Category Archives: Northern California

2015 Winter-Run Salmon Progress Report – Lessons Learned and Not Learned

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The Sacramento River Temperature Task Group’s report on water year 20151 released at the end of last year prematurely proclaimed successful operations for 2015 under its Temperature Control Plan (TCP). If the Group had waited a few more months, it would have reported utter failure, with the poorest survival and production of winter-run salmon yet recorded.2 Below, I excerpt from the Report, and offer some observations.

In summary, water year 2015 has been one of the driest years in decades and it followed three consecutive dry years throughout the state. Shasta Reservoir was projected to have end of year storage of 1.1 MAF in the May 90% forecast. Due to such low storage in Shasta Reservoir, Reclamation utilized Trinity River water to conserve Shasta Reservoir storage. The amount of water brought over from Trinity River through the Spring Creek Tunnel into Keswick Reservoir was a great benefit to the temperature operations on the Sacramento River. In all, Reclamation achieved meeting the TCP at Clear Creek (see Chart 1) of 57°F not to exceed 58°F through October 1, 2015, as indicated in the Temperature Management Plan, when 90% of the redds were emerging.

Comment: The Trinity water brought into Keswick Reservoir was 58-59°F, warmer than even the downstream criteria, resulting in more of the Shasta cold-water pool being used to cool it. The problem was recognized by the parties, as it resulted in demands to replace the existing Whiskeytown temperature curtain to cool the Trinity water before it was released into Keswick Reservoir. Achieving the 2015 goal of not exceeding 58°F turned out ineffective as well. Less than normal amounts of Trinity water have been brought into Keswick so far in 2016.

Despite the SRTTG best projection and modeling efforts to manage Sacramento River water temperature for winter-run spawning and egg incubation in water year (WY) 2014, winter-run brood year (BY) 2014 was considered a year class failure. One hundred percent of BY 2014 redds were exposed to temps above 56°F daily average temperature (DAT) at the Sacramento River above Clear Creek California Data Exchange Center monitoring station temperature compliance point (CCR) at some time period during WY 2014. Of significant concern were those eggs, alevin, and fry exposed to the elevated DAT above 56°F (and as high as 62.3°F) throughout September and October when the cold water pool out of Shasta Reservoir was depleted.

Comment: So the Task Group met the monthly average but allowed the daily average temperature to exceed 58°F in summer 2015 (Charts 2 and 3). The Report suggests improvement compared to 2014 conditions, but 2015 was also above 56°F. On 10% of the days in summer 2015, hourly water temperature exceeded 60°F at the CCR gage at Bonnyview Bridge in Redding during warm afternoons. On 60% of the days, water temperature reached or exceeded 59°F, the tolerance limit for salmon eggs and embryos. 3

Temperature monitoring results of 70 loggers indicated slight variation and stratification in temperature between in-river, backwater, and deep pools, but in general all winter-run salmon eggs and alevins were exposed to poor water quality due to warm water temperatures.

Comment: If they knew this, why did they allow it?

The plan called for real-time operations that targeted 57° at the Clear Creek compliance location not to exceed 58°F with minimized flows. By targeting 57°F not to exceed 58°F, where the majority of the redds were above Hwy 44, we were able to extend the use of the cold water pool.

Comment: By targeting the Clear Creek compliance location, the Task Group pretty much assured that adult winter-run salmon would seek out cooler waters near Redding, essentially confining their spawning to the uppermost 10 miles of their historic 60 mile spawning reach. The Group extended the cold-water pool by creating low survival conditions in the spawning reach. Reclamation was able to bring in warmer Trinity water for water supply (at the expense of Shasta’s cold-water pool) and did not have to sacrifice hydropower or peaking hydropower using Shasta Dam’s warm-water bypass (an operation which most likely would have been required if the target had been the appropriate 56°F). Reclamation was also able to meet its water supply commitment of 75% allocation to the Sacramento River settlement contractors in the fourth year of drought. So far in 2016, Reclamation has met its commitment of 100% allocation to the settlement contractors.

Perhaps more perplexing is what was left out of the report: water temperature and flow conditions in the salmon-migration and sturgeon-spawning reach in over 100 miles of the Sacramento River below Red Bluff. There was no mention of the Basin Plan’s targets for this reach of the river where water temperatures were too high (>22°C, 72°F) to allow adult salmon migration, while creating lethal conditions (>20°C, 68°F) for juvenile sturgeon4 (Chart 4). There was a complete disregard for the winter-run salmon objective of 56°C at Red Bluff in the Basin Plan, Water Right Order 90-05, and the NMFS BO: all 150 days from May through September failed to meet the objective (Chart 5). So far in 2016, the objective has yet to be met, despite the fact that Shasta was nearly full at the beginning of May.

