years are reasonable prescriptions for their depressed salmon and steelhead populations.

Graph of Reservoir releases from Shasta-Keswick

Figure 4. Reservoir releases from Shasta-Keswick in water year 2015. Only two small releases were made in the storm periods.

Figure 5. Shasta Reservoir storage in water year 2015. The two storm periods added nearly 1.5 million acre-feet of water to the reservoir.

Figure 6. Shasta Reservoir inflow in water year 2015.

Smolts are larger (3-6 inches in length) juveniles physiologically ready for entry to salt water. ↩

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