Hopefully, the Winter Run 2016 report will be more comprehensive and complete than the Report for 2015. The 2016 Report should include not only the consequences for spawning habitat near Redding, but should also analyze the condition of rearing and migratory habitat below Redding through the fall and winter. The report should also cover consequences to the other salmon, including the ten million federal hatchery salmon smolts released near Redding.

Chart 1. Map of 60 miles spawning reach below Keswick Dam on Sacramento River. Various temperature compliance points are noted. The NMFS BO specifies Bend Bridge with relaxation allowed in drier years. In 2015 the compliance point was above Hwy 44 bridge. Clear Creek 58F DAT was the compliance point in spring 2016. Balls Ferry 56°F is present compliance point in summer 2016.

Chart 1. Map of 60 miles spawning reach below Keswick Dam on Sacramento River. Various temperature compliance points are noted. The NMFS BO specifies Bend Bridge with relaxation allowed in drier years. In 2015 the compliance point was above Hwy 44 bridge. Clear Creek 58F DAT was the compliance point in spring 2016. Balls Ferry 56°F is present compliance point in summer 2016.

Chart 2. Summary of 2015 spring-summer monthly average temperature at Clear Creek compliance point.

Chart 2. Summary of 2015 spring-summer monthly average temperature at Clear Creek compliance point.

Chart 3. Summer 2015 spring-summer water temperatures at compliance locations. Note the red line is one degree above the target 56°F they noted.

Chart 3. Summer 2015 spring-summer water temperatures at compliance locations. Note the red line is one degree above the target 56°F they noted.

Chart 4. Water temperature and river flow at Wilkins Slough at RM 125 on the Sacramento River May-September 2015. Historical average flow shown by green triangles.

Chart 4. Water temperature and river flow at Wilkins Slough at RM 125 on the Sacramento River May-September 2015. Historical average flow shown by green triangles.

Chart 5. All 150 days from May through September were higher than the 56°F Basin Plan objective for Red Bluff.

Chart 5. All 150 days from May through September were higher than the 56°F Basin Plan objective for Red Bluff.

Sac River Salmon Opener a Bust

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The salmon season on the lower Sacramento River opened on July 16 with a yawn. As described in the Chico Enterprise, “the salmon aren’t biting”. One fish was confirmed caught. The article paraphrased an analysis by CDFW biologist Rob Titus, who referred to a plan to hold back releases from Shasta Reservoir to help juvenile salmon to migrate to the ocean. The article also stated that “the drought has had a deep impact on the fish population.”

CDFW could have told everyone to stay home. The river flow was too low and the water temperatures were too high for salmon to move up the river. In a July 2 post, I warned about the low flows and warm water. In the lower river, flow was only 4000 cfs. Water temperature reached 72-74°F on opening day (see chart below), high enough to block migrating salmon. No CDFW biologist mentioned that while 10,000 cfs was being released from Shasta at the time, only 4,000 cfs was reaching the lower river.1 No one mentioned that the State Water Board is not enforcing the State standard of 68°F for the lower Sacramento.

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  1. As of 7/23, Sacramento River flow below Wilkins Slough had increased only slightly, to about 4400 cfs. ↩

Barging Hatchery Smolts to the Bay

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In this blog I often recommend barging hatchery and even wild salmon from spawning rivers to the Bay up to 200 miles or more over conventional trucking or direct releases from hatcheries. The theory is that continuous recirculation of water in the barge (or boat) holding tank helps the young salmon remember from where they came and imprint the route back to their home river or hatchery.  Trucking directly to the Bay is believed to cause straying to non-natal rivers, resulting unnatural mixing of stocks, hatchery fish straying into wild fish spawning rivers, and less salmon returning to their home hatcheries where their eggs may be needed to meet quotas.  It is well documented that trucking and pen acclimation significantly increases the contribution of hatchery smolts to the ocean fishery up to two or three fold or more.  Concern over straying has kept the practice to a minimum.

Well it turns out from studies conducted with tagged hatchery salmon beginning with releases in 2008 that trucking, at least of American and Feather hatchery smolts, does not lead to significant amounts of straying.  Also, barging does not significantly reduce the already low straying rate.  So trucking to Bay net pens for acclimation remains the chosen strategy for the two largest State hatcheries, and probably the other two on the Mokelumne and Merced rivers.

The jury is still out on the Coleman and Livingston Stone federal hatcheries near Redding.  Straying rates are higher and the benefits of trucking over 200 miles seem questionable.  One concern I have is the high straying rate encountered for Coleman (Battle Creek) fish includes fish that move past Battle Creek further up in the Sacramento River and its upper tributaries.  Most of the spawning fish in these areas come from Coleman and Livingston Stone national fish hatcheries.  Because Coleman was built to mitigate for the loss of fish to those areas, I question their inclusion in the straying estimates.  The USFWS, which manages the two hatcheries, continues to be reluctant to truck and barge fish.

Though barging may not be needed for the Feather and American River hatcheries, it still holds potential for improving survival and reducing straying overall.  So far, there is no evidence that barging improves survival over trucking to Bay net pens.  I reviewed subsequent tag returns for a barge release group in early May 2012 with returns from two net pen groups released at the same time in the Bay.  I found the subsequent return percentage of the barge group  to be in between the two trucked pen release groups.  In the notes of the barge release, high predation by birds was noted.  In the photo of a barge release below many birds can be seen.  I wonder if the barge release would also benefit from the same pen acclimation that is employed after trucking, which significantly improves trucked fish release survival and subsequent contribution to the fishery.  (Note: I have been present at numerous truck releases to the Bay and have observed obvious extreme predation on the disoriented and confused hatchery fish, often released into warmer, saltier water than was present at the hatchery by a horde of well-trained and waiting birds and predatory fish.  Release to net pens at variable locations for acclimation and tow to open waters for underwater release seemed to greatly reduce predation, which proved true in subsequent tag returns.)

A closer look at the tag-release-recovery data and further experimentation would better answer the questions, concerns, and hypotheses.  There were nine barged groups released into the Bay from 2012-2014.  With some tags still out or not processed (tags are in noses of adult fish returns 2-4 years after release), information continues to come in.  The nearly million or so coded-wire-tags released from the nine barge groups swam with approximately 30 million other tagged fish from the six Central Valley hatcheries.  Furthermore, records are meticulously kept with other tagged groups from Washington and Oregon, as well as from other California watersheds (e.g., Klamath), by the Pacific States Marine Fisheries Commission.  An example of the type of information available is shown in the map-chart below for just the one barge release group from 2012.  The California Department of Fish and Wildlife has its own team and program to keep track of California immense database on releases and recoveries.  The Department’s report from November 2015 provides an excellent review of the whole process and results to date.

Barge in SF Bay

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Hatchery Reform and the Coleman National Fish Hatchery – Adaptive Management Plan

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The Coleman National Fish Hatchery (CNFH) on lower Battle Creek near Redding, CA (see map below) was constructed in 1942 to mitigate for the Shasta Dam project on the Sacramento built just upstream from Redding. It annually produces 12,000,000 fall-run salmon smolts and a million late–fall-run salmon smolts. Operation of CNFH is in need of reform because it fails to meet its mitigation goal and because it may interfere with the Battle Creek Restoration Program (BCRP1).

Efforts to improve salmon runs in recent drought years by trucking smolts to the lower river and Bay-Delta have resulted in increased straying of CNFH adult salmon to other Central Valley Rivers.2 Releasing millions of smolts into lower Battle Creek at the hatchery negatively affects wild smolts emigrating from Battle Creek through competition and stimulation of an annual spring striped bass feeding frenzy in the Sacramento River.3 Straying also limits adult salmon return to the hatchery and in some years makes it difficult for the hatchery to meet egg quotas. Plans to reduce these conflicts have drawn criticism from fishermen groups4 because of the potential of reducing smolt production and survival, and subsequent fishery harvests. CNFH production likely contributes a third or more of California’s ocean and freshwater salmon catch, and is a major contributor to natural salmon spawning in the Central Valley.

Recommendations

  1. In the Central Valley Salmon Recovery Plan (NMFS 2009/2011, p. 201), NMFS suggests moving the production hatchery to the Sacramento River from Battle Creek to reduce conflicts. The existing hatchery could be used as a conservation hatchery to support recovery of wild Battle Creek salmon and steelhead.
  2. Fall-run salmon smolt production should be trucked/barged to the Bay to maximize contribution to fisheries, recognizing substantial straying of fall-run occurs throughout the Central Valley. Barging smolts from above the mouth of the Feather River to the Bay should reduce straying to the Feather, American, and San Joaquin rivers and their tributaries.
  3. Fall-run CNFH fry can be trucked/barged to high quality lower river floodplain and tidal estuary habitats historically important to fall-run, but presently unavailable or unreachable. Such habitats were important and reachable before the dams were built.
  4. Late-fall-run and steelhead smolts should be released at the hatchery in wet winters, but barged to the Bay in dry years.

Coleman National Fish Hatchery Map

June Update and Possible Solution to 2016 Fish Woes

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Over the past month I related water issues involving Delta and longfin smelt, striped bass, green and white sturgeon, and winter-run and spring-run salmon. All of these species need river flow and cooler water over the next several months. Shasta releases to the upper Sacramento River need to be cold, stable, and sufficient to sustain winter-run salmon eggs in the river near Redding and to sustain moderate flows and cooler water temperatures for 200 miles of river to protect sturgeon and other lifestages of salmon. Sufficient flows needs to pass through the Delta to keep the low salinity zone downstream of the Delta in the cool waters of eastern Suisun Bay, away from Delta exports.

Shasta releases are now 8000 cfs, with Bend Bridge water temperature near the Red Bluff target of 56°F. In June and July of drought years 2012 and 2013, releases were 11,000-14,000 cfs. However, concern over carryover storage and sustaining cold-water releases through summer has led to a more conservative management strategy in 2016. The cold-water pool in Shasta Reservoir is being rationed to make it through the summer. Flows will rise over the next six weeks to 9,000 or 10,000 cfs to satisfy irrigation demands in the upper river.

Flows in the lower Sacramento River at Wilkins Slough need to be greater than 5000 cfs in summer, if only to keep water temperature down closer to the Basin Plan’s 68°F. Flows are now 3000-4000 cfs, with water temperatures up to 75°F. In dry years 2012 and 2013, flows at Wilkins Slough were 6000-9000 cfs, and water temperatures were cooler, as some of Shasta’s storage was allocated for Delta export. This year’s management strategy to hold back Shasta releases will, if continued, keep both Wilkins Slough flows and Delta exports down.

Delta outflows need to be sustained near 10,000 cfs to keep the low salinity zone and X2 (2 ppt salinity) near Collinsville in eastern Suisun Bay. However, July outflow to the Bay required by water quality standards will be only about 8000 cfs. To help save the last of the two smelt species, 10,000 cfs would be far better.

A reasonable solution is apparent: raise Shasta releases through most of the summer by 2000 cfs to 10,000-12,000 cfs and require that the extra release be passed down the river to and through the Delta. While such a management strategy would benefit the fish, it would decrease Shasta storage by 120,000 acre-ft of water per month. At present, Shasta is 90% full at 4.1 million acre-feet (the cold-water pool volume is about 2.4 maf). At 12,000 cfs, the total Shasta release would rise to 600,000 acre-feet per month, which is about the current total release from Oroville (Feather River) and Folsom (American River) reservoirs. NMFS and USBR have determined that a 10,000 cfs Shasta cold-water release can be sustained through the summer, while a 12,000 cfs release could be problematic. Protests would no doubt come from water users who would want the extra 2000 cfs. But note that of the 20,000 cfs being released today from the three main Sacramento Valley reservoirs, only 8000 cfs is reaching the Bay.1

This solution of raising total reservoir releases to 22,000-24,000 and Bay outflow to 10,000 cfs is reasonable to help the fish after four years of drought. In 2014-2015, water quality standards were drastically reduced, with catastrophic effects to fish. The continuing legacy of these catastrophic effects creates the urgency to do better in 2016.

If higher releases from Shasta become problematic for whatever reason, then some compromise should be achievable, noting that water deliveries of Shasta water are to be provided only after the needs of the fish are first considered, including conservation of Shasta’s cold-water pool through the summer and early fall (Water Rights Orders 90-05 and 92-02). Further, Central Valley water rights are provided via the Trinity River trans-basin diversion to Keswick Reservoir on the Sacramento River below Shasta Dam, but the Trinity supply is much in doubt because Trinity storage has failed to recover after the drought, unlike Shasta storage. A lack of Trinity supply this summer will further limit water available for irrigation in the Central Valley. Yet another constraint is whether the available storage in Oroville and Folsom reservoirs is able to satisfy Delta demands without compromising the needs of endangered fish in the Feather and American rivers.

Sorting out these conflicts and needs is the responsibility of the State Water Resources Control Board. The Board’s top priority should be the basic needs of the endangered salmon, sturgeon, and smelts of the Central Valley. At minimum, the Board should require the following conditions this summer:

  1. Below Shasta – Stable flows of 9,000 to 10,000 cfs and 56°F average daily water temperatures near Red Bluff (Jellys Ferry or Bend Bridge).
  2. Lower Sacramento River – minimum 5000 cfs at Wilkins Slough (RM 125 on the Sacramento River)
  3. Delta Outflow – 9,000 cfs in July, 5,000 cfs in August, and 4,000 cfs in September.
  1.  A further complication is that South Delta export criteria allow an increase from 35% of inflow to 65% starting July 1.  Exports in June are limited to 5000 cfs.  In July, exports can be raised to 65% of inflow, but only if outflow is kept at 8000 cfs.  Delta ag diversions are also near 4000 cfs.  Thus July Delta inflow of  20,000 cfs or more (compared to the present inflow of 15,000 cfs) would be needed to allow 10,000 cfs of Delta export.   ↩